Starting phenix.real_space_refine on Sat Aug 23 05:26:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1u_41829/08_2025/8u1u_41829.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1u_41829/08_2025/8u1u_41829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u1u_41829/08_2025/8u1u_41829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1u_41829/08_2025/8u1u_41829.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1u_41829/08_2025/8u1u_41829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1u_41829/08_2025/8u1u_41829.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 1.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 543 atoms to isotropic. 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 75 5.16 5 C 6065 2.51 5 N 1603 2.21 5 O 1764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9507 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2952 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 9, 'TRANS': 356} Chain breaks: 1 Chain: "B" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1726 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 211} Chain breaks: 2 Chain: "C" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "D" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.31, per 1000 atoms: 0.24 Number of scatterers: 9507 At special positions: 0 Unit cell: (91.377, 120.821, 144.173, 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 75 16.00 O 1764 8.00 N 1603 7.00 C 6065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 57 " distance=2.02 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS A 117 " distance=2.03 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 91 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 220 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 900 " - " ASN A 52 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 274.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 38.1% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 127 through 159 Processing helix chain 'A' and resid 164 through 182 Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 197 through 233 removed outlier: 4.102A pdb=" N MET A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 242 through 267 Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 286 through 303 Processing helix chain 'A' and resid 303 through 324 Processing helix chain 'A' and resid 329 through 362 removed outlier: 3.599A pdb=" N ILE A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 367 through 397 removed outlier: 3.874A pdb=" N HIS A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N CYS A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Proline residue: A 393 - end of helix Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.898A pdb=" N LYS A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N HIS A 406 " --> pdb=" O LYS A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 33 removed outlier: 3.761A pdb=" N GLU B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 removed outlier: 3.845A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.442A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 242 through 255 Processing helix chain 'B' and resid 270 through 281 Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.690A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 329 through 351 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 8 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 56 through 59 removed outlier: 4.195A pdb=" N GLY E 59 " --> pdb=" O SER E 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 56 through 59' Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 211 through 215 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 273 Processing sheet with id=AA4, first strand: chain 'B' and resid 185 through 191 removed outlier: 3.618A pdb=" N MET B 198 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 189 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ALA