Starting phenix.real_space_refine on Mon Dec 30 07:35:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dou_27623/12_2024/8dou_27623.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dou_27623/12_2024/8dou_27623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dou_27623/12_2024/8dou_27623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dou_27623/12_2024/8dou_27623.map" model { file = "/net/cci-nas-00/data/ceres_data/8dou_27623/12_2024/8dou_27623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dou_27623/12_2024/8dou_27623.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.073 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 2287 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 32 5.16 5 C 7090 2.51 5 N 1676 2.21 5 O 1864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10666 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "C" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "D" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.55, per 1000 atoms: 0.61 Number of scatterers: 10666 At special positions: 0 Unit cell: (94.08, 101.92, 138.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 4 15.00 O 1864 8.00 N 1676 7.00 C 7090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 51.3% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 removed outlier: 4.214A pdb=" N LEU A 21 " --> pdb=" O PRO A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 99 through 112 removed outlier: 3.757A pdb=" N ASN A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.770A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 removed outlier: 4.071A pdb=" N THR A 141 " --> pdb=" O PRO A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 Processing helix chain 'A' and resid 173 through 190 removed outlier: 3.959A pdb=" N LYS A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 224 through 241 removed outlier: 4.104A pdb=" N ASN A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 22 through 48 removed outlier: 5.195A pdb=" N TRP B 31 " --> pdb=" O TRP B 27 " (cutoff:3.500A) Proline residue: B 32 - end of helix removed outlier: 3.905A pdb=" N ILE B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 56 through 87 removed outlier: 3.706A pdb=" N TYR B 60 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 101 through 129 removed outlier: 3.772A pdb=" N VAL B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 4.528A pdb=" N LYS B 135 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 removed outlier: 4.012A pdb=" N VAL B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.603A pdb=" N ILE B 191 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.617A pdb=" N TYR B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 223 through 256 Proline residue: B 235 - end of helix removed outlier: 4.586A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.507A pdb=" N LEU C 63 " --> pdb=" O GLY C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 111 removed outlier: 4.437A pdb=" N ILE C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 129 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.600A pdb=" N TYR C 142 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 159 removed outlier: 4.015A pdb=" N GLU C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 191 removed outlier: 3.984A pdb=" N GLN C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 206 removed outlier: 4.058A pdb=" N ILE C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 315 through 318 Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 22 through 48 removed outlier: 4.985A pdb=" N TRP D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Proline residue: D 32 - end of helix removed outlier: 3.809A pdb=" N ILE D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 44 " --> pdb=" O THR D 40 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N HIS D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 57 through 84 removed outlier: 3.859A pdb=" N GLY D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Proline residue: D 70 - end of helix removed outlier: 3.593A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 95 removed outlier: 3.786A pdb=" N THR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS D 94 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 129 removed outlier: 3.947A pdb=" N VAL D 105 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 139 removed outlier: 4.171A pdb=" N LYS D 135 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR D 138 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 139 " --> pdb=" O TYR D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 163 removed outlier: 3.505A pdb=" N ILE D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 180 Processing helix chain 'D' and resid 188 through 192 removed outlier: 3.541A pdb=" N LEU D 192 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.626A pdb=" N TYR D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.516A pdb=" N VAL D 215 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 256 Proline residue: D 235 - end of helix removed outlier: 5.733A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASP D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 37 removed outlier: 6.625A pdb=" N LYS A 9 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 2 " --> pdb=" O ILE A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 37 removed outlier: 6.625A pdb=" N LYS A 9 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 77 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 