Starting phenix.real_space_refine on Sat Aug 23 14:17:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo5_43364/08_2025/8vo5_43364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo5_43364/08_2025/8vo5_43364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vo5_43364/08_2025/8vo5_43364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo5_43364/08_2025/8vo5_43364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vo5_43364/08_2025/8vo5_43364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo5_43364/08_2025/8vo5_43364.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 77 5.16 5 C 7936 2.51 5 N 2166 2.21 5 O 2436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12624 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3789 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 469} Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.76, per 1000 atoms: 0.22 Number of scatterers: 12624 At special positions: 0 Unit cell: (154.5, 81.37, 138.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 6 15.00 Mg 3 11.99 O 2436 8.00 N 2166 7.00 C 7936 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: 0.83 Conformation dependent library (CDL) restraints added in 386.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2964 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 37 sheets defined 36.4% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 86 through 89 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.752A pdb=" N LYS A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.730A pdb=" N TYR A 335 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.765A pdb=" N GLY A 476 " --> pdb=" O ASP A 473 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 477 " --> pdb=" O HIS A 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 477' Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.812A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.599A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 296 removed outlier: 4.044A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.787A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.629A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.876A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.554A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.956A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 removed outlier: 3.578A pdb=" N LEU C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 296 removed outlier: 4.071A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.581A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.565A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.866A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.504A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.532A pdb=" N LEU D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 296 removed outlier: 4.191A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.174A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 352 through 356 removed outlier: 3.766A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 5.615A pdb=" N TYR A 23 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER A 36 " --> pdb=" O TYR A 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 111 through 113 removed outlier: 3.702A pdb=" N ALA A 123 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY A 113 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS A 121 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 189 Processing sheet with id=AA7, first strand: chain 'A' and resid 152 through 154 removed outlier: 6.451A pdb=" N HIS A 154 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL A 165 " --> pdb=" O HIS A 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA9, first strand: chain 'A' and resid 213 through 217 Processing sheet with id=AB1, first strand: chain 'A' and resid 231 through 234 Processing sheet with id=AB2, first strand: chain 'A' and resid 305 through 308 removed outlier: 3.881A pdb=" N ALA A 261 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.479A pdb=" N ASN A 272 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 284 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AB5, first strand: chain 'A' and resid 337 through 340 removed outlier: 3.767A pdb=" N GLU A 339 " --> pdb=" O THR A 346 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR A 346 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 13.840A pdb=" N ILE A 345 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N SER A 357 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU A 347 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE A 354 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 366 " --> pdb=" O PHE A 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 385 through 386 Processing sheet with id=AB7, first strand: chain 'A' and resid 394 through 397 removed outlier: 5.463A pdb=" N PHE A 394 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 407 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AB9, first