Starting phenix.real_space_refine on Sat Dec 28 02:05:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hj2_33481/12_2024/8hj2_33481.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hj2_33481/12_2024/8hj2_33481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hj2_33481/12_2024/8hj2_33481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hj2_33481/12_2024/8hj2_33481.map" model { file = "/net/cci-nas-00/data/ceres_data/8hj2_33481/12_2024/8hj2_33481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hj2_33481/12_2024/8hj2_33481.cif" } resolution = 3.8 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= 0.000 sd= 0.002 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 40 5.16 5 C 4712 2.51 5 N 1306 2.21 5 O 1409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7467 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2423 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 86 Chain: "G" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 230 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 4, 'TRANS': 41} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 1966 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 10, 'TRANS': 271} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 11, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 165 Chain: "A" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1887 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 4.76, per 1000 atoms: 0.64 Number of scatterers: 7467 At special positions: 0 Unit cell: (85.696, 102.336, 119.808, 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 40 16.00 O 1409 8.00 N 1306 7.00 C 4712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 122 " - pdb=" SG CYS R 149 " distance=2.06 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: 2.03 Conformation dependent library (CDL) restraints added in 1.2 seconds 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 41.0% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 18 through 24 removed outlier: 4.180A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 4.057A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.844A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 56 removed outlier: 6.083A pdb=" N ILE R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU R 41 " --> pdb=" O PHE R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 91 removed outlier: 4.067A pdb=" N PHE R 67 " --> pdb=" O THR R 63 " (cutoff:3.500A) Proline residue: R 85 - end of helix removed outlier: 3.931A pdb=" N LEU R 90 " --> pdb=" O SER R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 133 removed outlier: 3.661A pdb=" N PHE R 105 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE R 107 " --> pdb=" O GLN R 103 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER R 114 " --> pdb=" O SER R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 141 Processing helix chain 'R' and resid 142 through 162 removed outlier: 4.301A pdb=" N PHE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 165 No H-bonds generated for 'chain 'R' and resid 163 through 165' Processing helix chain 'R' and resid 178 through 184 Processing helix chain 'R' and resid 188 through 197 Processing helix chain 'R' and resid 199 through 232 removed outlier: 3.847A pdb=" N PHE R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 279 Proline residue: R 267 - end of helix Processing helix chain 'R' and resid 282 through 295 Processing helix chain 'R' and resid 295 through 308 removed outlier: 4.438A pdb=" N CYS R 301 " --> pdb=" O SER R 297 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL R 302 " --> pdb=" O PHE R 298 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 323 Processing helix chain 'A' and resid 10 through 40 removed outlier: 4.074A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.590A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 283 through 293 removed outlier: 3.527A pdb=" N LEU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.301A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 3.641A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 321 through 340 removed outlier: 3.803A pdb=" N THR