B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 51 Processing sheet with id=AA6, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.560A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.076A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.302A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.903A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.618A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.648A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 6 through 10 Processing sheet with id=AB4, first strand: chain 'E' and resid 14 through 15 removed outlier: 6.825A pdb=" N MET E 37 " --> pdb=" O TYR E 53 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR E 53 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP E 39 " --> pdb=" O VAL E 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AB6, first strand: chain 'E' and resid 138 through 139 removed outlier: 6.717A pdb=" N LEU E 165 " --> pdb=" O TYR E 181 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR E 181 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP E 167 " --> pdb=" O LEU E 179 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1383 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: 1.51 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3029 1.34 - 1.46: 2225 1.46 - 1.58: 4346 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 9705 Sorted by residual: bond pdb=" C ARG E 209 " pdb=" N LEU E 210 " ideal model delta sigma weight residual 1.333 1.384 -0.050 1.33e-02 5.65e+03 1.44e+01 bond pdb=" C SER E 208 " pdb=" N ARG E 209 " ideal model delta sigma weight residual 1.331 1.285 0.045 1.34e-02 5.57e+03 1.14e+01 bond pdb=" N THR B 4 " pdb=" CA THR B 4 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.24e+00 bond pdb=" CA SER A 58 " pdb=" CB SER A 58 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.63e-02 3.76e+03 3.21e+00 bond pdb=" N ALA D 7 " pdb=" CA ALA D 7 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 9700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 12320 1.31 - 2.62: 652 2.62 - 3.93: 111 3.93 - 5.24: 34 5.24 - 6.55: 13 Bond angle restraints: 13130 Sorted by residual: angle pdb=" C ARG E 182 " pdb=" N MET E 183 " pdb=" CA MET E 183 " ideal model delta sigma weight residual 121.54 128.09 -6.55 1.91e+00 2.74e-01 1.18e+01 angle pdb=" C GLN C 9 " pdb=" N GLU C 10 " pdb=" CA GLU C 10 " ideal model delta sigma weight residual 121.14 115.58 5.56 1.75e+00 3.27e-01 1.01e+01 angle pdb=" CG ARG C 214 " pdb=" CD ARG C 214 " pdb=" NE ARG C 214 " ideal model delta sigma weight residual 112.00 118.51 -6.51 2.20e+00 2.07e-01 8.75e+00 angle pdb=" CA SER A 58 " pdb=" C SER A 58 " pdb=" O SER A 58 " ideal model delta sigma weight residual 119.79 116.46 3.33 1.18e+00 7.18e-01 7.94e+00 angle pdb=" CA GLU C 10 " pdb=" CB GLU C 10 " pdb=" CG GLU C 10 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.62e+00 ... (remaining 13125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5289 17.67 - 35.33: 416 35.33 - 53.00: 59 53.00 - 70.66: 16 70.66 - 88.32: 8 Dihedral angle restraints: 5788 sinusoidal: 2282 harmonic: 3506 Sorted by residual: dihedral pdb=" CB CYS A 121 " pdb=" SG CYS A 121 " pdb=" SG CYS A 368 " pdb=" CB CYS A 368 " ideal model delta sinusoidal sigma weight residual 93.00 -178.68 -88.32 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CA ASP C 291 " pdb=" C ASP C 291 " pdb=" N PHE C 292 " pdb=" CA PHE C 292 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ILE A 47 " pdb=" C ILE A 47 " pdb=" N LEU A 48 " pdb=" CA LEU A 48 " ideal model delta harmonic sigma weight residual 180.00 153.01 26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 5785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1141 0.049 - 0.099: 280 0.099 - 0.148: 68 0.148 - 0.197: 6 0.197 - 0.247: 1 Chirality restraints: 1496 Sorted by residual: chirality pdb=" C1 NAG A 900 " pdb=" ND2 