strand: chain 'A' and resid 452 through 457 removed outlier: 3.712A pdb=" N CYS A 456 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS A 460 " --> pdb=" O CYS A 456 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE A 463 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LYS A 471 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ALA A 480 " --> pdb=" O LYS A 471 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.904A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AC3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'B' and resid 41 through 42 removed outlier: 4.075A pdb=" N GLN B 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 41 through 42 removed outlier: 4.075A pdb=" N GLN B 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AC7, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AC8, first strand: chain 'B' and resid 169 through 170 removed outlier: 5.845A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AD1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.750A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AD3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AD4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AD5, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.027A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AD8, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AD9, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.765A pdb=" N ILE D 165 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 238 through 241 523 hydrogen bonds defined for protein. 1311 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: 2.01 Time building geometry restraints manager: 1.08 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: 4156 1.34 - 1.46: 2330 1.46 - 1.58: 6274 1.58 - 1.69: 9 1.69 - 1.81: 128 Bond restraints: 12897 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.76e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.32e+00 bond pdb=" N THR A 318 " pdb=" CA THR A 318 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.29e+00 bond pdb=" CG HIC C 73 " pdb=" CD2 HIC C 73 " ideal model delta sigma weight residual 1.369 1.411 -0.042 2.00e-02 2.50e+03 4.43e+00 ... (remaining 12892 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 17160 1.76 - 3.53: 266 3.53 - 5.29: 42 5.29 - 7.06: 17 7.06 - 8.82: 2 Bond angle restraints: 17487 Sorted by residual: angle pdb=" C THR A 318 " pdb=" CA THR A 318 " pdb=" CB THR A 318 " ideal model delta sigma weight residual 109.54 102.94 6.60 1.84e+00 2.95e-01 1.29e+01 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 115.90 -5.40 1.70e+00 3.46e-01 1.01e+01 angle pdb=" C PHE C 124 " pdb=" N GLU C 125 " pdb=" CA GLU C 125 " ideal model delta sigma weight residual 122.79 117.38 5.41 1.78e+00 3.16e-01 9.25e+00 angle pdb=" N GLU C 364 " pdb=" CA GLU C 364 " pdb=" CB GLU C 364 " ideal model delta sigma weight residual 110.16 114.62 -4.46 1.48e+00 4.57e-01 9.09e+00 angle pdb=" N GLU A 339 " pdb=" CA GLU A 339 " pdb=" C GLU A 339 " ideal model delta sigma weight residual 109.59 104.82 4.77 1.61e+00 3.86e-01 8.79e+00 ... (remaining 17482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 7263 23.67 - 47.34: 423 47.34 - 71.01: 37 71.01 - 94.68: 4 94.68 - 118.35: 3 Dihedral angle restraints: 7730 sinusoidal: 3102 harmonic: 4628 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.36 118.35 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -174.23 114.23 1 2.00e+01 2.50e-03 3.38e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -171.13 111.13 1 2.00e+01 2.50e-03 3.27e+01 ... (remaining 7727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1569 0.055 - 0.110: 307 0.110 - 0.165: 44 0.165 - 0.220: 1 0.220 - 0.276: 1 Chirality restraints: 1922 Sorted by residual: chirality pdb=" CA GLU A 339 " pdb=" N GLU A 339 " pdb=" C GLU A 339 " pdb=" CB GLU A 339 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA THR A 318 " pdb=" N THR A 318 " pdb=" C THR A 318 " pdb=" CB THR A 318 " both_signs ideal model delta sigma weight residual False 2.53 2.73 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ASP D 157 " pdb=" N ASP D 157 " pdb=" C ASP D 157 " pdb=" CB ASP D 157 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1919 not shown) Planarity restraints: 2258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 163 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO D 164 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO C 164 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 324 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C GLN A 324 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN A 324 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A 325 " -0.010 2.00e-02 2.50e+03 ... (remaining 2255 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1765 2.76 - 3.29: 11820 3.29 - 3.83: 20390 3.83 - 4.36: 25493 4.36 - 4.90: 44088 Nonbonded interactions: 103556 Sorted by model distance: nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.220 2.170 nonbonded pdb=" OG SER D 155 " pdb=" OG1 THR D 303 " model vdw 2.221 3.040 nonbonded pdb=" OD2 ASP D 222 " pdb=" ND2 ASN D 225 " model vdw 2.235 3.120 nonbonded pdb=" OE1 GLU D 259 " pdb=" NH1 ARG D 312 " model vdw 2.248 3.120 nonbonded pdb=" OD1 ASP A 486 " pdb=" OG SER A 489 " model vdw 2.249 3.040 ... (remaining 103551 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 'B' selection = chain 'C' 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=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: 6.