Starting phenix.real_space_refine on Thu Mar 14 23:06:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1u_41829/03_2024/8u1u_41829.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1u_41829/03_2024/8u1u_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1u_41829/03_2024/8u1u_41829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1u_41829/03_2024/8u1u_41829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1u_41829/03_2024/8u1u_41829.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1u_41829/03_2024/8u1u_41829.pdb" } resolution = 3.1 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= 0.007 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 5.36, per 1000 atoms: 0.56 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 - 3.50 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 Links applied NAG-ASN " NAG A 900 " - " ASN A 52 " Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.15 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: 2.79 Time building geometry restraints manager: 3.44 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: 99.49 - 106.43: 184 106.43 - 113.36: 5281 113.36 - 120.30: 3652 120.30 - 127.23: 3911 127.23 - 134.17: 102 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 2.440 nonbonded pdb=" OG1 THR C 29 " pdb=" OE1 GLN C 32 " model vdw 2.036 2.440 nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 166 " model vdw 2.038 2.440 nonbonded pdb=" O VAL A 158 " pdb=" NZ LYS A 161 " model vdw 2.071 2.520 nonbonded pdb=" OG SER A 176 " pdb=" OG SER A 215 " model vdw 2.119 2.440 ... (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 ========== 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 5.500 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.130 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.790 ------------------------------------------------------------------------------- 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 9705 Z= 0.288 Angle : 0.711 6.549 13130 Z= 0.384 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 : 6.13 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 (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 (0.24), 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 TRP 0.014 0.002 TRP C 82 HIS 0.008 0.002 HIS A 327 PHE 0.037 0.002 PHE A 346 TYR 0.019 0.002 TYR D 40 ARG 0.021 0.001 ARG C 214 *********************** 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 fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.066 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: 0.2968 time to fit residues: 74.8460 Evaluate side-chains 158 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.0050 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN C 88 ASN C 176 GLN C 220 GLN C 259 GLN E 80 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9705 Z= 0.225 Angle : 0.578 6.251 13130 Z= 0.311 Chirality : 0.042 0.171 1496 Planarity : 0.004 0.035 1649 Dihedral : 5.318 49.611 1322 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.67 % Allowed : 5.91 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.38 (0.24), residues: 1188 helix: 1.66 (0.26), residues: 406 sheet: -0.36 (0.30), residues: 290 loop : -0.47 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 297 HIS 0.004 0.001 HIS A 388 PHE 0.032 0.001 PHE A 346 TYR 0.022 0.001 TYR B 230 ARG 0.007 0.001 ARG C 214 *********************** 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 172 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 165 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8243 (m-30) cc_final: 0.7805 (m-30) REVERT: B 21 ARG cc_start: 0.8088 (ptp90) cc_final: 0.7878 (mtm-85) REVERT: B 24 ARG cc_start: 0.7846 (ttt180) cc_final: 0.7420 (ttp80) REVERT: B 246 SER cc_start: 0.8776 (m) cc_final: 0.8550 (t) REVERT: C 260 GLU cc_start: 0.8542 (tt0) cc_final: 0.8310 (tt0) REVERT: D 21 MET cc_start: 0.8280 (tmm) cc_final: 0.7989 (tmm) REVERT: E 210 LEU cc_start: 0.8842 (mm) cc_final: 0.8361 (mm) outliers start: 7 outliers final: 2 residues processed: 168 average time/residue: 0.2546 time to fit residues: 56.7340 Evaluate side-chains 148 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LYS 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 59 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN D 18 GLN E 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9705 Z= 0.276 Angle : 0.562 6.749 13130 Z= 0.302 Chirality : 0.043 0.173 1496 Planarity : 0.003 0.035 1649 Dihedral : 5.214 50.391 1322 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.53 % Allowed : 9.25 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.37 (0.24), residues: 1188 helix: 1.71 (0.26), residues: 407 sheet: -0.49 (0.29), residues: 301 loop : -0.44 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 80 HIS 0.004 0.001 HIS C 62 PHE 0.028 0.002 PHE A 346 TYR 0.015 0.001 TYR B 230 ARG 0.005 0.001 ARG C 214 *********************** 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 172 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8187 (m-30) cc_final: 0.7767 (m-30) REVERT: A 398 PHE cc_start: 0.7740 (m-80) cc_final: 0.7495 (m-80) REVERT: B 21 ARG cc_start: 0.8129 (ptp90) cc_final: 0.7869 (mtm-85) REVERT: B 24 ARG cc_start: 0.7866 (ttt180) cc_final: 0.7445 (ttp80) REVERT: C 172 GLU cc_start: 0.8474 (tp30) cc_final: 0.8054 (tm-30) REVERT: E 210 LEU cc_start: 0.8809 (mm) cc_final: 0.8476 (mm) outliers start: 16 outliers final: 13 residues processed: 167 average time/residue: 0.2497 time to fit residues: 55.8526 Evaluate side-chains 158 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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 74 SER 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 96 MET Chi-restraints excluded: chain E residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 0.0270 chunk 51 optimal weight: 0.0570 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9705 Z= 0.159 Angle : 0.518 6.561 13130 Z= 0.276 Chirality : 0.040 0.149 1496 Planarity : 0.003 0.034 1649 Dihedral : 4.960 50.708 1322 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.33 % Allowed : 12.20 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.55 (0.25), residues: 1188 helix: 1.92 (0.26), residues: 414 sheet: -0.43 (0.30), residues: 286 loop : -0.41 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 80 HIS 0.003 0.001 HIS D 44 PHE 0.022 0.001 PHE A 346 TYR 0.015 0.001 TYR E 181 ARG 0.005 0.000 ARG B 32 *********************** 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 177 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 PHE cc_start: 0.7768 (m-80) cc_final: 0.7552 (m-80) REVERT: B 21 ARG cc_start: 0.8106 (ptp90) cc_final: 0.7862 (mtm-85) REVERT: B 24 ARG cc_start: 0.7794 (ttt180) cc_final: 0.7356 (ttp80) REVERT: B 247 MET cc_start: 0.8107 (mtp) cc_final: 0.7578 (mtm) REVERT: C 172 GLU cc_start: 0.8439 (tp30) cc_final: 0.8045 (tm-30) REVERT: D 18 GLN cc_start: 0.5390 (OUTLIER) cc_final: 0.5164 (tp40) outliers start: 14 outliers final: 9 residues processed: 172 average time/residue: 0.2590 time to fit residues: 58.9409 Evaluate side-chains 155 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 354 PHE Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.0070 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN B 306 GLN C 259 GLN D 18 GLN E 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9705 Z= 0.205 Angle : 0.542 7.935 13130 Z= 0.286 Chirality : 0.041 0.155 1496 Planarity : 0.003 0.034 1649 Dihedral : 4.937 50.934 1322 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.24 % Allowed : 12.77 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.25), residues: 1188 helix: 1.92 (0.26), residues: 414 sheet: -0.45 (0.30), residues: 288 loop : -0.45 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 80 HIS 0.004 0.001 HIS A 84 PHE 0.022 0.001 PHE A 346 TYR 0.014 0.001 TYR E 181 ARG 0.004 0.000 ARG B 32 *********************** 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 165 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8263 (m-30) cc_final: 0.7791 (m-30) REVERT: A 405 LYS cc_start: 0.7513 (mmpt) cc_final: 0.7310 (mmpt) REVERT: B 21 ARG cc_start: 0.8125 (ptp90) cc_final: 0.7872 (mtm-85) REVERT: B 24 ARG cc_start: 0.7805 (ttt180) cc_final: 0.7368 (ttp80) REVERT: C 172 GLU cc_start: 0.8457 (tp30) cc_final: 0.8112 (tm-30) outliers start: 13 outliers final: 11 residues processed: 160 average time/residue: 0.2587 time to fit residues: 54.5865 Evaluate side-chains 154 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 C residue 10 GLU Chi-restraints excluded: chain C residue 153 ASP 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 61 ILE Chi-restraints excluded: chain E residue 123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 0.0270 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN C 88 ASN D 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9705 Z= 0.321 Angle : 0.585 7.188 13130 Z= 0.310 Chirality : 0.043 0.174 1496 Planarity : 0.003 0.034 1649 Dihedral : 5.158 50.666 1322 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.72 % Allowed : 13.