ASN A 52 " pdb=" C2 NAG A 900 " pdb=" O5 NAG A 900 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE E 61 " pdb=" N ILE E 61 " pdb=" C ILE E 61 " pdb=" CB ILE E 61 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CA ILE C 81 " pdb=" N ILE C 81 " pdb=" C ILE C 81 " pdb=" CB ILE C 81 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 1493 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 85 " 0.214 9.50e-02 1.11e+02 9.59e-02 5.75e+00 pdb=" NE ARG A 85 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 85 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 85 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 85 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 346 " 0.018 2.00e-02 2.50e+03 1.60e-02 4.51e+00 pdb=" CG PHE A 346 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A 346 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 346 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 346 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 346 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 346 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 203 " 0.011 2.00e-02 2.50e+03 1.41e-02 3.47e+00 pdb=" CG PHE E 203 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE E 203 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE E 203 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE E 203 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE E 203 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 203 " 0.009 2.00e-02 2.50e+03 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 103 2.58 - 3.16: 8320 3.16 - 3.74: 14938 3.74 - 4.32: 21612 4.32 - 4.90: 36045 Nonbonded interactions: 81018 Sorted by model distance: nonbonded pdb=" O LEU A 304 " pdb=" OG1 THR A 308 " model vdw 2.003 3.040 nonbonded pdb=" OG1 THR C 29 " pdb=" OE1 GLN C 32 " model vdw 2.036 3.040 nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 166 " model vdw 2.038 3.040 nonbonded pdb=" O VAL A 158 " pdb=" NZ LYS A 161 " model vdw 2.071 3.120 nonbonded pdb=" OG SER A 176 " pdb=" OG SER A 215 " model vdw 2.119 3.040 ... (remaining 81013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.830 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9713 Z= 0.201 Angle : 0.719 6.954 13147 Z= 0.388 Chirality : 0.046 0.247 1496 Planarity : 0.005 0.096 1649 Dihedral : 13.153 84.395 3503 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.24), residues: 1188 helix: 1.58 (0.26), residues: 402 sheet: -0.52 (0.29), residues: 301 loop : -0.47 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 214 TYR 0.019 0.002 TYR D 40 PHE 0.037 0.002 PHE A 346 TRP 0.014 0.002 TRP C 82 HIS 0.008 0.002 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 9705) covalent geometry : angle 0.71072 (13130) SS BOND : bond 0.00450 ( 7) SS BOND : angle 3.10498 ( 14) hydrogen bonds : bond 0.14184 ( 498) hydrogen bonds : angle 6.48780 ( 1383) link_NAG-ASN : bond 0.00008 ( 1) link_NAG-ASN : angle 3.39863 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8244 (m-30) cc_final: 0.7916 (m-30) REVERT: A 201 MET cc_start: 0.8427 (mmm) cc_final: 0.8195 (tpp) REVERT: A 284 ASN cc_start: 0.7560 (t0) cc_final: 0.6988 (t0) REVERT: B 21 ARG cc_start: 0.8101 (ptp90) cc_final: 0.7843 (mtm-85) REVERT: B 252 SER cc_start: 0.9135 (t) cc_final: 0.8933 (t) REVERT: D 21 MET cc_start: 0.8337 (tmm) cc_final: 0.7880 (tmm) REVERT: D 46 LYS cc_start: 0.9153 (mmmm) cc_final: 0.8913 (mmpt) REVERT: E 177 GLN cc_start: 0.8936 (pt0) cc_final: 0.8567 (pt0) REVERT: E 193 ARG cc_start: 0.8651 (ptt90) cc_final: 0.8451 (ptt90) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1174 time to fit residues: 29.9656 Evaluate side-chains 158 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 299 ASN B 52 GLN B 195 HIS B 255 ASN B 306 GLN C 176 GLN C 220 GLN C 259 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.091226 restraints weight = 15665.041| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.69 