7 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS A 75 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 166 removed outlier: 6.397A pdb=" N PHE A 163 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL A 197 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 165 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A 50 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA A 211 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU A 222 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU A 213 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 265 removed outlier: 3.688A pdb=" N ILE A 282 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU A 329 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG C 392 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 371 removed outlier: 8.615A pdb=" N ILE A 363 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LEU A 349 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASN A 365 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N VAL A 347 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS A 367 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 310 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 394 removed outlier: 4.050A pdb=" N ASN A 390 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR C 331 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG A 392 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 329 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS C 327 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY C 326 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 288 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR C 279 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N SER C 266 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE C 281 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU C 264 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU C 283 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL C 262 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP C 285 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY C 269 " --> pdb=" O SER C 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 164 through 165 removed outlier: 3.726A pdb=" N VAL C 197 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU C 50 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE C 212 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLY C 51 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU C 221 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 308 through 313 502 hydrogen bonds defined for protein. 1434 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: 3.20 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1656 1.30 - 1.43: 2980 1.43 - 1.56: 6254 1.56 - 1.69: 6 1.69 - 1.82: 52 Bond restraints: 10948 Sorted by residual: bond pdb=" C HIS B 212 " pdb=" O HIS B 212 " ideal model delta sigma weight residual 1.237 1.168 0.068 1.16e-02 7.43e+03 3.46e+01 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" N ILE D 211 " pdb=" CA ILE D 211 " ideal model delta sigma weight residual 1.459 1.531 -0.071 1.33e-02 5.65e+03 2.88e+01 bond pdb=" C5 ADP C 501 " pdb=" C6 ADP C 501 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" N LEU D 139 " pdb=" CA LEU D 139 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.16e-02 7.43e+03 1.50e+01 ... (remaining 10943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 14512 1.83 - 3.65: 214 3.65 - 5.48: 61 5.48 - 7.31: 20 7.31 - 9.13: 11 Bond angle restraints: 14818 Sorted by residual: angle pdb=" N THR B 128 " pdb=" CA THR B 128 " pdb=" C THR B 128 " ideal model delta sigma weight residual 111.07 117.99 -6.92 1.07e+00 8.73e-01 4.18e+01 angle pdb=" O PHE B 126 " pdb=" C PHE B 126 " pdb=" N ILE B 127 " ideal model delta sigma weight residual 122.12 116.24 5.88 1.06e+00 8.90e-01 3.08e+01 angle pdb=" C TYR B 114 " pdb=" CA TYR B 114 " pdb=" CB TYR B 114 " ideal model delta sigma weight residual 110.96 119.46 -8.50 1.54e+00 4.22e-01 3.05e+01 angle pdb=" CA TYR B 114 " pdb=" C TYR B 114 " pdb=" O TYR B 114 " ideal model delta sigma weight residual 121.00 115.24 5.76 1.05e+00 9.07e-01 3.01e+01 angle pdb=" C PHE B 126 " pdb=" N ILE B 127 " pdb=" CA ILE B 127 " ideal model delta sigma weight residual 120.72 114.17 6.55 1.22e+00 6.72e-01 2.88e+01 ... (remaining 14813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.15: 6079 27.15 - 54.30: 298 54.30 - 81.44: 13 81.44 - 108.59: 1 108.59 - 135.74: 5 Dihedral angle restraints: 6396 sinusoidal: 2616 harmonic: 3780 Sorted by residual: dihedral pdb=" O2A ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PA ADP C 501 " pdb=" PB ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 75.74 -135.74 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" O2A ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PA ADP A 501 " pdb=" PB ADP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 68.82 -128.82 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" O1B ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PB ADP A 501 " pdb=" PA ADP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 65.56 -125.56 1 2.00e+01 2.50e-03 3.80e+01 ... (remaining 6393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1411 0.058 - 0.116: 220 0.116 - 0.174: 19 0.174 - 0.233: 2 0.233 - 0.291: 2 Chirality restraints: 1654 Sorted by residual: chirality pdb=" CB ILE D 211 " pdb=" CA ILE D 211 " pdb=" CG1 ILE D 211 " pdb=" CG2 ILE D 211 