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.930 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 0.056 12897 Z= 0.161 Angle : 0.596 8.820 17487 Z= 0.320 Chirality : 0.045 0.276 1922 Planarity : 0.004 0.075 2258 Dihedral : 14.130 118.353 4766 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.21), residues: 1587 helix: 0.22 (0.25), residues: 483 sheet: -0.02 (0.29), residues: 331 loop : -0.15 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 28 TYR 0.010 0.001 TYR A 230 PHE 0.015 0.001 PHE C 124 TRP 0.018 0.002 TRP A 171 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00344 (12897) covalent geometry : angle 0.59588 (17487) hydrogen bonds : bond 0.21549 ( 516) hydrogen bonds : angle 8.30434 ( 1311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.562 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.6005 time to fit residues: 88.4064 Evaluate side-chains 104 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.147043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122049 restraints weight = 16736.365| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.44 r_work: 0.3354 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12897 Z= 0.254 Angle : 0.668 8.071 17487 Z= 0.342 Chirality : 0.050 0.179 1922 Planarity : 0.005 0.049 2258 Dihedral : 7.713 116.606 1791 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.93 % Allowed : 7.74 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.21), residues: 1587 helix: 0.16 (0.24), residues: 480 sheet: -0.16 (0.28), residues: 337 loop : -0.19 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 300 TYR 0.013 0.001 TYR A 111 PHE 0.013 0.002 PHE D 31 TRP 0.018 0.002 TRP A 171 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00625 (12897) covalent geometry : angle 0.66798 (17487) hydrogen bonds : bond 0.05252 ( 516) hydrogen bonds : angle 6.06234 ( 1311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: C 122 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8255 (mp) REVERT: C 288 ASP cc_start: 0.6894 (OUTLIER) cc_final: 0.6658 (m-30) REVERT: C 325 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6518 (ptm) REVERT: C 364 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: D 82 MET cc_start: 0.9058 (tpt) cc_final: 0.8567 (tpt) outliers start: 26 outliers final: 9 residues processed: 129 average time/residue: 0.6000 time to fit residues: 83.7596 Evaluate side-chains 116 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 305 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 123 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 119 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN B 41 GLN B 162 ASN B 354 GLN C 59 GLN D 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.149984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125473 restraints weight = 16908.404| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.53 r_work: 0.3428 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12897 Z= 0.141 Angle : 0.566 7.151 17487 Z= 0.287 Chirality : 0.045 0.163 1922 Planarity : 0.004 0.045 2258 Dihedral : 7.376 110.310 1791 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.23 % Allowed : 9.52 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.21), residues: 1587 helix: 0.43 (0.24), residues: 480 sheet: -0.09 (0.29), residues: 329 loop : -0.10 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 28 TYR 0.027 0.001 TYR A 111 PHE 0.014 0.001 PHE A 216 TRP 0.014 0.002 TRP D 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00338 (12897) covalent geometry : angle 0.56566 (17487) hydrogen bonds : bond 0.03949 ( 516) hydrogen bonds : angle 5.55588 ( 1311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 300 ARG cc_start: 0.5775 (mpt180) cc_final: 0.5567 (mmt-90) REVERT: B 47 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7381 (mmm) REVERT: B 65 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8571 (pp) REVERT: C 122 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8197 (mp) REVERT: C 288 ASP cc_start: 0.6675 (OUTLIER) cc_final: 0.6431 (m-30) REVERT: C 364 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: D 82 MET cc_start: 0.9003 (tpt) cc_final: 0.8556 (tpt) outliers start: 30 outliers final: 11 residues processed: 133 average time/residue: 0.6066 time to fit residues: 87.8263 Evaluate side-chains 121 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 97 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 