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1188 helix: 1.82 (0.26), residues: 408 sheet: -0.57 (0.30), residues: 304 loop : -0.52 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 82 HIS 0.004 0.001 HIS E 223 PHE 0.024 0.001 PHE A 346 TYR 0.015 0.001 TYR E 181 ARG 0.005 0.000 ARG A 89 *********************** 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 166 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8254 (m-30) cc_final: 0.7861 (m-30) REVERT: B 24 ARG cc_start: 0.7887 (ttt180) cc_final: 0.7480 (ttp80) REVERT: C 172 GLU cc_start: 0.8484 (tp30) cc_final: 0.8137 (tm-30) REVERT: C 228 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7886 (p0) REVERT: D 42 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7861 (tm-30) REVERT: E 210 LEU cc_start: 0.8789 (mm) cc_final: 0.8378 (mm) outliers start: 18 outliers final: 14 residues processed: 161 average time/residue: 0.2685 time to fit residues: 56.8186 Evaluate side-chains 158 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 232 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 228 ASP 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 123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN C 259 GLN D 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9705 Z= 0.210 Angle : 0.540 7.043 13130 Z= 0.286 Chirality : 0.041 0.161 1496 Planarity : 0.003 0.033 1649 Dihedral : 4.995 50.741 1322 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.00 % Allowed : 13.44 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.45 (0.25), residues: 1188 helix: 1.93 (0.26), residues: 409 sheet: -0.57 (0.30), residues: 293 loop : -0.48 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 80 HIS 0.003 0.001 HIS A 406 PHE 0.020 0.001 PHE A 310 TYR 0.015 0.001 TYR E 181 ARG 0.004 0.000 ARG A 89 *********************** 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 171 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.6112 (t80) cc_final: 0.5632 (t80) REVERT: A 167 ASP cc_start: 0.8206 (m-30) cc_final: 0.7804 (m-30) REVERT: B 21 ARG cc_start: 0.8104 (ptp90) cc_final: 0.7856 (mtm-85) REVERT: B 24 ARG cc_start: 0.7836 (ttt180) cc_final: 0.7396 (ttp80) REVERT: C 172 GLU cc_start: 0.8456 (tp30) cc_final: 0.8129 (tm-30) REVERT: C 228 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7944 (p0) REVERT: E 210 LEU cc_start: 0.8744 (mm) cc_final: 0.8370 (mm) outliers start: 21 outliers final: 15 residues processed: 166 average time/residue: 0.2707 time to fit residues: 60.0087 Evaluate side-chains 158 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 146 LEU Chi-restraints excluded: chain C residue 228 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 99 CYS Chi-restraints excluded: chain E residue 123 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN D 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9705 Z= 0.224 Angle : 0.552 7.198 13130 Z= 0.293 Chirality : 0.041 0.162 1496 Planarity : 0.003 0.033 1649 Dihedral : 4.955 50.791 1322 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.48 % Allowed : 13.82 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.45 (0.25), residues: 1188 helix: 1.94 (0.26), residues: 409 sheet: -0.49 (0.31), residues: 288 loop : -0.54 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 80 HIS 0.003 0.001 HIS A 327 PHE 0.020 0.001 PHE A 346 TYR 0.014 0.001 TYR E 181 ARG 0.005 0.000 ARG A 89 *********************** 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 170 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 26 MET cc_start: 0.9160 (mmm) cc_final: 0.8633 (tpp) REVERT: A 167 ASP cc_start: 0.8218 (m-30) cc_final: 0.7837 (m-30) REVERT: B 24 ARG cc_start: 0.7837 (ttt180) cc_final: 0.7397 (ttp80) REVERT: C 172 GLU cc_start: 0.8450 (tp30) cc_final: 0.8132 (tm-30) REVERT: C 228 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7905 (p0) REVERT: D 18 GLN cc_start: 0.5041 (OUTLIER) cc_final: 0.4764 (tp40) REVERT: E 210 LEU cc_start: 0.8747 (mm) cc_final: 0.8374 (mm) outliers start: 26 outliers final: 21 residues processed: 163 average time/residue: 0.2647 time to fit residues: 56.8814 Evaluate side-chains 165 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU 