Starting phenix.real_space_refine on Mon Mar 11 06:50:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj2_33481/03_2024/8hj2_33481.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj2_33481/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj2_33481/03_2024/8hj2_33481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj2_33481/03_2024/8hj2_33481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj2_33481/03_2024/8hj2_33481.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj2_33481/03_2024/8hj2_33481.pdb" } 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 Residue "B ASP 76": "OD1" <-> "OD2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 360": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.61, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 2.62 Conformation dependent library (CDL) restraints added in 1.5 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: 0.78 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: 2.33 Time building geometry restraints manager: 2.90 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: 93.31 - 101.47: 12 101.47 - 109.62: 1002 109.62 - 117.78: 4630 117.78 - 125.94: 4607 125.94 - 134.10: 129 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 2.440 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.265 2.440 nonbonded pdb=" O VAL R 111 " pdb=" OG SER R 114 " model vdw 2.268 2.440 nonbonded pdb=" O ASP B 228 " pdb=" OG SER B 245 " model vdw 2.271 2.440 nonbonded pdb=" OG1 THR N 91 " pdb=" O VAL N 124 " model vdw 2.312 2.440 ... (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 ========== 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: 0.710 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: 3.710 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.040 Find NCS groups from input model: 0.190 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: 30.740 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 0.844 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: 0.2261 time to fit residues: 90.3403 Evaluate side-chains 277 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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: 0.9980 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 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: 0.7501 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7617 Z= 0.198 Angle : 0.633 8.297 10380 Z= 0.335 Chirality : 0.045 0.182 1199 Planarity : 0.005 0.068 1341 Dihedral : 5.613 20.420 1100 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.75 % Allowed : 15.22 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.25), residues: 1013 helix: 0.76 (0.25), residues: 409 sheet: -0.41 (0.35), residues: 210 loop : -1.99 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 169 HIS 0.004 0.001 HIS R 174 PHE 0.022 0.002 PHE R 272 TYR 0.017 0.001 TYR A 350 ARG 0.009 0.001 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 309 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 290 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 143 THR cc_start: 0.6991 (p) cc_final: 0.6550 (t) REVERT: B 205 ASP cc_start: 0.8287 (p0) cc_final: 0.8054 (p0) REVERT: B 241 PHE cc_start: 0.8495 (p90) cc_final: 0.8251 (p90) REVERT: B 262 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.7074 (mmt) REVERT: N 34 MET cc_start: 0.7635 (mmm) cc_final: 0.7331 (mmt) REVERT: R 153 ILE cc_start: 0.8946 (mt) cc_final: 0.8738 (mt) REVERT: A 209 GLU cc_start: 0.7011 (pp20) cc_final: 0.6713 (pp20) REVERT: A 220 HIS cc_start: 0.7975 (t70) cc_final: 0.7368 (t70) REVERT: A 332 ARG cc_start: 0.8643 (ttp80) cc_final: 0.8416 (ttp80) outliers start: 19 outliers final: 12 residues processed: 295 average time/residue: 0.1913 time to fit residues: 74.6803 Evaluate side-chains 296 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 283 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 THR 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 N residue 89 GLU 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: 0.6980 chunk 75 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 0.052 7617 Z= 0.228 Angle : 0.607 8.017 10380 Z= 0.325 Chirality : 0.044 0.167 1199 Planarity : 0.004 0.045 1341 Dihedral : 5.108 18.638 1100 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.78 % Allowed : 16.96 % Favored : 78.26 % 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: -0.21 (0.26), residues: 1013 helix: 1.60 (0.26), residues: 402 sheet: -0.38 (0.35), residues: 219 loop : -1.88 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.005 0.001 HIS A 352 PHE 0.015 0.002 PHE R 272 TYR 0.012 0.001 TYR A 350 ARG 0.004 0.000 ARG N 19 *********************** 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 