A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 384 removed outlier: 3.574A pdb=" N ARG A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.513A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.529A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.068A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.005A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.585A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.447A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, 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: 6.298A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.340A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 208 through 214 removed outlier: 5.969A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 2487 1.35 - 1.48: 2049 1.48 - 1.62: 3027 1.62 - 1.75: 0 1.75 - 1.88: 54 Bond restraints: 7617 Sorted by residual: bond pdb=" CB CYS R 149 " pdb=" SG CYS R 149 " ideal model delta sigma weight residual 1.808 1.884 -0.076 3.30e-02 9.18e+02 5.35e+00 bond pdb=" CB CYS R 122 " pdb=" SG CYS R 122 " ideal model delta sigma weight residual 1.808 1.884 -0.076 3.30e-02 9.18e+02 5.29e+00 bond pdb=" CB VAL B 296 " pdb=" CG2 VAL B 296 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.77e+00 bond pdb=" CB VAL R 207 " pdb=" CG1 VAL R 207 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.61e+00 bond pdb=" CA ALA B 231 " pdb=" CB ALA B 231 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.78e-02 3.16e+03 4.08e+00 ... (remaining 7612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 10176 3.58 - 7.15: 182 7.15 - 10.73: 18 10.73 - 14.30: 2 14.30 - 17.88: 2 Bond angle restraints: 10380 Sorted by residual: angle pdb=" CG ARG R 147 " pdb=" CD ARG R 147 " pdb=" NE ARG R 147 " ideal model delta sigma weight residual 112.00 129.88 -17.88 2.20e+00 2.07e-01 6.61e+01 angle pdb=" N THR A 315 " pdb=" CA THR A 315 " pdb=" C THR A 315 " ideal model delta sigma weight residual 109.81 122.54 -12.73 2.21e+00 2.05e-01 3.32e+01 angle pdb=" C LEU R 140 " pdb=" N VAL R 141 " pdb=" CA VAL R 141 " ideal model delta sigma weight residual 121.65 116.60 5.05 9.40e-01 1.13e+00 2.89e+01 angle pdb=" N VAL A 224 " pdb=" CA VAL A 224 " pdb=" C VAL A 224 " ideal model delta sigma weight residual 106.21 111.13 -4.92 1.07e+00 8.73e-01 2.11e+01 angle pdb=" CA ARG R 147 " pdb=" CB ARG R 147 " pdb=" CG ARG R 147 " ideal model delta sigma weight residual 114.10 122.91 -8.81 2.00e+00 2.50e-01 1.94e+01 ... (remaining 10375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4050 17.38 - 34.76: 349 34.76 - 52.14: 44 52.14 - 69.51: 5 69.51 - 86.89: 6 Dihedral angle restraints: 4454 sinusoidal: 1465 harmonic: 2989 Sorted by residual: dihedral pdb=" CB CYS R 122 " pdb=" SG CYS R 122 " pdb=" SG CYS R 149 " pdb=" CB CYS R 149 " ideal model delta sinusoidal sigma weight residual 93.00 179.89 -86.89 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CA VAL R 111 " pdb=" C VAL R 111 " pdb=" N LEU R 112 " pdb=" CA LEU R 112 " ideal model delta harmonic sigma weight residual 180.00 -152.69 -27.31 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ASN B 237 " pdb=" C ASN B 237 " pdb=" N GLY B 238 " pdb=" CA GLY B 238 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 4451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1052 0.096 - 0.192: 133 0.192 - 0.288: 10 0.288 - 0.383: 3 0.383 - 0.479: 1 Chirality restraints: 1199 Sorted by residual: chirality pdb=" CB ILE B 123 " pdb=" CA ILE B 123 " pdb=" CG1 ILE B 123 " pdb=" CG2 ILE B 123 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CG LEU N 45 " pdb=" CB LEU N 45 " pdb=" CD1 LEU N 45 " pdb=" CD2 LEU N 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1196 not shown) Planarity restraints: 1341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 321 " 0.065 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO A 322 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 169 " 0.030 2.00e-02 2.50e+03 2.15e-02 1.15e+01 pdb=" CG TRP B 169 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP B 169 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 169 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 169 