156 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN B 354 GLN C 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124572 restraints weight = 16676.266| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.37 r_work: 0.3432 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12897 Z= 0.138 Angle : 0.554 7.124 17487 Z= 0.279 Chirality : 0.045 0.161 1922 Planarity : 0.004 0.043 2258 Dihedral : 7.244 108.705 1791 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.53 % Allowed : 12.05 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.21), residues: 1587 helix: 0.49 (0.24), residues: 483 sheet: -0.06 (0.29), residues: 329 loop : -0.04 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 28 TYR 0.008 0.001 TYR A 458 PHE 0.010 0.001 PHE D 31 TRP 0.013 0.001 TRP D 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00335 (12897) covalent geometry : angle 0.55396 (17487) hydrogen bonds : bond 0.03684 ( 516) hydrogen bonds : angle 5.32190 ( 1311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.407 Fit side-chains REVERT: A 300 ARG cc_start: 0.5772 (mpt180) cc_final: 0.5484 (mmt-90) REVERT: B 47 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7372 (mmm) REVERT: B 65 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8607 (pp) REVERT: C 28 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.7994 (tpp80) REVERT: C 211 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.8196 (m-30) REVERT: C 288 ASP cc_start: 0.6483 (OUTLIER) cc_final: 0.6260 (m-30) REVERT: C 364 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: D 82 MET cc_start: 0.8982 (tpt) cc_final: 0.8553 (tpt) outliers start: 34 outliers final: 13 residues processed: 138 average time/residue: 0.6148 time to fit residues: 92.1338 Evaluate side-chains 123 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 305 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 131 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 128 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.149441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125761 restraints weight = 16745.375| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.46 r_work: 0.3440 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12897 Z= 0.121 Angle : 0.542 7.099 17487 Z= 0.270 Chirality : 0.044 0.167 1922 Planarity : 0.004 0.041 2258 Dihedral : 7.094 106.164 1791 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.46 % Allowed : 13.54 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.22), residues: 1587 helix: 0.59 (0.25), residues: 483 sheet: -0.04 (0.29), residues: 329 loop : 0.00 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 28 TYR 0.007 0.001 TYR B 306 PHE 0.013 0.001 PHE A 216 TRP 0.012 0.001 TRP D 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00290 (12897) covalent geometry : angle 0.54210 (17487) hydrogen bonds : bond 0.03404 ( 516) hydrogen bonds : angle 5.17360 ( 1311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.523 Fit side-chains REVERT: A 190 THR cc_start: 0.7595 (OUTLIER) cc_final: 0.7334 (p) REVERT: A 300 ARG cc_start: 0.5751 (mpt180) cc_final: 0.5518 (mmt-90) REVERT: B 47 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7459 (mmm) REVERT: B 65 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8599 (pp) REVERT: C 28 ARG cc_start: 0.8332 (ttm-80) cc_final: 0.7999 (tpp80) REVERT: C 211 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8185 (m-30) REVERT: C 288 ASP cc_start: 0.6468 (m-30) cc_final: 0.6214 (m-30) REVERT: C 364 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: D 82 MET cc_start: 0.9010 (tpt) cc_final: 0.8604 (tpt) REVERT: D 225 ASN cc_start: 0.8223 (m110) cc_final: 0.8003 (m110) outliers start: 33 outliers final: 13 residues processed: 136 average time/residue: 0.6107 time to fit residues: 90.6294 Evaluate side-chains 122 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 305 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 0.0000 chunk 101 optimal weight: 3.9990 chunk 148 optimal weight: 0.0470 chunk 98 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 overall best weight: 0.6244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.149218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.125515 restraints weight = 16621.751| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.46 r_work: 0.3370 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12897 Z= 0.122 Angle : 0.545 10.376 17487 Z= 0.270 Chirality : 0.044 0.164 1922 Planarity : 0.004 0.040 2258 Dihedral : 7.008 104.309 1791 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.31 % Allowed : 14.51 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.22), residues: 1587 helix: 0.64 (0.25), residues: 483 sheet: -0.01 (0.29), residues: 329 loop : 0.00 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 28 TYR 0.008 0.001 TYR B 306 PHE 0.009 0.001 PHE D 31 TRP 0.012 0.001 TRP D 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00293 (12897) covalent geometry : angle 