321 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 288 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 124 TYR cc_start: 0.7922 (m-80) cc_final: 0.7617 (m-80) REVERT: B 143 THR cc_start: 0.7044 (p) cc_final: 0.6540 (t) REVERT: B 241 PHE cc_start: 0.8575 (p90) cc_final: 0.8281 (p90) REVERT: B 261 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8024 (mm) REVERT: N 34 MET cc_start: 0.7849 (mmm) cc_final: 0.7567 (mmt) REVERT: N 60 TYR cc_start: 0.7608 (m-80) cc_final: 0.7263 (m-80) REVERT: N 115 TYR cc_start: 0.7787 (t80) cc_final: 0.7414 (t80) REVERT: R 153 ILE cc_start: 0.8876 (mt) cc_final: 0.8653 (mt) REVERT: R 217 ILE cc_start: 0.8706 (mm) cc_final: 0.8440 (mt) REVERT: R 275 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7018 (tt0) REVERT: A 209 GLU cc_start: 0.7122 (pp20) cc_final: 0.6522 (pp20) REVERT: A 220 HIS cc_start: 0.8028 (t70) cc_final: 0.7315 (t70) outliers start: 33 outliers final: 25 residues processed: 296 average time/residue: 0.1948 time to fit residues: 76.4646 Evaluate side-chains 313 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 287 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR 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 270 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 89 GLU 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 111 VAL 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 222 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 300 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.0050 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 123 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7617 Z= 0.186 Angle : 0.584 12.373 10380 Z= 0.306 Chirality : 0.043 0.161 1199 Planarity : 0.004 0.047 1341 Dihedral : 4.769 17.730 1100 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.80 % Allowed : 20.14 % Favored : 74.06 % 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 (0.27), residues: 1013 helix: 2.00 (0.26), residues: 404 sheet: -0.33 (0.34), residues: 219 loop : -1.73 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.006 0.001 HIS A 352 PHE 0.023 0.002 PHE R 107 TYR 0.020 0.001 TYR R 211 ARG 0.003 0.000 ARG N 67 *********************** 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 331 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 291 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: B 124 TYR cc_start: 0.7951 (m-80) cc_final: 0.7619 (m-80) REVERT: B 143 THR cc_start: 0.6907 (p) cc_final: 0.6584 (t) REVERT: B 205 ASP cc_start: 0.8298 (p0) cc_final: 0.8039 (p0) REVERT: B 241 PHE cc_start: 0.8557 (p90) cc_final: 0.8320 (p90) REVERT: B 261 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8045 (mm) REVERT: N 29 PHE cc_start: 0.7380 (t80) cc_final: 0.7166 (t80) REVERT: N 34 MET cc_start: 0.7800 (mmm) cc_final: 0.7425 (mmt) REVERT: N 60 TYR cc_start: 0.7672 (m-80) cc_final: 0.7394 (m-80) REVERT: N 87 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7775 (tttt) REVERT: N 115 TYR cc_start: 0.7748 (t80) cc_final: 0.7359 (t80) REVERT: R 153 ILE cc_start: 0.8768 (mt) cc_final: 0.8546 (mt) REVERT: R 170 LYS cc_start: 0.7458 (mttm) cc_final: 0.7251 (mttp) REVERT: R 198 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6669 (mpt) REVERT: R 211 TYR cc_start: 0.7646 (m-80) cc_final: 0.7359 (t80) REVERT: R 217 ILE cc_start: 0.8707 (mm) cc_final: 0.8446 (mt) REVERT: R 275 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6924 (tt0) REVERT: A 209 GLU cc_start: 0.7056 (pp20) cc_final: 0.6785 (pp20) REVERT: A 220 HIS cc_start: 0.7934 (t70) cc_final: 0.7383 (t70) outliers start: 40 outliers final: 30 residues processed: 304 average time/residue: 0.1888 time to fit residues: 76.1133 Evaluate side-chains 316 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 283 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 72 SER Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 164 THR 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 322 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU 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 146 LEU 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 215 PHE Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain A residue 45 LEU 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 Chi-restraints excluded: chain A residue 300 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 40.0000 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 86 optimal weight: 0.0870 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.7162 ------------------------------------------------------------------------------- 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 268 ASN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7617 Z= 