Starting phenix.real_space_refine on Thu May 15 02:58:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo5_43364/05_2025/8vo5_43364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo5_43364/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vo5_43364/05_2025/8vo5_43364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo5_43364/05_2025/8vo5_43364.map" model { file = "/net/cci-nas-00/data/ceres_data/8vo5_43364/05_2025/8vo5_43364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo5_43364/05_2025/8vo5_43364.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.14, per 1000 atoms: 0.72 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: 3.17 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.77 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: 4.15 Time building geometry restraints manager: 3.70 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: 6.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 32.430 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.260 ------------------------------------------------------------------------------- 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 : 7.37 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 (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: -0.12 (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 TRP 0.018 0.002 TRP A 171 HIS 0.003 0.001 HIS A 108 PHE 0.015 0.001 PHE C 124 TYR 0.010 0.001 TYR A 230 ARG 0.007 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.21549 ( 516) hydrogen bonds : angle 8.30434 ( 1311) covalent geometry : bond 0.00344 (12897) covalent geometry : angle 0.59588 (17487) *********************** 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 : 1.412 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 1.3428 time to fit residues: 198.6037 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 : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.0470 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.0370 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN B 162 ASN B 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.149734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.124317 restraints weight = 16642.115| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.51 r_work: 0.3391 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12897 Z= 0.172 Angle : 0.603 7.450 17487 Z= 0.307 Chirality : 0.046 0.179 1922 Planarity : 0.004 0.050 2258 Dihedral : 7.405 112.121 1791 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.49 % Allowed : 7.14 % Favored : 91.37 % 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 (0.21), residues: 1587 helix: 0.39 (0.24), residues: 480 sheet: -0.05 (0.28), residues: 331 loop : -0.05 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 171 HIS 0.005 0.001 HIS D 161 PHE 0.010 0.001 PHE D 31 TYR 0.011 0.001 TYR A 458 ARG 0.006 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 516) hydrogen bonds : angle 5.95906 ( 1311) covalent geometry : bond 0.00416 (12897) covalent geometry : angle 0.60319 (17487) *********************** 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 135 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: C 288 ASP cc_start: 0.6628 (m-30) cc_final: 0.6395 (m-30) REVERT: C 325 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6169 (ptm) REVERT: D 82 MET cc_start: 0.9039 (tpt) cc_final: 0.8690 (tpt) outliers start: 20 outliers final: 7 residues processed: 128 average time/residue: 1.3236 time to fit residues: 184.0098 Evaluate side-chains 111 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 249 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 123 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 0.0470 chunk 25 optimal weight: 0.3980 chunk 147 optimal weight: 0.0970 chunk 36 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 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 = 0.3889 r_free = 0.3889 target = 0.151288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.126762 restraints weight = 16842.149| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.53 r_work: 0.3441 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1187 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= 0.127 Angle : 0.551 7.066 17487 Z= 0.278 Chirality : 0.045 0.166 1922 Planarity : 0.004 0.044 2258 Dihedral : 7.192 107.995 1791 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.71 % Allowed : 9.45 % Favored : 88.84 % 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: 0.15 (0.21), residues: 1587 helix: 0.57 (0.25), residues: 480 sheet: -0.02 (0.29), residues: 331 loop : 0.01 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 340 HIS 0.004 0.001 HIS B 161 PHE 0.014 0.001 PHE A 216 TYR 0.022 0.001 TYR A 111 ARG 0.008 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 516) hydrogen bonds : angle 5.49725 ( 1311) covalent geometry : bond 0.00303 (12897) covalent geometry : angle 0.55063 (17487) *********************** 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 139 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.407 Fit side-chains revert: symmetry clash REVERT: A 300 ARG cc_start: 0.5758 (mpt180) cc_final: 0.5545 (mmt-90) REVERT: B 47 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7391 (mmm) REVERT: B 65 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8649 (pp) REVERT: C 288 ASP cc_start: 0.6433 (OUTLIER) cc_final: 0.6182 (m-30) REVERT: C 325 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6532 (ptm) REVERT: D 82 MET cc_start: 0.9016 (tpt) cc_final: 0.8631 (tpt) outliers start: 23 outliers final: 10 residues processed: 128 average time/residue: 1.2261 time to fit residues: 