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 169 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 169 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 169 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 169 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 169 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 350 " -0.019 2.00e-02 2.50e+03 2.22e-02 9.86e+00 pdb=" CG TYR A 350 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 350 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 350 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 350 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 350 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 350 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 350 " -0.001 2.00e-02 2.50e+03 ... (remaining 1338 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1625 2.77 - 3.31: 7265 3.31 - 3.84: 12585 3.84 - 4.37: 14090 4.37 - 4.90: 24254 Nonbonded interactions: 59819 Sorted by model distance: nonbonded pdb=" O SER R 116 " pdb=" OG SER R 119 " model vdw 2.242 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.265 3.040 nonbonded pdb=" O VAL R 111 " pdb=" OG SER R 114 " model vdw 2.268 3.040 nonbonded pdb=" O ASP B 228 " pdb=" OG SER B 245 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR N 91 " pdb=" O VAL N 124 " model vdw 2.312 3.040 ... (remaining 59814 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.480 Find NCS groups from input model: 0.060 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 0.007 0.076 7617 Z= 0.495 Angle : 1.203 17.880 10380 Z= 0.665 Chirality : 0.066 0.479 1199 Planarity : 0.008 0.101 1341 Dihedral : 13.410 82.535 2511 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -2.19 (0.23), residues: 1013 helix: -1.03 (0.21), residues: 400 sheet: -0.66 (0.35), residues: 214 loop : -2.24 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.005 TRP B 169 HIS 0.010 0.003 HIS A 347 PHE 0.044 0.004 PHE N 29 TYR 0.054 0.004 TYR A 350 ARG 0.023 0.002 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: B 280 LYS cc_start: 0.7598 (tttt) cc_final: 0.7239 (ttmt) REVERT: B 293 ASN cc_start: 0.8829 (p0) cc_final: 0.8589 (p0) REVERT: N 60 TYR cc_start: 0.7306 (m-80) cc_final: 0.6746 (m-80) REVERT: A 209 GLU cc_start: 0.7146 (pp20) cc_final: 0.6860 (pp20) REVERT: A 252 ASP cc_start: 0.8020 (t0) cc_final: 0.7664 (t0) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2249 time to fit residues: 89.6273 Evaluate side-chains 277 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.0770 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 176 GLN R 213 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7617 Z= 0.205 Angle : 0.639 8.031 10380 Z= 0.340 Chirality : 0.045 0.167 1199 Planarity : 0.005 0.066 1341 Dihedral : 5.563 20.275 1100 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.33 % Allowed : 13.77 % Favored : 82.90 % 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: -0.74 (0.25), residues: 1013 helix: 0.82 (0.25), residues: 409 sheet: -0.36 (0.35), residues: 218 loop : -2.00 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 169 HIS 0.005 0.001 HIS R 174 PHE 0.022 0.002 PHE R 272 TYR 0.016 0.001 TYR B 85 ARG 0.007 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 292 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 ASP cc_start: 0.8434 (p0) cc_final: 0.8227 (p0) REVERT: B 241 PHE cc_start: 0.8522 (p90) cc_final: 0.8251 (p90) REVERT: B 262 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6986 (mmt) REVERT: N 34 MET cc_start: 0.7750 (mmm) cc_final: 0.7474 (mmt) REVERT: N 60 TYR cc_start: 0.7605 (m-80) cc_final: 0.7094 (m-80) REVERT: N 67 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6228 (ttp80) REVERT: R 137 TYR cc_start: 0.8729 (t80) cc_final: 0.7960 (t80) REVERT: R 153 ILE cc_start: 0.8949 (mt) cc_final: 0.8740 (mt) REVERT: A 209 GLU cc_start: 0.7006 (pp20) cc_final: 0.6709 (pp20) REVERT: A 220 HIS cc_start: 0.7913 (t70) cc_final: 0.7288 (t70) outliers start: 23 outliers final: 15 residues processed: 298 average time/residue: 0.2040 time to fit residues: 79.6762 Evaluate side-chains 300 