0.272 Angle : 0.620 9.041 10380 Z= 0.331 Chirality : 0.044 0.154 1199 Planarity : 0.004 0.049 1341 Dihedral : 4.834 16.623 1100 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.23 % Allowed : 20.72 % Favored : 73.04 % 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: 0.17 (0.27), residues: 1013 helix: 2.10 (0.26), residues: 397 sheet: -0.28 (0.35), residues: 219 loop : -1.79 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.005 0.001 HIS A 352 PHE 0.013 0.002 PHE R 272 TYR 0.017 0.002 TYR R 211 ARG 0.010 0.001 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 324 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 281 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 TYR cc_start: 0.7994 (m-80) cc_final: 0.7597 (m-80) REVERT: B 205 ASP cc_start: 0.8314 (p0) cc_final: 0.8048 (p0) REVERT: B 241 PHE cc_start: 0.8664 (p90) cc_final: 0.8434 (p90) REVERT: N 34 MET cc_start: 0.8030 (mmm) cc_final: 0.7672 (mmt) REVERT: N 60 TYR cc_start: 0.7655 (m-80) cc_final: 0.7409 (m-80) REVERT: N 115 TYR cc_start: 0.7780 (t80) cc_final: 0.7395 (t80) REVERT: R 153 ILE cc_start: 0.8872 (mt) cc_final: 0.8651 (mt) REVERT: R 170 LYS cc_start: 0.7701 (mttm) cc_final: 0.7433 (mttp) REVERT: R 198 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.6890 (mpt) REVERT: R 211 TYR cc_start: 0.7663 (m-80) cc_final: 0.7396 (t80) REVERT: R 217 ILE cc_start: 0.8684 (mm) cc_final: 0.8417 (mt) REVERT: A 284 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7205 (mm110) outliers start: 43 outliers final: 35 residues processed: 295 average time/residue: 0.1914 time to fit residues: 74.5973 Evaluate side-chains 312 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 276 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 72 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 91 HIS 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 284 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 89 GLU 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 111 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 215 PHE Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 300 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7617 Z= 0.234 Angle : 0.615 8.317 10380 Z= 0.324 Chirality : 0.043 0.159 1199 Planarity : 0.004 0.048 1341 Dihedral : 4.715 16.084 1100 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.38 % Allowed : 21.88 % Favored : 71.74 % 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: 0.26 (0.27), residues: 1013 helix: 2.14 (0.26), residues: 400 sheet: -0.26 (0.35), residues: 219 loop : -1.71 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.024 0.002 PHE N 29 TYR 0.020 0.002 TYR A 37 ARG 0.004 0.000 ARG N 19 *********************** 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 320 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 276 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7728 (mp10) REVERT: B 124 TYR cc_start: 0.8021 (m-80) cc_final: 0.7644 (m-80) REVERT: B 205 ASP cc_start: 0.8304 (p0) cc_final: 0.8024 (p0) REVERT: N 34 MET cc_start: 0.8047 (mmm) cc_final: 0.7670 (mmt) REVERT: N 60 TYR cc_start: 0.7602 (m-80) cc_final: 0.7402 (m-80) REVERT: N 73 ASP cc_start: 0.8001 (m-30) cc_final: 0.7409 (m-30) REVERT: N 87 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7781 (tttt) REVERT: N 115 TYR cc_start: 0.7783 (t80) cc_final: 0.7405 (t80) REVERT: R 153 ILE cc_start: 0.8846 (mt) cc_final: 0.8615 (mt) REVERT: R 198 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.6827 (mpt) REVERT: R 211 TYR cc_start: 0.7668 (m-80) cc_final: 0.7384 (t80) REVERT: R 217 ILE cc_start: 0.8680 (mm) cc_final: 0.8415 (mt) outliers start: 44 outliers final: 37 residues processed: 290 average time/residue: 0.1885 time to fit residues: 72.3691 Evaluate side-chains 316 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 276 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 72 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 GLN 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 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU 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 114 SER 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 215 PHE Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain A residue 45 LEU 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 Chi-restraints excluded: chain A residue 300 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7617 Z= 0.195 Angle : 0.612 13.179 10380 Z= 0.315 Chirality : 0.043 0.165 1199 Planarity : 0.004 0.050 1341 Dihedral : 4.531 16.137 1100 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.94 % Allowed : 23.33 % Favored : 70.72 % 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: 0.44 (0.27), residues: 