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 160 LYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 225 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 74 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 123 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.0870 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 0.0770 chunk 32 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN B 269 ASN B 294 ASN C 88 ASN D 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9705 Z= 0.173 Angle : 0.544 7.348 13130 Z= 0.290 Chirality : 0.041 0.147 1496 Planarity : 0.003 0.033 1649 Dihedral : 4.866 50.858 1322 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.91 % Allowed : 14.87 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.25), residues: 1188 helix: 1.96 (0.26), residues: 415 sheet: -0.47 (0.31), residues: 288 loop : -0.56 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 80 HIS 0.003 0.001 HIS A 388 PHE 0.019 0.001 PHE A 310 TYR 0.015 0.001 TYR E 181 ARG 0.006 0.000 ARG C 214 *********************** 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 fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8191 (m-30) cc_final: 0.7816 (m-30) REVERT: B 21 ARG cc_start: 0.8093 (ptp90) cc_final: 0.7879 (mtm-85) REVERT: B 24 ARG cc_start: 0.7817 (ttt180) cc_final: 0.7384 (ttp80) REVERT: C 172 GLU cc_start: 0.8428 (tp30) cc_final: 0.8127 (tm-30) REVERT: C 228 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7688 (p0) REVERT: E 210 LEU cc_start: 0.8709 (mm) cc_final: 0.8360 (mm) outliers start: 20 outliers final: 14 residues processed: 160 average time/residue: 0.2654 time to fit residues: 56.1640 Evaluate side-chains 153 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 332 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 37 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 0.0030 chunk 77 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN C 259 GLN D 18 GLN E 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9705 Z= 0.214 Angle : 0.557 7.475 13130 Z= 0.296 Chirality : 0.041 0.156 1496 Planarity : 0.003 0.032 1649 Dihedral : 4.897 51.019 1322 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.72 % Allowed : 15.06 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.46 (0.25), residues: 1188 helix: 1.95 (0.26), residues: 415 sheet: -0.46 (0.31), residues: 286 loop : -0.59 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 80 HIS 0.003 0.001 HIS A 327 PHE 0.020 0.001 PHE A 346 TYR 0.014 0.001 TYR E 181 ARG 0.005 0.000 ARG A 89 ********************** 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 159 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 167 ASP cc_start: 0.8205 (m-30) cc_final: 0.7829 (m-30) REVERT: B 24 ARG cc_start: 0.7817 (ttt180) cc_final: 0.7392 (ttp80) REVERT: B 193 ASP cc_start: 0.7853 (t0) cc_final: 0.7600 (t0) REVERT: B 279 LYS cc_start: 0.8763 (pttm) cc_final: 0.8554 (pttm) REVERT: C 172 GLU cc_start: 0.8428 (tp30) cc_final: 0.8128 (tm-30) REVERT: C 228 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7691 (p0) REVERT: C 262 MET cc_start: 0.9023 (mmm) cc_final: 0.8805 (tpt) REVERT: E 210 LEU cc_start: 0.8715 (mm) cc_final: 0.8362 (mm) outliers start: 18 outliers final: 14 residues processed: 156 average time/residue: 0.2713 time to fit residues: 55.6926 Evaluate side-chains 154 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 332 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 37 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN D 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.087054 restraints weight = 15761.442| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.63 r_work: 0.2977 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9705 Z= 0.296 Angle : 0.595 8.227 13130 Z= 0.318 Chirality : 0.043 0.179 1496 Planarity : 0.003 0.032 1649 Dihedral : 5.047 51.307 1322 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.62 % Allowed : 15.25 % 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 (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: 0.38 (0.25), residues: 1188 helix: 1.89 (0.26), residues: 409 sheet: -0.45 (0.30), residues: 299 loop : -0.65 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 80 HIS 0.004 0.001 HIS A 84 PHE 0.022 0.001 PHE A 346 TYR 0.016 0.001 TYR E 181 ARG 0.006 0.000 ARG A 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.87 seconds wall clock time: 44 minutes 59.40 seconds (2699.40 seconds total)