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA THR B 128 " pdb=" N THR B 128 " pdb=" C THR B 128 " pdb=" CB THR B 128 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA TYR B 114 " pdb=" N TYR B 114 " pdb=" C TYR B 114 " pdb=" CB TYR B 114 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.30e-01 ... (remaining 1651 not shown) Planarity restraints: 1816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 139 " -0.018 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C LEU D 139 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU D 139 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE D 140 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 114 " 0.026 2.00e-02 2.50e+03 1.61e-02 5.21e+00 pdb=" CG TYR B 114 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 114 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 114 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 114 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 114 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 114 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 114 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 92 " -0.013 2.00e-02 2.50e+03 1.61e-02 4.51e+00 pdb=" CG PHE B 92 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 92 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 92 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B 92 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 92 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 92 " 0.000 2.00e-02 2.50e+03 ... (remaining 1813 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1828 2.77 - 3.30: 9797 3.30 - 3.83: 16897 3.83 - 4.37: 18279 4.37 - 4.90: 33388 Nonbonded interactions: 80189 Sorted by model distance: nonbonded pdb=" OG SER A 114 " pdb=" OE1 GLU A 117 " model vdw 2.233 3.040 nonbonded pdb=" O PHE A 134 " pdb=" OH TYR A 142 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP C 294 " pdb=" OH TYR C 315 " model vdw 2.264 3.040 nonbonded pdb=" O PHE C 134 " pdb=" OH TYR C 142 " model vdw 2.267 3.040 nonbonded pdb=" O ILE C 154 " pdb=" OG1 THR C 158 " model vdw 2.270 3.040 ... (remaining 80184 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.15 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.250 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 : 0.003 0.110 10948 Z= 0.186 Angle : 0.632 9.135 14818 Z= 0.343 Chirality : 0.042 0.291 1654 Planarity : 0.003 0.038 1816 Dihedral : 14.699 135.740 3980 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.34 % Allowed : 0.43 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1292 helix: 1.82 (0.23), residues: 595 sheet: 1.26 (0.43), residues: 170 loop : -1.64 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 181 HIS 0.005 0.000 HIS B 212 PHE 0.037 0.001 PHE B 92 TYR 0.036 0.001 TYR B 114 ARG 0.003 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 1.306 Fit side-chains REVERT: A 343 TYR cc_start: 0.7548 (m-80) cc_final: 0.6931 (m-80) REVERT: B 129 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7077 (mt) outliers start: 4 outliers final: 0 residues processed: 170 average time/residue: 0.2037 time to fit residues: 51.0313 Evaluate side-chains 133 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.0970 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 55 ASN B 218 ASN C 361 HIS C 368 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 10948 Z= 0.397 Angle : 0.708 8.443 14818 Z= 0.360 Chirality : 0.047 0.170 1654 Planarity : 0.004 0.034 1816 Dihedral : 8.236 155.539 1424 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.55 % Allowed : 12.76 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1292 helix: 1.17 (0.22), residues: 599 sheet: 0.37 (0.41), residues: 189 loop : -1.79 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 71 HIS 0.005 0.002 HIS D 223 PHE 0.028 0.002 PHE C 369 TYR 0.027 0.002 TYR B 243 ARG 0.006 0.001 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 1.160 Fit side-chains REVERT: A 318 GLU cc_start: 0.6998 (mp0) cc_final: 0.6736 (mp0) REVERT: B 16 ASN cc_start: 0.8585 (p0) cc_final: 0.8346 (p0) REVERT: B 205 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.6060 (ttm) REVERT: B 220 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7758 (mm) outliers start: 18 outliers final: 12 residues processed: 160 average time/residue: 0.2283 time to fit residues: 51.9290 Evaluate side-chains 134 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 174 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 0.0050 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 357 GLN B 218 ASN C 31 HIS C 157 HIS C 187 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10948 Z= 0.234 Angle : 0.598 7.519 14818 Z= 0.300 Chirality : 0.042 0.134 1654 Planarity : 0.004 0.033 1816 Dihedral : 7.942 170.737 1422 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.33 % Allowed : 15.60 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1292 helix: 1.47 (0.22), residues: 588 sheet: 0.71 (0.43), residues: 177 loop : -1.87 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 181 HIS 0.012 0.001 HIS C 187 PHE 0.017 0.001 PHE B 152 TYR 0.021 0.001 TYR B 243 ARG 0.007 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.271 Fit side-chains REVERT: A 5 PHE cc_start: 0.6923 (t80) cc_final: 0.6701 (t80) REVERT: A 318 GLU cc_start: 0.6994 (mp0) cc_final: 0.6784 (mp0) REVERT: B 16 ASN cc_start: 0.8545 (p0) cc_final: 0.8200 (p0) REVERT: B 220 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7693 (mm) REVERT: C 