Starting phenix.real_space_refine on Mon May 12 17:09:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6n_36924/05_2025/8k6n_36924.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6n_36924/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k6n_36924/05_2025/8k6n_36924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6n_36924/05_2025/8k6n_36924.map" model { file = "/net/cci-nas-00/data/ceres_data/8k6n_36924/05_2025/8k6n_36924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6n_36924/05_2025/8k6n_36924.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.33, per 1000 atoms: 0.57 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: 2.90 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.96 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: 2.41 Time building geometry restraints manager: 3.30 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: 1.320 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.510 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (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 TRP 0.031 0.002 TRP S 111 HIS 0.007 0.001 HIS D 26 PHE 0.018 0.002 PHE B 235 TYR 0.027 0.002 TYR D 27 ARG 0.002 0.000 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.15379 ( 444) hydrogen bonds : angle 6.22289 ( 1293) SS BOND : bond 0.00684 ( 2) SS BOND : angle 2.31912 ( 4) covalent geometry : bond 0.00396 ( 9484) covalent geometry : angle 0.66222 (12847) *********************** 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 : 1.177 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: 0.2394 time to fit residues: 52.8773 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 : 0.983 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.172817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.142018 restraints weight = 13016.478| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.45 r_work: 0.3723 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9486 Z= 0.163 Angle : 0.618 10.121 12851 Z= 0.321 Chirality : 0.043 0.164 1466 Planarity : 0.004 0.041 1618 Dihedral : 5.088 87.185 1284 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.57 % Allowed : 9.22 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1168 helix: 2.13 (0.26), residues: 419 sheet: -0.24 (0.31), residues: 276 loop : -1.46 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 169 HIS 0.004 0.001 HIS D 26 PHE 0.015 0.002 PHE B 235 TYR 0.029 0.002 TYR D 27 ARG 0.004 0.000 ARG S 38 Details of bonding type rmsd hydrogen bonds : bond 0.06303 ( 444) hydrogen bonds : angle 5.11085 ( 1293) SS BOND : bond 0.00775 ( 2) SS BOND : angle 2.61481 ( 4) covalent geometry : bond 0.00360 ( 9484) covalent geometry : angle 0.61612 (12847) *********************** 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 172 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7262 (t0) cc_final: 0.7005 (t0) REVERT: B 340 ASN cc_start: 0.7584 (t0) cc_final: 0.7299 (t0) REVERT: E 179 LEU cc_start: 0.7525 (tp) cc_final: 0.7246 (tt) REVERT: E 226 ILE cc_start: 0.8209 (tp) cc_final: 0.7882 (tp) REVERT: E 248 ASN cc_start: 0.7253 (m-40) cc_final: 0.6899 (m-40) REVERT: S 140 MET cc_start: 0.5187 (mtp) cc_final: 0.4816 (mtp) outliers start: 16 outliers final: 12 residues processed: 161 average time/residue: 0.2333 time to fit residues: 52.2913 Evaluate side-chains 168 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 178 LEU 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 11 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 HIS ** S 231 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 = 0.4224 r_free = 0.4224 target = 0.170971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140057 restraints weight = 13077.930| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.44 r_work: 0.3694 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9486 Z= 0.199 Angle : 0.620 7.720 12851 Z= 0.326 Chirality : 0.044 0.176 1466 Planarity : 0.004 0.041 1618 Dihedral : 5.158 88.858 1281 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.75 % Allowed : 12.66 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1168 helix: 2.22 (0.26), residues: 411 sheet: -0.32 (0.30), residues: 286 loop : -1.52 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 169 HIS 0.008 0.001 HIS D 26 PHE 0.019 0.002 PHE B 235 TYR 0.021 0.002 TYR D 27 ARG 0.002 0.000 ARG S 38 Details of bonding type rmsd hydrogen bonds : bond 0.06564 ( 444) hydrogen bonds : angle 5.01502 ( 1293) SS BOND : bond 0.00697 ( 2) SS BOND : angle 2.03781 ( 4) covalent geometry : bond 0.00452 ( 9484) covalent geometry : angle 0.61898 (12847) *********************** 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 185 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7347 (t0) cc_final: 0.7054 (t0) REVERT: E 153 VAL cc_start: 0.8189 (p) cc_final: 0.7919 (m) REVERT: E 226 ILE cc_start: 0.8305 (tp) cc_final: 0.7942 (tp) REVERT: E 248 ASN cc_start: 0.7291 (m-40) cc_final: 0.6917 (m-40) REVERT: E 328 MET cc_start: 0.6088 (tmm) cc_final: 0.5843 (tmm) outliers start: 28 outliers final: 23 residues processed: 170 average time/residue: 0.2083 time to fit residues: 49.1648 Evaluate side-chains 178 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 277 GLU Chi-restraints excluded: chain A residue 286 ILE 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 325 MET 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 250 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 172 THR Chi-restraints excluded: chain S residue 178 LEU 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 88 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ** 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 = 0.4225 r_free = 0.4225 target = 0.171515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.140831 restraints weight = 13072.724| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.49 r_work: 0.3702 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9486 Z= 0.167 Angle : 0.589 7.342 12851 Z= 0.310 Chirality : 0.042 0.164 1466 Planarity : 0.004 0.038 1618 Dihedral : 5.101 89.225 1281 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.94 % Allowed : 15.60 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1168 helix: 2.27 (0.26), residues: 411 sheet: -0.37 (0.31), residues: 281 loop : -1.51 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 169 HIS 0.009 0.001 HIS D 26 PHE 0.016 0.002 PHE B 235 TYR 0.017 0.002 TYR D 27 ARG 0.002 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.06024 ( 444) hydrogen bonds : angle 4.83537 ( 1293) SS BOND : bond 0.00700 ( 2) SS BOND : angle 1.85321 ( 4) covalent geometry : bond 0.00372 ( 9484) covalent geometry : angle 0.58860 (12847) *********************** 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: 30 poor density : 154 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7200 (t0) cc_final: 0.6907 (t0) REVERT: A 341 THR cc_start: 0.8123 (m) cc_final: 0.7917 (m) REVERT: D 32 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.7471 (t) REVERT: E 69 SER cc_start: 0.8133 (m) cc_final: 0.7930 (m) REVERT: E 153 VAL cc_start: 0.8259 (p) cc_final: 0.7927 (m) REVERT: E 226 ILE cc_start: 0.8285 (tp) cc_final: 0.7915 (tp) REVERT: E 248 ASN cc_start: 0.7226 (m-40) cc_final: 0.6875 (m-40) REVERT: E 328 MET cc_start: 0.6001 (tmm) cc_final: 0.5624 (tmm) outliers start: 30 outliers final: 24 residues processed: 169 average time/residue: 0.1986 time to fit residues: 46.9784 Evaluate side-chains 177 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 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 307 VAL 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 250 VAL 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 E residue 331 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 79 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 43 optimal weight: 0.0170 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.0670 chunk 36 optimal weight: 0.0770 overall best weight: 0.2714 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.174365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.143742 restraints weight = 13104.798| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.48 r_work: 0.3754 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9486 Z= 0.111 Angle : 0.546 6.867 12851 Z= 0.287 Chirality : 0.040 0.129 1466 Planarity : 0.004 0.034 1618 Dihedral : 4.889 89.758 1281 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.85 % Allowed : 17.57 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1168 helix: 2.32 (0.26), residues: 417 sheet: -0.26 (0.30), residues: 299 loop : -1.37 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 332 HIS 0.007 0.001 HIS D 26 PHE 0.011 0.001 PHE A 190 TYR 0.016 0.001 TYR D 27 ARG 0.002 0.000 ARG E 187 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 444) hydrogen bonds : angle 4.49984 ( 1293) SS