r_work: 0.3030 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9713 Z= 0.148 Angle : 0.602 7.243 13147 Z= 0.324 Chirality : 0.043 0.168 1496 Planarity : 0.004 0.034 1649 Dihedral : 5.354 49.936 1322 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.48 % Allowed : 5.82 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.24), residues: 1188 helix: 1.59 (0.26), residues: 408 sheet: -0.50 (0.30), residues: 289 loop : -0.34 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 214 TYR 0.021 0.001 TYR B 230 PHE 0.033 0.001 PHE A 346 TRP 0.010 0.001 TRP C 82 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9705) covalent geometry : angle 0.59659 (13130) SS BOND : bond 0.00468 ( 7) SS BOND : angle 1.97597 ( 14) hydrogen bonds : bond 0.04378 ( 498) hydrogen bonds : angle 5.40167 ( 1383) link_NAG-ASN : bond 0.00228 ( 1) link_NAG-ASN : angle 3.41567 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8610 (m-30) cc_final: 0.8194 (m-30) REVERT: A 284 ASN cc_start: 0.7626 (t0) cc_final: 0.7409 (t0) REVERT: A 401 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8022 (mm-30) REVERT: B 24 ARG cc_start: 0.7932 (ttt180) cc_final: 0.7205 (ttp80) REVERT: C 172 GLU cc_start: 0.8886 (tp30) cc_final: 0.8569 (tm-30) REVERT: C 175 GLN cc_start: 0.8088 (mp10) cc_final: 0.7850 (mp10) REVERT: D 21 MET cc_start: 0.8452 (tmm) cc_final: 0.7940 (tmm) REVERT: E 210 LEU cc_start: 0.8979 (mm) cc_final: 0.8414 (mm) outliers start: 5 outliers final: 1 residues processed: 166 average time/residue: 0.1004 time to fit residues: 22.0446 Evaluate side-chains 148 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 84 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 0.0010 chunk 72 optimal weight: 0.9980 chunk 116 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 187 GLN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN E 80 ASN E 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.088932 restraints weight = 15748.139| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.68 r_work: 0.3001 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9713 Z= 0.159 Angle : 0.567 7.649 13147 Z= 0.305 Chirality : 0.043 0.169 1496 Planarity : 0.003 0.034 1649 Dihedral : 5.186 49.966 1322 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.33 % Allowed : 9.34 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.24), residues: 1188 helix: 1.72 (0.26), residues: 407 sheet: -0.52 (0.29), residues: 299 loop : -0.49 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 41 TYR 0.016 0.001 TYR E 181 PHE 0.028 0.001 PHE A 346 TRP 0.011 0.001 TRP A 80 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9705) covalent geometry : angle 0.56287 (13130) SS BOND : bond 0.00355 ( 7) SS BOND : angle 1.78761 ( 14) hydrogen bonds : bond 0.04052 ( 498) hydrogen bonds : angle 5.21497 ( 1383) link_NAG-ASN : bond 0.00004 ( 1) link_NAG-ASN : angle 2.71836 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8605 (m-30) cc_final: 0.8141 (m-30) REVERT: A 284 ASN cc_start: 0.7678 (t0) cc_final: 0.7269 (t0) REVERT: A 398 PHE cc_start: 0.8048 (m-80) cc_final: 0.7772 (m-80) REVERT: A 401 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8137 (mm-30) REVERT: B 24 ARG cc_start: 0.7945 (ttt180) cc_final: 0.7242 (ttp80) REVERT: C 23 LYS cc_start: 0.9062 (ttpp) cc_final: 0.8824 (tptt) REVERT: C 32 GLN cc_start: 0.8291 (mp10) cc_final: 0.7971 (mp10) REVERT: C 172 GLU cc_start: 0.8909 (tp30) cc_final: 0.8584 (tm-30) REVERT: C 175 GLN cc_start: 0.8112 (mp10) cc_final: 0.7844 (mp10) REVERT: D 21 MET cc_start: 0.8570 (tmm) cc_final: 0.8288 (tmm) REVERT: E 46 LYS cc_start: 0.8987 (mmtp) cc_final: 0.8773 (mmmm) REVERT: E 210 LEU cc_start: 0.8954 (mm) cc_final: 0.8384 (mm) outliers start: 14 outliers final: 10 residues processed: 164 average time/residue: 0.1079 time to fit residues: 23.2895 Evaluate side-chains 157 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 