125 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8152 (mt) outliers start: 27 outliers final: 11 residues processed: 151 average time/residue: 0.2066 time to fit residues: 46.1170 Evaluate side-chains 140 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 128 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 60 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 361 HIS ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 218 ASN C 157 HIS C 202 ASN D 55 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 10948 Z= 0.356 Angle : 0.664 7.751 14818 Z= 0.337 Chirality : 0.045 0.152 1654 Planarity : 0.004 0.031 1816 Dihedral : 8.044 174.100 1422 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.62 % Allowed : 16.72 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1292 helix: 1.20 (0.22), residues: 593 sheet: 0.12 (0.42), residues: 186 loop : -2.05 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 71 HIS 0.005 0.001 HIS D 212 PHE 0.019 0.002 PHE B 180 TYR 0.021 0.002 TYR B 243 ARG 0.004 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 1.194 Fit side-chains REVERT: A 5 PHE cc_start: 0.7003 (t80) cc_final: 0.6791 (t80) REVERT: A 129 SER cc_start: 0.8263 (t) cc_final: 0.8051 (t) REVERT: A 303 ASP cc_start: 0.7551 (p0) cc_final: 0.7270 (p0) REVERT: A 318 GLU cc_start: 0.7124 (mp0) cc_final: 0.6913 (mp0) REVERT: B 12 GLN cc_start: 0.8306 (mp10) cc_final: 0.8050 (mp10) REVERT: B 16 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8246 (p0) REVERT: B 205 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.6077 (ttm) REVERT: B 220 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7802 (mm) REVERT: C 18 GLN cc_start: 0.7343 (pm20) cc_final: 0.7142 (pm20) outliers start: 42 outliers final: 26 residues processed: 162 average time/residue: 0.2115 time to fit residues: 50.2976 Evaluate side-chains 156 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 250 ASN A 357 GLN B 16 ASN B 218 ASN C 157 HIS D 177 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10948 Z= 0.198 Angle : 0.592 9.192 14818 Z= 0.294 Chirality : 0.041 0.145 1654 Planarity : 0.004 0.052 1816 Dihedral : 7.691 168.368 1422 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.45 % Allowed : 18.71 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1292 helix: 1.46 (0.22), residues: 592 sheet: -0.09 (0.42), residues: 191 loop : -1.89 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 8 HIS 0.002 0.001 HIS C 361 PHE 0.016 0.001 PHE B 92 TYR 0.018 0.001 TYR B 243 ARG 0.003 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 1.211 Fit side-chains REVERT: B 12 GLN cc_start: 0.8268 (mp10) cc_final: 0.7400 (mp10) REVERT: B 16 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8157 (p0) REVERT: B 220 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7683 (mm) REVERT: C 18 GLN cc_start: 0.7106 (pm20) cc_final: 0.6903 (pm20) REVERT: C 125 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8117 (mt) outliers start: 40 outliers final: 24 residues processed: 167 average time/residue: 0.2058 time to fit residues: 50.5152 Evaluate side-chains 156 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 218 ASN C 157 HIS D 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10948 Z= 0.186 Angle : 0.595 9.740 14818 Z= 0.295 Chirality : 0.042 0.134 1654 Planarity : 0.004 0.042 1816 Dihedral : 7.518 163.985 1422 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.02 % Allowed : 19.74 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1292 helix: 1.55 (0.23), residues: 592 sheet: -0.01 (0.42), residues: 193 loop : -1.90 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 181 HIS 0.003 0.001 HIS C 361 PHE 0.019 0.001 PHE D 92 TYR 0.022 0.001 TYR B 243 ARG 0.005 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 1.265 Fit side-chains REVERT: B 12 GLN cc_start: 0.8310 (mp10) cc_final: 0.7467 (mp10) REVERT: B 16 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.8131 (p0) REVERT: B 205 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5660 (ttm) REVERT: B 220 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7676 (mm) REVERT: C 125 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8105 (mt) REVERT: C 294 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6781 (m-30) outliers start: 35 outliers final: 19 residues processed: 148 average time/residue: 0.2003 time to fit residues: 44.5220 Evaluate side-chains 151 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 168 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 218 ASN C 157 HIS C 350 HIS D 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10948 Z= 0.231 Angle : 0.607 9.427 14818 Z= 0.301 Chirality : 0.042 0.138 1654 Planarity : 0.003 0.034 1816 Dihedral : 7.454 162.234 1422 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.88 % Allowed : 19.40 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1292 helix: 1.51 (0.22), residues: 592 sheet: -0.12 (0.41), residues: 196 loop : -1.96 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 181 HIS 0.004 0.001 HIS C 350 PHE 0.018 0.001 PHE C 30 TYR 0.023 0.001 TYR B 243 ARG 0.005 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 1.194 Fit side-chains REVERT: B 12 GLN cc_start: 0.8238 (mp10) cc_final: 0.7521 (mp10) REVERT: B 16 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8083 (p0) REVERT: B 205 MET cc_start: 0.6273 (OUTLIER) cc_final: 0.5833 (ttm) REVERT: B 220 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7697 (mm) REVERT: C 125 