171.8733 Evaluate side-chains 118 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 337 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 288 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 325 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 305 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 75 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 D 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120660 restraints weight = 16744.663| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.50 r_work: 0.3348 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 12897 Z= 0.286 Angle : 0.670 8.264 17487 Z= 0.342 Chirality : 0.051 0.163 1922 Planarity : 0.005 0.053 2258 Dihedral : 7.760 116.111 1791 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.83 % Allowed : 11.68 % Favored : 85.49 % 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: -0.27 (0.21), residues: 1587 helix: 0.14 (0.24), residues: 483 sheet: -0.17 (0.28), residues: 335 loop : -0.25 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 340 HIS 0.007 0.001 HIS B 161 PHE 0.014 0.002 PHE D 31 TYR 0.011 0.002 TYR A 111 ARG 0.007 0.001 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.05091 ( 516) hydrogen bonds : angle 5.62673 ( 1311) covalent geometry : bond 0.00716 (12897) covalent geometry : angle 0.66990 (17487) *********************** 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 148 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 1.458 Fit side-chains REVERT: A 300 ARG cc_start: 0.5783 (mpt180) cc_final: 0.5541 (mmt-90) REVERT: B 47 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7473 (mmm) REVERT: B 65 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8626 (pp) REVERT: C 28 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.8088 (tpp80) REVERT: C 122 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8213 (mp) REVERT: D 82 MET cc_start: 0.9074 (tpt) cc_final: 0.8623 (tpt) outliers start: 38 outliers final: 16 residues processed: 133 average time/residue: 1.3359 time to fit residues: 193.6776 Evaluate side-chains 123 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE 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 A residue 190 THR 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 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 D residue 123 MET Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 211 ASP 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 69 optimal weight: 0.7980 chunk 152 optimal weight: 0.3980 chunk 112 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.146569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122709 restraints weight = 16629.062| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.41 r_work: 0.3411 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12897 Z= 0.162 Angle : 0.578 7.208 17487 Z= 0.292 Chirality : 0.046 0.166 1922 Planarity : 0.004 0.050 2258 Dihedral : 7.446 110.283 1791 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.60 % Allowed : 13.47 % Favored : 83.93 % 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: -0.12 (0.21), residues: 1587 helix: 0.34 (0.24), residues: 483 sheet: -0.14 (0.29), residues: 329 loop : -0.18 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.005 0.001 HIS B 161 PHE 0.012 0.001 PHE A 216 TYR 0.009 0.001 TYR B 306 ARG 0.010 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 516) hydrogen bonds : angle 5.37664 ( 1311) covalent geometry : bond 0.00399 (12897) covalent geometry : angle 0.57844 (17487) *********************** 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: 35 poor density : 108 time to evaluate : 1.453 Fit side-chains REVERT: A 300 ARG cc_start: 0.5775 (mpt180) cc_final: 0.5461 (mmt-90) REVERT: B 47 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7380 (mmm) REVERT: B 65 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8594 (pp) REVERT: C 28 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.8010 (tpp80) REVERT: C 122 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8149 (mp) REVERT: D 82 MET cc_start: 0.8980 (tpt) cc_final: 0.8499 (tpt) outliers start: 35 outliers final: 16 residues processed: 133 average time/residue: 1.2393 time to fit residues: 180.4637 Evaluate side-chains 125 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU 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 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 215 LYS Chi-restraints excluded: chain B residue 288 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 D residue 123 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 123 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.143274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119040 restraints weight = 16900.327| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.44 r_work: 0.3368 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 12897 Z= 0.284 Angle : 0.672 9.847 17487 Z= 0.341 Chirality : 0.050 0.169 1922 Planarity : 0.005 0.055 2258 Dihedral : 7.847 116.250 1791 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.12 % Allowed : 13.99 % Favored : 82.89 % 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: -0.42 (0.21), residues: 1587 helix: 0.07 (0.24), residues: 483 sheet: -0.23 (0.29), residues: 335 loop : -0.39 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 340 HIS 0.006 0.001 HIS B 161 PHE 0.014 0.002 PHE D 31 TYR 0.015 0.002 TYR A 111 ARG 0.007 0.001 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.04988 ( 516) hydrogen bonds : angle 5.56063 ( 1311) covalent geometry : bond 0.00705 (12897) covalent geometry : angle 0.67214 (17487) *********************** 