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 283 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 131 ILE Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.4980 chunk 75 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7617 Z= 0.202 Angle : 0.601 7.885 10380 Z= 0.322 Chirality : 0.044 0.169 1199 Planarity : 0.004 0.044 1341 Dihedral : 5.031 17.484 1100 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.49 % Allowed : 17.54 % Favored : 77.97 % 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: -0.16 (0.26), residues: 1013 helix: 1.63 (0.26), residues: 402 sheet: -0.33 (0.35), residues: 217 loop : -1.85 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.003 0.001 HIS A 352 PHE 0.016 0.002 PHE R 191 TYR 0.013 0.001 TYR B 85 ARG 0.007 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 293 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 PHE cc_start: 0.8600 (p90) cc_final: 0.8331 (p90) REVERT: B 261 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7953 (mm) REVERT: N 3 GLN cc_start: 0.6773 (tt0) cc_final: 0.6541 (tm-30) REVERT: N 34 MET cc_start: 0.7886 (mmm) cc_final: 0.7634 (mmt) REVERT: N 60 TYR cc_start: 0.7691 (m-80) cc_final: 0.7306 (m-80) REVERT: N 67 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6367 (ttp80) REVERT: N 87 LYS cc_start: 0.7958 (tttt) cc_final: 0.7482 (tttt) REVERT: R 137 TYR cc_start: 0.8748 (t80) cc_final: 0.8017 (t80) REVERT: R 153 ILE cc_start: 0.8843 (mt) cc_final: 0.8614 (mt) REVERT: R 217 ILE cc_start: 0.8715 (mm) cc_final: 0.8471 (mt) REVERT: R 275 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6990 (tt0) REVERT: A 209 GLU cc_start: 0.7050 (pp20) cc_final: 0.6699 (pp20) REVERT: A 220 HIS cc_start: 0.7903 (t70) cc_final: 0.7295 (t70) outliers start: 31 outliers final: 17 residues processed: 300 average time/residue: 0.2024 time to fit residues: 80.0754 Evaluate side-chains 302 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 283 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 105 PHE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 0.0270 chunk 10 optimal weight: 0.0870 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7617 Z= 0.170 Angle : 0.580 7.471 10380 Z= 0.307 Chirality : 0.043 0.159 1199 Planarity : 0.004 0.047 1341 Dihedral : 4.653 16.852 1100 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.20 % Allowed : 19.42 % Favored : 76.38 % 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: 0.22 (0.27), residues: 1013 helix: 2.14 (0.26), residues: 399 sheet: -0.21 (0.35), residues: 218 loop : -1.81 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.005 0.001 HIS A 352 PHE 0.028 0.002 PHE N 29 TYR 0.020 0.001 TYR R 211 ARG 0.005 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 283 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ASP cc_start: 0.8222 (t0) cc_final: 0.7874 (t0) REVERT: B 241 PHE cc_start: 0.8515 (p90) cc_final: 0.8294 (p90) REVERT: B 251 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7492 (mtm-85) REVERT: B 280 LYS cc_start: 0.7493 (tttt) cc_final: 0.7223 (ttmt) REVERT: N 3 GLN cc_start: 0.6794 (tt0) cc_final: 0.6576 (tm-30) REVERT: N 34 MET cc_start: 0.7798 (mmm) cc_final: 0.7471 (mmt) REVERT: N 60 TYR cc_start: 0.7749 (m-80) cc_final: 0.7433 (m-80) REVERT: N 67 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6746 (ttp80) REVERT: N 115 TYR cc_start: 0.7714 (t80) cc_final: 0.7314 (t80) REVERT: R 275 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6850 (tt0) outliers start: 29 outliers final: 17 residues processed: 297 average time/residue: 0.2066 time to fit residues: 80.7490 Evaluate side-chains 292 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 274 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 105 PHE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 30.0000 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 0.0980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7617 Z= 0.191 Angle : 0.604 12.554 10380 Z= 0.316 Chirality : 0.043 0.156 1199 Planarity : 0.004 0.049 1341 Dihedral : 4.572 17.380 1100 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.49 % Allowed : 21.59 % Favored : 73.91 % 