0.54451 (17487) hydrogen bonds : bond 0.03356 ( 516) hydrogen bonds : angle 5.07822 ( 1311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.608 Fit side-chains REVERT: A 190 THR cc_start: 0.7582 (OUTLIER) cc_final: 0.7318 (p) REVERT: A 300 ARG cc_start: 0.5774 (mpt180) cc_final: 0.5512 (mmt-90) REVERT: B 47 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7422 (mmm) REVERT: B 65 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8571 (pp) REVERT: C 28 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.8016 (tpp80) REVERT: C 122 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8112 (mp) REVERT: C 211 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8150 (m-30) REVERT: C 288 ASP cc_start: 0.6615 (OUTLIER) cc_final: 0.6375 (m-30) REVERT: C 364 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: D 82 MET cc_start: 0.9020 (tpt) cc_final: 0.8669 (tpt) outliers start: 31 outliers final: 14 residues processed: 129 average time/residue: 0.5424 time to fit residues: 76.8271 Evaluate side-chains 126 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 305 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 26 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.124046 restraints weight = 16668.487| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.46 r_work: 0.3429 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12897 Z= 0.154 Angle : 0.568 9.855 17487 Z= 0.283 Chirality : 0.046 0.168 1922 Planarity : 0.004 0.046 2258 Dihedral : 7.116 104.658 1791 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.68 % Allowed : 14.81 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.21), residues: 1587 helix: 0.55 (0.24), residues: 483 sheet: -0.08 (0.29), residues: 329 loop : -0.04 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 28 TYR 0.009 0.001 TYR A 111 PHE 0.015 0.001 PHE A 216 TRP 0.013 0.001 TRP D 340 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00376 (12897) covalent geometry : angle 0.56754 (17487) hydrogen bonds : bond 0.03660 ( 516) hydrogen bonds : angle 5.14586 ( 1311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.7590 (OUTLIER) cc_final: 0.7329 (p) REVERT: B 47 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7442 (mmm) REVERT: B 65 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8532 (pp) REVERT: B 334 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6870 (pp20) REVERT: C 28 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.8021 (tpp80) REVERT: C 122 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8127 (mp) REVERT: C 211 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8200 (m-30) REVERT: C 288 ASP cc_start: 0.6521 (OUTLIER) cc_final: 0.6279 (m-30) REVERT: C 364 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: D 82 MET cc_start: 0.8992 (tpt) cc_final: 0.8557 (tpt) outliers start: 36 outliers final: 19 residues processed: 134 average time/residue: 0.5848 time to fit residues: 85.8352 Evaluate side-chains 131 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 305 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 150 optimal weight: 0.5980 chunk 111 optimal weight: 0.4980 chunk 110 optimal weight: 0.3980 chunk 31 optimal weight: 0.0070 chunk 15 optimal weight: 0.0980 chunk 156 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 152 optimal weight: 0.0870 overall best weight: 0.1776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 HIS C 225 ASN D 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.148810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124778 restraints weight = 16638.396| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.44 r_work: 0.3420 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12897 Z= 0.089 Angle : 0.522 9.644 17487 Z= 0.258 Chirality : 0.043 0.165 1922 Planarity : 0.004 0.038 2258 Dihedral : 6.772 99.981 1791 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.49 % Allowed : 16.07 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.22), residues: 1587 helix: 0.77 (0.25), residues: 483 sheet: 0.03 (0.28), residues: 339 loop : 0.08 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 28 TYR 0.007 0.001 TYR C 69 PHE 0.007 0.001 PHE D 31 TRP 0.010 0.001 TRP B 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00200 (12897) covalent geometry : angle 0.52177 (17487) hydrogen bonds : bond 0.02776 ( 516) hydrogen bonds : angle 4.91839 ( 1311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.7522 (OUTLIER) cc_final: 0.7266 (p) REVERT: B 47 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7853 (mmt) REVERT: B 65 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8607 (pp) REVERT: C 28 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.8024 (tpp80) REVERT: C 288 ASP cc_start: 0.6370 (m-30) cc_final: 0.6129 (m-30) REVERT: D 82 MET cc_start: 0.8996 (tpt) cc_final: 0.8693 (tpt) outliers start: 20 outliers final: 8 residues processed: 131 average time/residue: 0.5751 time to fit residues: 82.5120 Evaluate side-chains 117 