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8120 (mt) REVERT: C 294 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6912 (m-30) outliers start: 45 outliers final: 28 residues processed: 160 average time/residue: 0.2131 time to fit residues: 50.8960 Evaluate side-chains 159 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 218 ASN C 157 HIS D 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10948 Z= 0.248 Angle : 0.627 9.415 14818 Z= 0.310 Chirality : 0.042 0.143 1654 Planarity : 0.004 0.035 1816 Dihedral : 7.418 161.472 1422 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.53 % Allowed : 19.57 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1292 helix: 1.42 (0.22), residues: 596 sheet: -0.18 (0.41), residues: 196 loop : -1.98 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 8 HIS 0.004 0.001 HIS C 350 PHE 0.029 0.001 PHE B 152 TYR 0.025 0.001 TYR B 243 ARG 0.007 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 1.235 Fit side-chains REVERT: B 12 GLN cc_start: 0.8306 (mp10) cc_final: 0.7637 (mp10) REVERT: B 205 MET cc_start: 0.6219 (OUTLIER) cc_final: 0.5877 (ttm) REVERT: B 220 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7706 (mm) REVERT: C 125 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8170 (mt) outliers start: 41 outliers final: 31 residues processed: 159 average time/residue: 0.2000 time to fit residues: 47.3453 Evaluate side-chains 162 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 HIS ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 218 ASN C 157 HIS D 177 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10948 Z= 0.235 Angle : 0.639 10.293 14818 Z= 0.317 Chirality : 0.042 0.196 1654 Planarity : 0.004 0.032 1816 Dihedral : 7.407 163.174 1422 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.62 % Allowed : 19.66 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1292 helix: 1.35 (0.22), residues: 602 sheet: -0.21 (0.41), residues: 196 loop : -2.02 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 8 HIS 0.005 0.001 HIS A 268 PHE 0.038 0.001 PHE B 152 TYR 0.024 0.001 TYR B 243 ARG 0.007 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 1.082 Fit side-chains REVERT: B 12 GLN cc_start: 0.8243 (mp10) cc_final: 0.7456 (mp10) REVERT: B 16 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8203 (p0) REVERT: B 205 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5842 (ttm) REVERT: B 220 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7695 (mm) REVERT: C 125 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8178 (mt) outliers start: 42 outliers final: 33 residues processed: 159 average time/residue: 0.1930 time to fit residues: 45.9172 Evaluate side-chains 163 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 9.9990 chunk 57 optimal weight: 0.0060 chunk 84 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 218 ASN C 157 HIS ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10948 Z= 0.253 Angle : 0.650 8.948 14818 Z= 0.323 Chirality : 0.043 0.180 1654 Planarity : 0.004 0.037 1816 Dihedral : 7.458 166.282 1422 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.45 % Allowed : 19.48 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.24), residues: 1292 helix: 1.36 (0.22), residues: 596 sheet: -0.26 (0.41), residues: 196 loop : -2.03 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 8 HIS 0.005 0.001 HIS C 350 PHE 0.023 0.001 PHE B 152 TYR 0.025 0.001 TYR B 243 ARG 0.010 0.000 ARG B 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 1.300 Fit side-chains REVERT: B 12 GLN cc_start: 0.8237 (mp10) cc_final: 0.7445 (mp10) REVERT: B 16 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8202 (p0) REVERT: B 17 ARG cc_start: 0.7538 (mmm160) cc_final: 0.7225 (mmm160) REVERT: B 85 PHE cc_start: 0.6214 (OUTLIER) cc_final: 0.5881 (t80) REVERT: B 205 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.5854 (ttm) REVERT: C 125 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8191 (mt) outliers start: 40 outliers final: 31 residues processed: 161 average time/residue: 0.2111 time to fit residues: 50.4914 Evaluate side-chains 164 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 0.0980 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 213 HIS B 218 ASN C 157 HIS ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 HIS D 177 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.188346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.157499 restraints weight = 14763.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.158363 restraints weight = 14767.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.160529 restraints weight = 12206.205| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3966 r_free = 0.3966 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3904 r_free = 0.3904 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10948 Z= 0.200 Angle : 0.633 8.888 14818 Z= 0.313 Chirality : 0.042 0.175 1654 Planarity : 0.004 0.034 1816 Dihedral : 7.437 169.997 1422 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.45 % Allowed : 19.83 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1292 helix: 1.39 (0.22), residues: 602 sheet: -0.22 (0.41), residues: 191 loop : -1.96 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 71 HIS 0.004 0.001 HIS C 350 PHE 0.032 0.001 PHE B 152 TYR 0.024 0.001 TYR B 243 ARG 0.012 0.000 ARG B 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2033.56 seconds wall clock time: 38 minutes 1.62 seconds (2281.62 seconds total)