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: 0.34 (0.27), residues: 1013 helix: 2.25 (0.26), residues: 399 sheet: -0.08 (0.35), residues: 218 loop : -1.80 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.006 0.001 HIS A 220 PHE 0.019 0.002 PHE R 272 TYR 0.016 0.001 TYR R 211 ARG 0.004 0.000 ARG R 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 274 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 301 LYS cc_start: 0.7292 (mptt) cc_final: 0.6990 (mttm) REVERT: N 34 MET cc_start: 0.7898 (mmm) cc_final: 0.7596 (mmt) REVERT: N 60 TYR cc_start: 0.7747 (m-80) cc_final: 0.7468 (m-80) REVERT: N 67 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6691 (ttp80) REVERT: N 74 ASN cc_start: 0.6898 (m-40) cc_final: 0.6565 (p0) REVERT: N 115 TYR cc_start: 0.7778 (t80) cc_final: 0.7354 (t80) REVERT: R 126 ASP cc_start: 0.8712 (t0) cc_final: 0.8463 (t0) REVERT: R 137 TYR cc_start: 0.8739 (t80) cc_final: 0.7917 (t80) REVERT: R 211 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.7212 (t80) outliers start: 31 outliers final: 24 residues processed: 286 average time/residue: 0.2061 time to fit residues: 77.7536 Evaluate side-chains 296 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 105 PHE Chi-restraints excluded: chain R residue 117 MET Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 211 TYR Chi-restraints excluded: chain R residue 215 PHE Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 282 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7617 Z= 0.276 Angle : 0.639 8.525 10380 Z= 0.342 Chirality : 0.045 0.185 1199 Planarity : 0.004 0.049 1341 Dihedral : 4.764 16.645 1100 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.51 % Allowed : 22.61 % Favored : 71.88 % 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 (0.27), residues: 1013 helix: 2.08 (0.26), residues: 403 sheet: -0.13 (0.36), residues: 212 loop : -1.84 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.006 0.001 HIS A 220 PHE 0.025 0.002 PHE R 107 TYR 0.022 0.002 TYR A 37 ARG 0.010 0.001 ARG R 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 275 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: B 124 TYR cc_start: 0.8084 (m-80) cc_final: 0.7691 (m-80) REVERT: B 251 ARG cc_start: 0.7827 (mtt90) cc_final: 0.7521 (mtm-85) REVERT: N 34 MET cc_start: 0.8032 (mmm) cc_final: 0.7732 (mmt) REVERT: N 60 TYR cc_start: 0.7763 (m-80) cc_final: 0.7487 (m-80) REVERT: N 74 ASN cc_start: 0.7096 (m-40) cc_final: 0.6723 (p0) REVERT: N 115 TYR cc_start: 0.7819 (t80) cc_final: 0.7332 (t80) REVERT: R 126 ASP cc_start: 0.8762 (t0) cc_final: 0.8556 (t0) REVERT: R 137 TYR cc_start: 0.8784 (t80) cc_final: 0.8005 (t80) REVERT: R 198 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6811 (mpt) REVERT: R 211 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.7234 (t80) REVERT: R 275 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6997 (tt0) outliers start: 38 outliers final: 28 residues processed: 289 average time/residue: 0.2027 time to fit residues: 77.1750 Evaluate side-chains 296 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 266 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 117 MET Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 198 MET Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 211 TYR Chi-restraints excluded: chain R residue 215 PHE Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 282 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 0.0770 chunk 96 optimal weight: 0.0010 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7617 Z= 0.171 Angle : 0.600 8.840 10380 Z= 0.313 Chirality : 0.043 0.165 1199 Planarity : 0.004 0.052 1341 Dihedral : 4.398 15.739 1100 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.20 % Allowed : 24.49 % Favored : 71.30 % 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: 0.42 (0.27), residues: 1013 helix: 2.31 (0.26), residues: 402 sheet: -0.11 (0.35), residues: 215 loop : -1.73 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 PHE 0.029 0.002 PHE R 107 TYR 0.017 0.001 TYR R 211 ARG 0.009 0.000 ARG R 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 279 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: B 124 TYR cc_start: 0.7869 (m-80) cc_final: 0.7518 (m-80) REVERT: B 251 ARG cc_start: 0.7728 (mtt90) cc_final: 0.7470 (mtm-85) REVERT: B 301 LYS cc_start: 0.7179 (mptt) cc_final: 0.6899 (mttm) REVERT: N 5 GLN cc_start: 0.7965 (mp10) cc_final: 0.7753 (mm-40) REVERT: N 34 MET cc_start: 0.7911 (mmm) cc_final: 0.7663 (mmt) REVERT: N 60 TYR cc_start: 0.7781 (m-80) cc_final: 0.7537 (m-80) REVERT: N 67 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6839 (ttp80) REVERT: N 87 LYS cc_start: 0.7837 (tttt) cc_final: 0.7456 (tptm) REVERT: N 115 TYR cc_start: 0.7792 (t80) cc_final: 0.7245 (t80) REVERT: R 127 ARG cc_start: 0.8264 (mmp-170) cc_final: 0.7911 (tpp-160) REVERT: R 137 TYR cc_start: 0.8718 (t80) cc_final: 0.7849 (t80) REVERT: R 211 TYR cc_start: 0.7703 (OUTLIER) cc_final: 0.7068 (t80) REVERT: R 275 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6853 (tt0) outliers start: 29 outliers final: 22 residues processed: 288 average time/residue: 0.1953 time to fit residues: 74.0975 Evaluate side-chains 290 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 105 PHE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 211 TYR Chi-restraints excluded: chain R residue 215 PHE Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 282 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 47 optimal weight: 0.0670 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7617 Z= 0.170 Angle : 0.598 7.799 10380 Z= 0.312 Chirality : 0.044 0.195 1199 Planarity : 0.004 0.052 1341 Dihedral : 4.242 15.213 1100 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.35 % Allowed : 26.52 % Favored : 69.13 % 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: 0.58 (0.27), residues: 1013 helix: 2.49 (0.26), residues: 400 sheet: 0.01 (0.35), residues: 215 loop : -1.70 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 PHE 0.025 0.002 PHE R 107 TYR 0.021 0.001 TYR A 37 ARG 0.009 0.000 ARG R 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: B 124 TYR cc_start: 0.7907 (m-80) cc_final: 0.7504 (m-80) REVERT: B 262 MET cc_start: 0.6880 (mmt) cc_final: 0.6679 (mmt) REVERT: B 301 LYS cc_start: 0.7198 (mptt) cc_final: 0.6827 (mttm) REVERT: N 34 MET cc_start: 0.7838 (mmm) cc_final: 0.7633 (mmt) REVERT: N 60 TYR cc_start: 0.7804 (m-80) cc_final: 0.7569 (m-80) REVERT: N 67 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6935 (ttp80) REVERT: N 87 LYS cc_start: 0.7792 (tttt) cc_final: 0.7426 (tptm) REVERT: N 115 TYR cc_start: 0.7778 (t80) cc_final: 0.7240 (t80) REVERT: R 127 ARG cc_start: 0.8276 (mmp-170) cc_final: 0.7873 (tpp-160) REVERT: R 137 TYR cc_start: 0.8690 (t80) cc_final: 0.7804 (t80) REVERT: R 211 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.7005 (t80) REVERT: R 275 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6865 (tt0) outliers start: 30 outliers final: 22 residues processed: 274 average time/residue: 0.2126 time to fit residues: 75.9829 Evaluate side-chains 286 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 105 PHE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 211 TYR Chi-restraints excluded: chain R residue 215 PHE Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 282 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 0.0670 chunk 57 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7617 Z= 0.182 Angle : 0.613 8.007 10380 Z= 0.317 Chirality : 0.044 0.233 1199 Planarity : 0.004 0.052 1341 Dihedral : 4.178 15.587 1100 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.62 % Allowed : 27.97 % Favored : 68.41 % 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: 0.64 (0.27), residues: 1013 helix: 2.53 (0.26), residues: 400 sheet: 0.10 (0.36), residues: 215 loop : -1.68 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS A 220 PHE 0.024 0.002 PHE R 107 TYR 0.021 0.001 TYR A 37 ARG 0.007 0.000 ARG R 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 260 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 124 TYR cc_start: 0.7925 (m-80) cc_final: 0.7488 (m-80) REVERT: B 301 LYS cc_start: 0.7208 (mptt) cc_final: 0.6840 (mttm) REVERT: N 34 MET cc_start: 0.7837 (mmm) cc_final: 0.7581 (mmt) REVERT: N 60 TYR