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 305 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 33 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.146325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122333 restraints weight = 16629.812| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.42 r_work: 0.3408 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12897 Z= 0.207 Angle : 0.618 9.539 17487 Z= 0.310 Chirality : 0.048 0.168 1922 Planarity : 0.004 0.045 2258 Dihedral : 7.193 103.401 1791 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.64 % Allowed : 16.07 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.21), residues: 1587 helix: 0.44 (0.24), residues: 483 sheet: 0.03 (0.28), residues: 342 loop : -0.05 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 28 TYR 0.019 0.001 TYR B 69 PHE 0.017 0.002 PHE A 216 TRP 0.016 0.002 TRP D 340 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00513 (12897) covalent geometry : angle 0.61784 (17487) hydrogen bonds : bond 0.04183 ( 516) hydrogen bonds : angle 5.19992 ( 1311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.490 Fit side-chains REVERT: A 190 THR cc_start: 0.7602 (OUTLIER) cc_final: 0.7329 (p) REVERT: B 47 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.7425 (mmm) REVERT: B 65 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8534 (pp) REVERT: B 334 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6889 (pp20) REVERT: C 28 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8117 (tpp80) REVERT: C 288 ASP cc_start: 0.6574 (m-30) cc_final: 0.6335 (m-30) REVERT: D 47 MET cc_start: 0.2445 (tmm) cc_final: 0.2107 (tmm) REVERT: D 82 MET cc_start: 0.9003 (tpt) cc_final: 0.8521 (tpt) outliers start: 22 outliers final: 13 residues processed: 125 average time/residue: 0.5978 time to fit residues: 81.4214 Evaluate side-chains 123 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 305 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 8 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121727 restraints weight = 16644.960| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.40 r_work: 0.3385 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12897 Z= 0.224 Angle : 0.626 9.702 17487 Z= 0.318 Chirality : 0.049 0.176 1922 Planarity : 0.004 0.047 2258 Dihedral : 7.501 109.541 1791 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.08 % Allowed : 16.00 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.21), residues: 1587 helix: 0.26 (0.24), residues: 483 sheet: -0.21 (0.28), residues: 339 loop : -0.19 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 28 TYR 0.020 0.001 TYR B 69 PHE 0.012 0.002 PHE D 31 TRP 0.015 0.002 TRP D 340 HIS 0.007 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00557 (12897) covalent geometry : angle 0.62560 (17487) hydrogen bonds : bond 0.04333 ( 516) hydrogen bonds : angle 5.33641 ( 1311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.421 Fit side-chains REVERT: B 47 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7502 (mmm) REVERT: B 65 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8493 (pp) REVERT: B 334 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6973 (pp20) REVERT: C 28 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.8124 (tpp80) REVERT: C 122 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8143 (mp) REVERT: C 325 MET cc_start: 0.8052 (ptp) cc_final: 0.7825 (ptp) REVERT: D 47 MET cc_start: 0.2570 (tmm) cc_final: 0.2229 (tmm) REVERT: D 82 MET cc_start: 0.9022 (tpt) cc_final: 0.8542 (tpt) outliers start: 28 outliers final: 18 residues processed: 126 average time/residue: 0.5668 time to fit residues: 77.7461 Evaluate side-chains 127 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 305 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN C 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.146575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.120803 restraints weight = 16865.622| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.54 r_work: 0.3342 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 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 : 0.003 0.042 12897 Z= 0.134 Angle : 0.571 9.670 17487 Z= 0.287 Chirality : 0.045 0.162 1922 Planarity : 0.004 0.041 2258 Dihedral : 7.191 104.663 1791 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.64 % Allowed : 16.67 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.21), residues: 1587 helix: 0.43 (0.24), residues: 483 sheet: -0.13 (0.28), residues: 339 loop : -0.04 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 28 TYR 0.014 0.001 TYR B 69 PHE 0.015 0.001 PHE A 216 TRP 0.012 0.001 TRP D 340 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00324 (12897) covalent geometry : angle 0.57085 (17487) hydrogen bonds : bond 0.03542 ( 516) hydrogen bonds : angle 5.17021 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3841.94 seconds wall clock time: 66 minutes 35.79 seconds (3995.79 seconds total)