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 145 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 1.332 Fit side-chains REVERT: A 151 ARG cc_start: 0.7489 (mtt90) cc_final: 0.7239 (mtt180) REVERT: B 47 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7466 (mmm) REVERT: B 65 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8579 (pp) REVERT: B 334 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6989 (pp20) REVERT: C 28 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.8070 (tpp80) REVERT: C 122 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8194 (mp) REVERT: D 82 MET cc_start: 0.9039 (tpt) cc_final: 0.8589 (tpt) REVERT: D 176 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8073 (mtt) REVERT: D 225 ASN cc_start: 0.8240 (m110) cc_final: 0.8020 (m110) outliers start: 42 outliers final: 21 residues processed: 133 average time/residue: 1.1959 time to fit residues: 174.4213 Evaluate side-chains 126 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR 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 169 VAL 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 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 249 THR Chi-restraints excluded: chain C residue 288 ASP 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 176 MET Chi-restraints excluded: chain D residue 211 ASP 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 55 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN D 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.148999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124217 restraints weight = 16707.815| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.52 r_work: 0.3413 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1627 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= 0.135 Angle : 0.567 9.528 17487 Z= 0.284 Chirality : 0.045 0.164 1922 Planarity : 0.004 0.046 2258 Dihedral : 7.364 107.699 1791 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.23 % Allowed : 15.62 % Favored : 82.14 % 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 (0.21), residues: 1587 helix: 0.40 (0.24), residues: 483 sheet: -0.12 (0.29), residues: 329 loop : -0.23 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.004 0.001 HIS B 161 PHE 0.010 0.001 PHE B 31 TYR 0.008 0.001 TYR B 306 ARG 0.008 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 516) hydrogen bonds : angle 5.27503 ( 1311) covalent geometry : bond 0.00328 (12897) covalent geometry : angle 0.56696 (17487) *********************** 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 144 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.346 Fit side-chains REVERT: B 47 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7447 (mmm) REVERT: B 65 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8613 (pp) REVERT: C 28 ARG cc_start: 0.8361 (ttm-80) cc_final: 0.8043 (tpp80) REVERT: C 122 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8171 (mp) REVERT: D 47 MET cc_start: 0.2604 (tmm) cc_final: 0.2265 (tmm) REVERT: D 82 MET cc_start: 0.9004 (tpt) cc_final: 0.8551 (tpt) REVERT: D 176 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8009 (mtt) outliers start: 30 outliers final: 14 residues processed: 135 average time/residue: 1.2778 time to fit residues: 187.8043 Evaluate side-chains 126 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 337 ASP Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 65 LEU 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 249 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 176 MET 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 82 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 128 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 111 optimal weight: 0.0370 overall best weight: 0.5436 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.148939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.125307 restraints weight = 16687.822| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.45 r_work: 0.3441 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12897 Z= 0.117 Angle : 0.550 10.278 17487 Z= 0.274 Chirality : 0.044 0.167 1922 Planarity : 0.004 0.042 2258 Dihedral : 7.101 104.486 1791 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.23 % Allowed : 15.85 % 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 (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: 0.09 (0.21), residues: 1587 helix: 0.54 (0.25), residues: 483 sheet: 0.08 (0.29), residues: 332 loop : -0.12 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 340 HIS 0.003 0.001 HIS B 161 PHE 0.010 0.001 PHE B 31 TYR 0.008 0.001 TYR C 143 ARG 0.008 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 516) hydrogen bonds : angle 5.11236 ( 1311) covalent geometry : bond 0.00280 (12897) covalent geometry : angle 0.54980 (17487) *********************** 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 148 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: B 47 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7831 (mmt) REVERT: B 65 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8634 (pp) REVERT: B 334 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6810 (pp20) REVERT: C 28 ARG cc_start: 0.8336 (ttm-80) cc_final: 0.8008 (tpp80) REVERT: C 122 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8131 (mp) REVERT: C 288 ASP cc_start: 0.6459 (OUTLIER) cc_final: 0.6217 (m-30) REVERT: D 47 MET cc_start: 0.2527 (tmm) cc_final: 0.2176 (tmm) REVERT: D 82 MET cc_start: 0.8975 (tpt) cc_final: 0.8617 (tpt) outliers start: 30 outliers final: 12 residues processed: 139 average time/residue: 1.2276 time to fit residues: 186.7464 