cc_start: 0.7811 (m-80) cc_final: 0.7585 (m-80) REVERT: N 67 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6937 (ttp80) REVERT: N 87 LYS cc_start: 0.7811 (tttt) cc_final: 0.7491 (tttt) REVERT: N 115 TYR cc_start: 0.7811 (t80) cc_final: 0.7279 (t80) REVERT: R 127 ARG cc_start: 0.8271 (mmp-170) cc_final: 0.7879 (tpp-160) REVERT: R 198 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6387 (mpt) REVERT: R 211 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7029 (t80) REVERT: R 275 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6837 (tt0) REVERT: A 211 LYS cc_start: 0.7663 (mmtm) cc_final: 0.7420 (mmtp) outliers start: 25 outliers final: 22 residues processed: 268 average time/residue: 0.2075 time to fit residues: 72.7834 Evaluate side-chains 286 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 198 MET Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 211 TYR Chi-restraints excluded: chain R residue 215 PHE Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 282 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 0.0010 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7617 Z= 0.182 Angle : 0.618 7.750 10380 Z= 0.320 Chirality : 0.044 0.186 1199 Planarity : 0.004 0.052 1341 Dihedral : 4.133 15.755 1100 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.48 % Allowed : 28.12 % Favored : 68.41 % 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: 0.73 (0.27), residues: 1013 helix: 2.60 (0.26), residues: 400 sheet: 0.16 (0.36), residues: 215 loop : -1.64 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 PHE 0.025 0.002 PHE R 107 TYR 0.021 0.001 TYR A 37 ARG 0.007 0.000 ARG R 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 SER cc_start: 0.9011 (t) cc_final: 0.8288 (p) REVERT: B 124 TYR cc_start: 0.7972 (m-80) cc_final: 0.7548 (m-80) REVERT: B 172 GLU cc_start: 0.8320 (pm20) cc_final: 0.8026 (pm20) REVERT: B 301 LYS cc_start: 0.7217 (mptt) cc_final: 0.6935 (mttm) REVERT: N 34 MET cc_start: 0.7834 (mmm) cc_final: 0.7587 (mmt) REVERT: N 60 TYR cc_start: 0.7796 (m-80) cc_final: 0.7552 (m-80) REVERT: N 67 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6955 (ttp80) REVERT: N 87 LYS cc_start: 0.7827 (tttt) cc_final: 0.7511 (tttt) REVERT: N 115 TYR cc_start: 0.7845 (t80) cc_final: 0.7336 (t80) REVERT: R 127 ARG cc_start: 0.8249 (mmp-170) cc_final: 0.7778 (tpp-160) REVERT: R 137 TYR cc_start: 0.8699 (t80) cc_final: 0.7822 (t80) REVERT: R 211 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.7025 (t80) REVERT: R 275 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6807 (tt0) REVERT: A 211 LYS cc_start: 0.7683 (mmtm) cc_final: 0.7465 (mmtp) outliers start: 24 outliers final: 21 residues processed: 272 average time/residue: 0.2055 time to fit residues: 73.1757 Evaluate side-chains 285 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 262 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 139 THR Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 211 TYR Chi-restraints excluded: chain R residue 215 PHE Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 282 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.0060 chunk 4 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.164875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138448 restraints weight = 12325.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.142769 restraints weight = 6790.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.145731 restraints weight = 4404.993| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7617 Z= 0.207 Angle : 0.618 7.568 10380 Z= 0.322 Chirality : 0.044 0.173 1199 Planarity : 0.004 0.052 1341 Dihedral : 4.187 16.217 1100 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.48 % Allowed : 28.99 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1013 helix: 2.64 (0.26), residues: 398 sheet: 0.17 (0.36), residues: 215 loop : -1.71 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.005 0.001 HIS A 220 PHE 0.024 0.002 PHE R 107 TYR 0.021 0.001 TYR A 37 ARG 0.007 0.000 ARG R 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2192.46 seconds wall clock time: 40 minutes 26.51 seconds (2426.51 seconds total)