193 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 102 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 0.0470 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN E 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.088311 restraints weight = 15887.887| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.67 r_work: 0.2988 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9713 Z= 0.160 Angle : 0.562 7.693 13147 Z= 0.301 Chirality : 0.042 0.165 1496 Planarity : 0.003 0.036 1649 Dihedral : 5.115 50.241 1322 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.62 % Allowed : 11.34 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.24), residues: 1188 helix: 1.81 (0.26), residues: 408 sheet: -0.50 (0.29), residues: 299 loop : -0.52 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 32 TYR 0.015 0.001 TYR E 181 PHE 0.025 0.001 PHE A 346 TRP 0.012 0.001 TRP A 80 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9705) covalent geometry : angle 0.55702 (13130) SS BOND : bond 0.00309 ( 7) SS BOND : angle 2.10805 ( 14) hydrogen bonds : bond 0.03889 ( 498) hydrogen bonds : angle 5.12875 ( 1383) link_NAG-ASN : bond 0.00030 ( 1) link_NAG-ASN : angle 2.30618 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 PHE cc_start: 0.8221 (m-80) cc_final: 0.7823 (m-80) REVERT: B 24 ARG cc_start: 0.7955 (ttt180) cc_final: 0.7235 (ttp80) REVERT: B 279 LYS cc_start: 0.8852 (pttm) cc_final: 0.8503 (pttp) REVERT: C 23 LYS cc_start: 0.9048 (ttpp) cc_final: 0.8783 (tptt) REVERT: C 172 GLU cc_start: 0.8931 (tp30) cc_final: 0.8569 (tm-30) REVERT: C 175 GLN cc_start: 0.8156 (mp10) cc_final: 0.7852 (mp10) REVERT: D 21 MET cc_start: 0.8594 (tmm) cc_final: 0.8275 (tmm) REVERT: E 46 LYS cc_start: 0.8982 (mmtp) cc_final: 0.8768 (mmmm) REVERT: E 210 LEU cc_start: 0.8871 (mm) cc_final: 0.8367 (mm) outliers start: 17 outliers final: 13 residues processed: 169 average time/residue: 0.1037 time to fit residues: 23.3921 Evaluate side-chains 161 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 193 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 53 optimal weight: 0.0670 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 110 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 72 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.091166 restraints weight = 15791.170| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.71 r_work: 0.3035 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9713 Z= 0.114 Angle : 0.539 7.553 13147 Z= 0.287 Chirality : 0.041 0.151 1496 Planarity : 0.003 0.036 1649 Dihedral : 4.962 50.462 1322 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.81 % Allowed : 12.01 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.24), residues: 1188 helix: 1.92 (0.26), residues: 414 sheet: -0.49 (0.30), residues: 286 loop : -0.51 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 89 TYR 0.015 0.001 TYR E 181 PHE 0.021 0.001 PHE A 346 TRP 0.012 0.001 TRP A 80 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9705) covalent geometry : angle 0.53568 (13130) SS BOND : bond 0.00246 ( 7) SS BOND : angle 1.72256 ( 14) hydrogen bonds : bond 0.03588 ( 498) hydrogen bonds : angle 4.98621 ( 1383) link_NAG-ASN : bond 0.00074 ( 1) link_NAG-ASN : angle 2.15298 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 26 MET cc_start: 0.9214 (mmm) cc_final: 0.8672 (tpp) REVERT: B 24 ARG cc_start: 0.7953 (ttt180) cc_final: 0.7248 (ttp80) REVERT: B 279 LYS cc_start: 0.8865 (pttm) cc_final: 0.8533 (pttm) REVERT: C 23 LYS cc_start: 0.9057 (ttpp) cc_final: 0.8780 (tptt) REVERT: C 32 GLN cc_start: 0.8130 (mp10) cc_final: 0.7732 (mp10) REVERT: C 172 GLU cc_start: 0.8924 (tp30) cc_final: 0.8492 (tm-30) REVERT: C 175 GLN cc_start: 0.8199 (mp10) cc_final: 0.7907 (mp10) REVERT: C 217 MET cc_start: 0.7940 (tpt) cc_final: 0.7656 (mmm) REVERT: D 21 MET cc_start: 0.8626 (tmm) cc_final: 0.8312 (tmm) REVERT: E 210 