BOND : bond 0.00526 ( 2) SS BOND : angle 1.33132 ( 4) covalent geometry : bond 0.00228 ( 9484) covalent geometry : angle 0.54542 (12847) *********************** 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 185 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7162 (t0) cc_final: 0.6842 (t0) REVERT: D 32 THR cc_start: 0.7664 (OUTLIER) cc_final: 0.7385 (t) REVERT: E 226 ILE cc_start: 0.8143 (tp) cc_final: 0.7767 (tp) REVERT: E 248 ASN cc_start: 0.7015 (m-40) cc_final: 0.6788 (m-40) REVERT: E 271 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7837 (p) REVERT: E 328 MET cc_start: 0.5835 (tmm) cc_final: 0.5330 (tmm) REVERT: E 329 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.8062 (m-40) REVERT: S 187 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8254 (tp) outliers start: 29 outliers final: 17 residues processed: 172 average time/residue: 0.2082 time to fit residues: 49.7345 Evaluate side-chains 173 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 322 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 307 VAL Chi-restraints excluded: chain B residue 325 MET 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 329 ASN Chi-restraints excluded: chain E residue 331 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 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 107 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.168500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.137561 restraints weight = 13092.477| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.50 r_work: 0.3663 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9486 Z= 0.246 Angle : 0.651 7.434 12851 Z= 0.344 Chirality : 0.045 0.188 1466 Planarity : 0.004 0.038 1618 Dihedral : 5.165 85.009 1281 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.14 % Allowed : 18.55 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1168 helix: 2.15 (0.26), residues: 411 sheet: -0.36 (0.31), residues: 275 loop : -1.54 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 169 HIS 0.009 0.001 HIS D 26 PHE 0.022 0.002 PHE A 337 TYR 0.017 0.002 TYR B 105 ARG 0.004 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.06861 ( 444) hydrogen bonds : angle 4.85976 ( 1293) SS BOND : bond 0.00770 ( 2) SS BOND : angle 2.03256 ( 4) covalent geometry : bond 0.00569 ( 9484) covalent geometry : angle 0.65032 (12847) *********************** 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 187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.018 Fit side-chains REVERT: A 262 ASP cc_start: 0.7262 (t0) cc_final: 0.6952 (t0) REVERT: B 118 ASP cc_start: 0.8049 (t70) cc_final: 0.7713 (t0) REVERT: D 32 THR cc_start: 0.7763 (OUTLIER) cc_final: 0.7502 (t) REVERT: E 69 SER cc_start: 0.8197 (m) cc_final: 0.7982 (m) REVERT: E 108 LEU cc_start: 0.8180 (tp) cc_final: 0.7975 (tp) REVERT: E 153 VAL cc_start: 0.8215 (p) cc_final: 0.7972 (m) REVERT: E 226 ILE cc_start: 0.8303 (tp) cc_final: 0.7930 (tp) REVERT: E 248 ASN cc_start: 0.7338 (m-40) cc_final: 0.7002 (m-40) REVERT: E 328 MET cc_start: 0.6036 (tmm) cc_final: 0.5624 (tmm) outliers start: 32 outliers final: 24 residues processed: 168 average time/residue: 0.2036 time to fit residues: 48.1447 Evaluate side-chains 183 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 74 SER Chi-restraints excluded: chain B residue 75 GLN 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 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 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 36 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.172924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.142319 restraints weight = 13115.241| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.49 r_work: 0.3730 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9486 Z= 0.138 Angle : 0.595 10.995 12851 Z= 0.309 Chirality : 0.041 0.139 1466 Planarity : 0.004 0.037 1618 Dihedral : 4.974 84.157 1281 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.24 % Allowed : 18.84 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1168 helix: 2.27 (0.27), residues: 411 sheet: -0.40 (0.30), residues: 292 loop : -1.44 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS D 26 PHE 0.014 0.001 PHE B 235 TYR 0.015 0.001 TYR S 102 ARG 0.003 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.05458 ( 444) hydrogen bonds : angle 4.59349 ( 1293) SS BOND : bond 0.00731 ( 2) SS BOND : angle 1.74978 ( 4) covalent