1013 helix: 2.29 (0.26), residues: 402 sheet: -0.14 (0.35), residues: 217 loop : -1.64 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.020 0.002 PHE B 199 TYR 0.018 0.001 TYR R 211 ARG 0.005 0.000 ARG N 19 *********************** 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 322 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 281 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: B 124 TYR cc_start: 0.8013 (m-80) cc_final: 0.7612 (m-80) REVERT: B 205 ASP cc_start: 0.8297 (p0) cc_final: 0.8013 (p0) REVERT: N 34 MET cc_start: 0.8053 (mmm) cc_final: 0.7725 (mmt) REVERT: N 60 TYR cc_start: 0.7614 (m-80) cc_final: 0.7398 (m-80) REVERT: N 87 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7698 (tttt) REVERT: N 115 TYR cc_start: 0.7782 (t80) cc_final: 0.7338 (t80) REVERT: R 153 ILE cc_start: 0.8753 (mt) cc_final: 0.8537 (mt) REVERT: R 217 ILE cc_start: 0.8696 (mm) cc_final: 0.8470 (mt) outliers start: 41 outliers final: 32 residues processed: 294 average time/residue: 0.2038 time to fit residues: 79.1533 Evaluate side-chains 308 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 274 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 72 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 105 PHE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 111 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 205 LEU Chi-restraints excluded: chain R residue 215 PHE Chi-restraints excluded: chain R residue 222 THR 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 Chi-restraints excluded: chain A residue 300 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7617 Z= 0.186 Angle : 0.608 10.809 10380 Z= 0.313 Chirality : 0.043 0.170 1199 Planarity : 0.004 0.051 1341 Dihedral : 4.420 16.081 1100 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 6.67 % Allowed : 22.90 % Favored : 70.43 % 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: 0.52 (0.27), residues: 1013 helix: 2.43 (0.26), residues: 399 sheet: -0.08 (0.35), residues: 217 loop : -1.66 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 PHE 0.034 0.002 PHE N 29 TYR 0.020 0.001 TYR A 37 ARG 0.005 0.000 ARG N 19 *********************** 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 320 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 274 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7707 (mp10) REVERT: B 124 TYR cc_start: 0.8000 (m-80) cc_final: 0.7592 (m-80) REVERT: B 172 GLU cc_start: 0.8288 (pm20) cc_final: 0.8037 (pm20) REVERT: B 205 ASP cc_start: 0.8314 (p0) cc_final: 0.8023 (p0) REVERT: N 34 MET cc_start: 0.8080 (mmm) cc_final: 0.7772 (mmt) REVERT: N 60 TYR cc_start: 0.7634 (m-80) cc_final: 0.7433 (m-80) REVERT: N 87 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7686 (tttt) REVERT: N 115 TYR cc_start: 0.7786 (t80) cc_final: 0.7328 (t80) REVERT: R 153 ILE cc_start: 0.8641 (mt) cc_final: 0.8429 (mt) REVERT: R 198 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6614 (mpt) REVERT: R 211 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.7085 (t80) outliers start: 46 outliers final: 36 residues processed: 286 average time/residue: 0.1972 time to fit residues: 74.1199 Evaluate side-chains 312 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 272 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 72 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 105 PHE 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 222 THR 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 Chi-restraints excluded: chain A residue 300 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.0040 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.0770 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.5550 ------------------------------------------------------------------------------- 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: 0.7463 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7617 Z= 0.178 Angle : 0.605 10.784 10380 Z= 0.310 Chirality : 0.043 0.175 1199 Planarity : 0.004 0.052 1341 Dihedral : 4.308 15.921 1100 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.07 % Allowed : 24.93 % Favored : 70.00 % 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: 0.63 (0.27), residues: 1013 helix: 2.55 (0.27), residues: 397 sheet: 0.01 (0.35), residues: 217 loop : -1.62 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.024 0.002 PHE N 29 TYR 0.021 0.001 TYR A 37 ARG 0.004 0.000 ARG B 68 *********************** 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 307 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 272 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: B 124 TYR cc_start: 0.7962 (m-80) cc_final: 0.7605 (m-80) REVERT: B 172 GLU cc_start: 0.8295 (pm20) cc_final: 0.8054 (pm20) REVERT: B 280 LYS cc_start: 0.7568 (tttt) cc_final: 0.7296 (ttmt) REVERT: N 29 PHE cc_start: 0.7416 (t80) cc_final: 0.7070 (t80) REVERT: N 34 MET cc_start: 0.8012 (mmm) cc_final: 0.7704 (mmt) REVERT: N 74 ASN cc_start: 0.7082 (m-40) cc_final: 0.6693 (p0) REVERT: N 87 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7662 (tttt) REVERT: N 115 TYR cc_start: 0.7799 (t80) cc_final: 0.7365 (t80) REVERT: R 153 ILE cc_start: 0.8567 (mt) cc_final: 0.8360 (mt) REVERT: R 198 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6542 (mpt) REVERT: R 211 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.7024 (t80) outliers start: 35 outliers final: 30 residues processed: 283 average time/residue: 0.2023 time to fit residues: 75.4578 Evaluate side-chains 303 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 269 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 75 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 63 THR 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 222 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 300 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 99 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 0.0010 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 0.3786 ------------------------------------------------------------------------------- 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: 0.7437 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7617 Z= 0.175 Angle : 0.623 13.096 10380 Z= 0.316 Chirality : 0.043 0.174 1199 Planarity : 0.003 0.052 1341 Dihedral : 4.215 15.778 1100 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.93 % Allowed : 26.23 % Favored : 68.84 % 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: 0.69 (0.27), residues: 1013 helix: 2.61 (0.26), residues: 399 sheet: -0.01 (0.36), residues: 220 loop : -1.62 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 PHE 0.024 0.001 PHE N 29 TYR 0.021 0.001 TYR A 37 ARG 0.004 0.000 ARG N 19 ********************** 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 301 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 267 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: B 68 ARG cc_start: 0.7966 (ttt-90) cc_final: 0.7463 (mtp-110) REVERT: B 75 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: B 124 TYR cc_start: 0.7902 (m-80) cc_final: 0.7546 (m-80) REVERT: B 172 GLU cc_start: 0.8318 (pm20) cc_final: 0.8082 (pm20) REVERT: B 205 ASP cc_start: 0.8270 (p0) cc_final: 0.8010 (p0) REVERT: N 34 MET cc_start: 0.8031 (mmm) cc_final: 0.7721 (mmt) REVERT: N 74 ASN cc_start: 0.7024 (m-40) cc_final: 0.6625 (p0) REVERT: N 87 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7558 (tttt) REVERT: N 115 TYR cc_start: 0.7836 (t80) cc_final: 0.7450 (t80) REVERT: R 153 ILE cc_start: 0.8546 (mt) cc_final: 0.8341 (mt) REVERT: R 198 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6418 (mpt) REVERT: R 211 TYR cc_start: 0.7577 (OUTLIER) cc_final: 0.6996 (t80) outliers start: 34 outliers final: 25 residues processed: 277 average time/residue: 0.1974 time to fit residues: 72.0145 Evaluate side-chains 291 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 262 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 75 GLN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 63 THR 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 A residue 224 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 300 ASP 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: 0.1980 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 4 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 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 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.164383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.138531 restraints weight = 12345.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.142826 restraints weight = 6637.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.145779 restraints weight = 4233.693| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3262 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= 0.191 Angle : 0.629 11.516 10380 Z= 0.320 Chirality : 0.043 0.166 1199 Planarity : 0.004 0.052 1341 Dihedral : 4.212 15.609 1100 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.07 % Allowed : 26.67 % Favored : 68.26 % 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: 2.65 (0.26), residues: 399 sheet: 0.05 (0.36), residues: 212 loop : -1.64 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.024 0.001 PHE N 29 TYR 0.022 0.001 TYR A 37 ARG 0.011 0.000 ARG R 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2154.67 seconds wall clock time: 39 minutes 30.06 seconds (2370.06 seconds total)