LEU cc_start: 0.8823 (mm) cc_final: 0.8340 (mm) outliers start: 19 outliers final: 14 residues processed: 166 average time/residue: 0.1066 time to fit residues: 23.3328 Evaluate side-chains 157 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 193 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 109 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.089631 restraints weight = 15742.172| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.64 r_work: 0.3001 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9713 Z= 0.160 Angle : 0.565 7.829 13147 Z= 0.301 Chirality : 0.042 0.173 1496 Planarity : 0.003 0.035 1649 Dihedral : 5.009 50.639 1322 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.91 % Allowed : 12.87 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.25), residues: 1188 helix: 1.92 (0.26), residues: 408 sheet: -0.50 (0.30), residues: 299 loop : -0.55 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.015 0.001 TYR E 181 PHE 0.022 0.001 PHE A 346 TRP 0.009 0.001 TRP C 82 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9705) covalent geometry : angle 0.56090 (13130) SS BOND : bond 0.00265 ( 7) SS BOND : angle 1.86148 ( 14) hydrogen bonds : bond 0.03763 ( 498) hydrogen bonds : angle 5.04021 ( 1383) link_NAG-ASN : bond 0.00030 ( 1) link_NAG-ASN : angle 1.89835 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 ARG cc_start: 0.7988 (ttt180) cc_final: 0.7285 (ttp80) REVERT: B 279 LYS cc_start: 0.8872 (pttm) cc_final: 0.8524 (pttm) REVERT: B 302 TYR cc_start: 0.8623 (t80) cc_final: 0.7816 (t80) REVERT: C 23 LYS cc_start: 0.9068 (ttpp) cc_final: 0.8791 (tptt) REVERT: C 172 GLU cc_start: 0.8915 (tp30) cc_final: 0.8493 (tm-30) REVERT: C 175 GLN cc_start: 0.8200 (mp10) cc_final: 0.7980 (mp10) REVERT: C 217 MET cc_start: 0.7981 (tpt) cc_final: 0.7687 (mmm) REVERT: D 21 MET cc_start: 0.8643 (tmm) cc_final: 0.8284 (tmm) REVERT: E 210 LEU cc_start: 0.8831 (mm) cc_final: 0.8352 (mm) outliers start: 20 outliers final: 18 residues processed: 166 average time/residue: 0.1161 time to fit residues: 25.4934 Evaluate side-chains 160 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 193 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 75 optimal weight: 0.0670 chunk 45 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.087415 restraints weight = 15925.792| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.66 r_work: 0.2984 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9713 Z= 0.182 Angle : 0.578 7.824 13147 Z= 0.307 Chirality : 0.043 0.166 1496 Planarity : 0.003 0.035 1649 Dihedral : 5.060 50.633 1322 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.38 % Allowed : 12.77 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.25), residues: 1188 helix: 1.89 (0.26), residues: 408 sheet: -0.58 (0.30), residues: 304 loop : -0.61 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 89 TYR 0.015 0.001 TYR E 181 PHE 0.022 0.001 PHE A 346 TRP 0.008 0.001 TRP C 82 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 9705) covalent geometry : angle 0.57449 (13130) SS BOND : bond 0.00292 ( 7) SS BOND : angle 1.81243 ( 14) hydrogen bonds : bond 0.03843 ( 498) hydrogen bonds : angle 5.06990 ( 1383) link_NAG-ASN : bond 0.00061 ( 1) link_NAG-ASN : angle 1.75236 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8269 (mt) REVERT: B 24 ARG cc_start: 0.8070 (ttt180) cc_final: 0.7320 (ttp80) REVERT: B 279 LYS cc_start: 0.8899 (pttm) cc_final: 0.8551 (pttm) REVERT: B 302 TYR cc_start: 0.8557 (t80) cc_final: 0.7761 (t80) REVERT: C 23 LYS cc_start: 0.9046 (ttpp) cc_final: 0.8792 (tptt) REVERT: C 32 GLN cc_start: 0.8138 (mp10) cc_final: 0.7804 (mp10) REVERT: C 172 GLU cc_start: 0.9080 (tp30) cc_final: 0.8566 (tm-30) REVERT: C 175 GLN cc_start: 0.8365 (mp10) cc_final: 0.8090 (mp10) REVERT: C 217 MET cc_start: 0.8162 (tpt) cc_final: 0.7837 (mmm) REVERT: D 21 MET cc_start: 0.8671 (tmm) cc_final: 0.8295 (tmm) REVERT: E 210 LEU cc_start: 0.8883 (mm) cc_final: 0.8362 (mm) outliers start: 25 outliers final: 20 residues processed: 167 average time/residue: 0.1032 time to fit residues: 23.0568 Evaluate side-chains 163 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 193 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 98 optimal weight: 0.0170 chunk 66 optimal weight: 2.9990 chunk 32 optimal weight: 0.0270 chunk 64 optimal weight: 0.6980 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.118199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.092301 restraints weight = 15705.986| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.65 r_work: 0.3062 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9713 Z= 0.108 Angle : 0.538 7.542 13147 Z= 0.286 Chirality : 0.041 0.142 1496 Planarity : 0.003 0.035 1649 Dihedral : 4.838 51.089 1322 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.62 % Allowed : 14.11 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.25), residues: 1188 helix: 2.01 (0.26), residues: 415 sheet: -0.57 (0.30), residues: 293 loop : -0.53 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.016 0.001 TYR E 181 PHE 0.020 0.001 PHE A 310 TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9705) covalent geometry : angle 0.53522 (13130) SS BOND : bond 0.00211 ( 7) SS BOND : angle 1.57123 ( 14) hydrogen bonds : bond 0.03375 ( 498) hydrogen bonds : angle 4.86811 ( 1383) link_NAG-ASN : bond 0.00167 ( 1) link_NAG-ASN : angle 1.94178 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 ARG cc_start: 0.7922 (ttt180) cc_final: 0.7232 (ttp80) REVERT: B 193 ASP cc_start: 0.8487 (m-30) cc_final: 0.8075 (t0) REVERT: C 23 LYS cc_start: 0.9038 (ttpp) cc_final: 0.8763 (tptt) REVERT: C 32 GLN cc_start: 0.8057 (mp10) cc_final: 0.7834 (mp10) REVERT: C 172 GLU cc_start: 0.8980 (tp30) cc_final: 0.8439 (tm-30) REVERT: C 215 GLU cc_start: 0.8602 (pt0) cc_final: 0.8210 (pm20) REVERT: C 217 MET cc_start: 0.7766 (tpt) cc_final: 0.7494 (mmm) REVERT: D 21 MET cc_start: 0.8667 (tmm) cc_final: 0.8294 (tmm) REVERT: E 210 LEU cc_start: 0.8788 (mm) cc_final: 0.8379 (mm) outliers start: 17 outliers final: 15 residues processed: 160 average time/residue: 0.1248 time to fit residues: 26.3661 Evaluate side-chains 150 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 193 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.087477 restraints weight = 15796.665| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.63 r_work: 0.2981 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9713 Z= 0.187 Angle : 0.598 8.910 13147 Z= 0.317 Chirality : 0.043 0.172 1496 Planarity : 0.003 0.033 1649 Dihedral : 5.047 51.283 1322 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.62 % Allowed : 14.49 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.25), residues: 1188 helix: 1.97 (0.26), residues: 408 sheet: -0.57 (0.30), residues: 288 loop : -0.63 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 89 TYR 0.018 0.001 TYR B 302 PHE 0.023 0.001 PHE A 346 TRP 0.022 0.001 TRP A 80 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 9705) covalent geometry : angle 0.59524 (13130) SS BOND : bond 0.00230 ( 7) SS BOND : angle 1.84994 ( 14) hydrogen bonds : bond 0.03835 ( 498) hydrogen bonds : angle 5.01013 ( 1383) link_NAG-ASN : bond 0.00010 ( 1) link_NAG-ASN : angle 1.62093 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8713 (m-30) cc_final: 0.8367 (m-30) REVERT: A 276 VAL cc_start: 0.8212 (t) cc_final: 0.7987 (p) REVERT: B 24 ARG cc_start: 0.8052 (ttt180) cc_final: 0.7311 (ttp80) REVERT: B 279 LYS cc_start: 0.8967 (pttm) cc_final: 0.8654 (pttm) REVERT: B 302 TYR cc_start: 0.8533 (t80) cc_final: 0.7779 (t80) REVERT: C 23 LYS cc_start: 0.9037 (ttpp) cc_final: 0.8764 (tptt) REVERT: C 32 GLN cc_start: 0.8162 (mp10) cc_final: 0.7886 (mp10) REVERT: C 172 GLU cc_start: 0.9128 (tp30) cc_final: 0.8685 (tm-30) REVERT: C 215 GLU cc_start: 