geometry : bond 0.00303 ( 9484) covalent geometry : angle 0.59433 (12847) *********************** 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 192 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7180 (t0) cc_final: 0.6874 (t0) REVERT: A 341 THR cc_start: 0.8111 (m) cc_final: 0.7899 (m) REVERT: D 32 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7477 (t) REVERT: E 69 SER cc_start: 0.8126 (m) cc_final: 0.7915 (m) REVERT: E 153 VAL cc_start: 0.8204 (p) cc_final: 0.7940 (m) REVERT: E 226 ILE cc_start: 0.8211 (tp) cc_final: 0.7836 (tp) REVERT: E 248 ASN cc_start: 0.7177 (m-40) cc_final: 0.6868 (m-40) REVERT: E 271 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7819 (p) REVERT: E 328 MET cc_start: 0.5852 (tmm) cc_final: 0.5382 (tmm) REVERT: E 329 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8064 (m-40) outliers start: 33 outliers final: 24 residues processed: 174 average time/residue: 0.2117 time to fit residues: 51.1461 Evaluate side-chains 185 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 75 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 325 MET 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 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 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 36 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 107 optimal weight: 0.0570 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.171461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.140743 restraints weight = 13318.705| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.53 r_work: 0.3703 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1850 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= 0.138 Angle : 0.597 9.488 12851 Z= 0.309 Chirality : 0.041 0.139 1466 Planarity : 0.004 0.037 1618 Dihedral : 4.912 82.839 1281 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.75 % Allowed : 19.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1168 helix: 2.30 (0.26), residues: 411 sheet: -0.43 (0.31), residues: 283 loop : -1.35 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 332 HIS 0.007 0.001 HIS D 26 PHE 0.014 0.001 PHE B 235 TYR 0.015 0.001 TYR S 102 ARG 0.004 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.05299 ( 444) hydrogen bonds : angle 4.53579 ( 1293) SS BOND : bond 0.00781 ( 2) SS BOND : angle 1.85311 ( 4) covalent geometry : bond 0.00304 ( 9484) covalent geometry : angle 0.59650 (12847) *********************** 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 186 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7218 (t0) cc_final: 0.6902 (t0) REVERT: D 32 THR cc_start: 0.7711 (OUTLIER) cc_final: 0.7479 (t) REVERT: E 69 SER cc_start: 0.8113 (m) cc_final: 0.7906 (m) REVERT: E 153 VAL cc_start: 0.8190 (p) cc_final: 0.7920 (m) REVERT: E 226 ILE cc_start: 0.8198 (tp) cc_final: 0.7816 (tp) REVERT: E 248 ASN cc_start: 0.7133 (m-40) cc_final: 0.6870 (m-40) REVERT: E 271 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7849 (p) REVERT: E 328 MET cc_start: 0.5840 (tmm) cc_final: 0.5359 (tmm) REVERT: E 329 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8041 (m-40) outliers start: 28 outliers final: 23 residues processed: 170 average time/residue: 0.2163 time to fit residues: 51.2348 Evaluate side-chains 182 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 75 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 325 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 79 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.171911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.141260 restraints weight = 13071.699| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.51 r_work: 0.3709 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.1911 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= 0.134 Angle : 0.604 10.588 12851 Z= 0.312 Chirality : 0.041 0.137 1466 Planarity : 0.004 0.037 1618 Dihedral : 4.856 81.586 1281 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.04 % Allowed : 19.82 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1168 helix: 2.32 (0.26), residues: 411 sheet: -0.41 (0.31), residues: 283 loop : -1.32 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.006 0.001 HIS D 26 PHE 0.014 0.001 PHE B 235 TYR 0.015 0.001 TYR S 102 ARG 0.003 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.05114 ( 444) hydrogen bonds : angle 4.49137 ( 1293) SS BOND : bond 0.00775 ( 2) SS BOND : angle 1.73564 ( 4) covalent geometry : bond 0.00294 ( 9484) covalent geometry : angle 0.60321 (12847) *********************** 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 184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7198 (t0) cc_final: 0.6875 (t0) REVERT: D 32 THR cc_start: 0.7695 (OUTLIER) cc_final: 0.7472 (t) REVERT: E 69 SER cc_start: 0.8052 (m) cc_final: 0.7850 (m) REVERT: E 153 VAL cc_start: 0.8176 (p) cc_final: 0.7900 (m) REVERT: E 226 ILE cc_start: 0.8180 (tp) cc_final: 0.7798 (tp) REVERT: E 248 ASN cc_start: 0.7105 (m-40) cc_final: 0.6852 (m-40) REVERT: E 271 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7807 (p) REVERT: E 328 MET cc_start: 0.5940 (tmm) cc_final: 0.5496 (tmm) REVERT: E 329 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8171 (m-40) outliers start: 31 outliers final: 24 residues processed: 166 average time/residue: 0.2088 time to fit residues: 48.0420 Evaluate side-chains 177 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 130 GLU 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 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 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 103 optimal weight: 5.9990 chunk 71 optimal weight: 0.2980 chunk 62 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.173959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.143411 restraints weight = 13189.655| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.51 r_work: 0.3733 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9486 Z= 0.133 Angle : 0.609 10.654 12851 Z= 0.314 Chirality : 0.042 0.136 1466 Planarity : 0.004 0.037 1618 Dihedral : 4.824 80.408 1281 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.75 % Allowed : 20.22 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1168 helix: 2.31 (0.26), residues: 411 sheet: -0.32 (0.31), residues: 287 loop : -1.30 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.006 0.001 HIS D 26 PHE 0.013 0.001 PHE B 235 TYR 0.014 0.001 TYR E 57 ARG 0.005 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 444) hydrogen bonds : angle 4.47148 ( 1293) SS BOND : bond 0.00751 ( 2) SS BOND : angle 1.66419 ( 4) covalent geometry : bond 0.00292 ( 9484) covalent geometry : angle 0.60828 (12847) ********************** 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 181 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7173 (mpt) cc_final: 0.6945 (mpt) REVERT: A 262 ASP cc_start: 0.7163 (t0) cc_final: 0.6852 (t0) REVERT: D 32 THR cc_start: 0.7686 (OUTLIER) cc_final: 0.7476 (t) REVERT: E 153 VAL cc_start: 0.8175 (p) cc_final: 0.7889 (m) REVERT: E 226 ILE cc_start: 0.8176 (tp) cc_final: 0.7800 (tp) REVERT: E 248 ASN cc_start: 0.7085 (m-40) cc_final: 0.6869 (m-40) REVERT: E 271 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7781 (p) REVERT: E 328 MET cc_start: 0.5864 (tmm) cc_final: 0.5434 (tmm) REVERT: E 329 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8139 (m-40) outliers start: 28 outliers final: 25 residues processed: 165 average time/residue: 0.2086 time to fit residues: 48.1279 Evaluate side-chains 180 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 130 GLU 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 118 MET 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 96 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.172104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.141462 restraints weight = 13106.772| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.52 r_work: 0.3716 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9486 Z= 0.139 Angle : 0.615 10.114 12851 Z= 0.316 Chirality : 0.042 0.137 1466 Planarity : 0.004 0.037 1618 Dihedral : 4.793 78.198 1281 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.94 % Allowed : 20.12 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1168 helix: 2.30 (0.26), residues: 411 sheet: -0.32 (0.31), residues: 280 loop : -1.33 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 332 HIS 0.005 0.001 HIS D 26 PHE 0.014 0.001 PHE B 235 TYR 0.015 0.001 TYR E 57 ARG 0.008 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.05172 ( 444) hydrogen bonds : angle 4.46115 ( 1293) SS BOND : bond 0.00758 ( 2) SS BOND : angle 1.68031 ( 4) covalent geometry : bond 0.00307 ( 9484) covalent geometry : angle 0.61417 (12847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8179.60 seconds wall clock time: 141 minutes 15.60 seconds (8475.60 seconds total)