0.8796 (pt0) cc_final: 0.8362 (pm20) REVERT: D 21 MET cc_start: 0.8676 (tmm) cc_final: 0.8255 (tmm) REVERT: D 42 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8168 (tm-30) REVERT: E 210 LEU cc_start: 0.8811 (mm) cc_final: 0.8479 (mm) outliers start: 17 outliers final: 14 residues processed: 158 average time/residue: 0.1088 time to fit residues: 22.8298 Evaluate side-chains 155 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 193 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 ASN ** 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 = 0.3496 r_free = 0.3496 target = 0.113716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.087942 restraints weight = 15774.106| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.64 r_work: 0.2988 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9713 Z= 0.170 Angle : 0.591 7.857 13147 Z= 0.313 Chirality : 0.043 0.177 1496 Planarity : 0.003 0.034 1649 Dihedral : 5.059 50.964 1322 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.62 % Allowed : 14.97 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.25), residues: 1188 helix: 1.97 (0.26), residues: 408 sheet: -0.56 (0.31), residues: 288 loop : -0.65 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 89 TYR 0.024 0.001 TYR B 302 PHE 0.020 0.001 PHE A 346 TRP 0.020 0.001 TRP A 80 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9705) covalent geometry : angle 0.58816 (13130) SS BOND : bond 0.00248 ( 7) SS BOND : angle 1.86141 ( 14) hydrogen bonds : bond 0.03757 ( 498) hydrogen bonds : angle 4.98156 ( 1383) link_NAG-ASN : bond 0.00011 ( 1) link_NAG-ASN : angle 1.62785 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8705 (m-30) cc_final: 0.8369 (m-30) REVERT: A 276 VAL cc_start: 0.8189 (t) cc_final: 0.7958 (p) REVERT: B 24 ARG cc_start: 0.8060 (ttt180) cc_final: 0.7311 (ttp80) REVERT: B 193 ASP cc_start: 0.8753 (m-30) cc_final: 0.8232 (t0) REVERT: C 23 LYS cc_start: 0.9016 (ttpp) cc_final: 0.8753 (tptt) REVERT: C 32 GLN cc_start: 0.8156 (mp10) cc_final: 0.7912 (mp10) REVERT: C 172 GLU cc_start: 0.9125 (tp30) cc_final: 0.8702 (tm-30) REVERT: C 215 GLU cc_start: 0.8796 (pt0) cc_final: 0.8354 (pm20) REVERT: C 217 MET cc_start: 0.8009 (tpt) cc_final: 0.7004 (mtp) REVERT: D 21 MET cc_start: 0.8684 (tmm) cc_final: 0.8334 (tmm) REVERT: D 42 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8175 (tm-30) REVERT: E 210 LEU cc_start: 0.8807 (mm) cc_final: 0.8442 (mm) outliers start: 17 outliers final: 16 residues processed: 157 average time/residue: 0.1397 time to fit residues: 28.8607 Evaluate side-chains 157 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 193 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 63 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.110331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.084409 restraints weight = 15817.076| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.62 r_work: 0.2930 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9713 Z= 0.275 Angle : 0.667 8.543 13147 Z= 0.353 Chirality : 0.046 0.213 1496 Planarity : 0.004 0.036 1649 Dihedral : 5.355 51.394 1322 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.53 % Allowed : 15.35 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.24), residues: 1188 helix: 1.72 (0.26), residues: 409 sheet: -0.64 (0.30), residues: 301 loop : -0.74 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 51 TYR 0.015 0.002 TYR A 210 PHE 0.023 0.002 PHE A 346 TRP 0.022 0.002 TRP A 80 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00648 ( 9705) covalent geometry : angle 0.66258 (13130) SS BOND : bond 0.00325 ( 7) SS BOND : angle 2.28519 ( 14) hydrogen bonds : bond 0.04265 ( 498) hydrogen bonds : angle 5.23039 ( 1383) link_NAG-ASN : bond 0.00185 ( 1) link_NAG-ASN : angle 1.62565 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.91 seconds wall clock time: 39 minutes 41.25 seconds (2381.25 seconds total)