Evaluate side-chains 125 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 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 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 D residue 123 MET Chi-restraints excluded: chain D residue 260 THR 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 147 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN D 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.149698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125218 restraints weight = 16793.126| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.51 r_work: 0.3350 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1766 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= 0.142 Angle : 0.575 11.569 17487 Z= 0.286 Chirality : 0.046 0.167 1922 Planarity : 0.004 0.043 2258 Dihedral : 7.133 104.094 1791 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.93 % Allowed : 16.82 % Favored : 81.25 % 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: 0.03 (0.21), residues: 1587 helix: 0.49 (0.25), residues: 483 sheet: -0.08 (0.28), residues: 339 loop : -0.08 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 340 HIS 0.004 0.001 HIS D 161 PHE 0.011 0.001 PHE D 31 TYR 0.008 0.001 TYR B 306 ARG 0.010 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 516) hydrogen bonds : angle 5.14444 ( 1311) covalent geometry : bond 0.00347 (12897) covalent geometry : angle 0.57536 (17487) *********************** 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 140 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.411 Fit side-chains REVERT: B 34 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8860 (tp) REVERT: B 47 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7402 (mmm) REVERT: B 65 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8608 (pp) REVERT: B 334 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6843 (pp20) REVERT: C 28 ARG cc_start: 0.8370 (ttm-80) cc_final: 0.8036 (tpp80) REVERT: C 72 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7834 (mt-10) REVERT: C 122 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8098 (mp) REVERT: C 288 ASP cc_start: 0.6610 (OUTLIER) cc_final: 0.6396 (m-30) REVERT: D 47 MET cc_start: 0.2547 (tmm) cc_final: 0.2197 (tmm) REVERT: D 82 MET cc_start: 0.9001 (tpt) cc_final: 0.8624 (tpt) outliers start: 26 outliers final: 15 residues processed: 131 average time/residue: 1.2224 time to fit residues: 175.4038 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 : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP 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 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 288 ASP Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 72 GLU 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 D residue 123 MET Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 298 VAL 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 80 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.149158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124464 restraints weight = 16788.905| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.53 r_work: 0.3342 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12897 Z= 0.151 Angle : 0.582 12.294 17487 Z= 0.290 Chirality : 0.046 0.166 1922 Planarity : 0.004 0.043 2258 Dihedral : 7.152 104.206 1791 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.93 % Allowed : 16.89 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.21), residues: 1587 helix: 0.47 (0.24), residues: 483 sheet: 0.01 (0.28), residues: 342 loop : -0.08 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 340 HIS 0.005 0.001 HIS D 161 PHE 0.014 0.001 PHE A 216 TYR 0.008 0.001 TYR A 111 ARG 0.010 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 516) hydrogen bonds : angle 5.16057 ( 1311) covalent geometry : bond 0.00371 (12897) covalent geometry : angle 0.58222 (17487) ********************** 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 133 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 1.423 Fit side-chains REVERT: B 34 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8865 (tp) REVERT: B 47 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7421 (mmm) REVERT: B 65 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8608 (pp) REVERT: B 334 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6856 (pp20) REVERT: C 28 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.8035 (tpp80) REVERT: C 122 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8118 (mp) REVERT: C 288 ASP cc_start: 0.6623 (OUTLIER) cc_final: 0.6413 (m-30) REVERT: D 47 MET cc_start: 0.2562 (tmm) cc_final: 0.2210 (tmm) REVERT: D 82 MET cc_start: 0.9000 (tpt) cc_final: 0.8564 (tpt) outliers start: 26 outliers final: 17 residues processed: 126 average time/residue: 1.2210 time to fit residues: 168.1303 Evaluate side-chains 129 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 117 ASP 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 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 249 THR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 298 VAL 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 75 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 147 optimal weight: 0.1980 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 92 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.150438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125660 restraints weight = 16836.892| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.55 r_work: 0.3420 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1824 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= 0.126 Angle : 0.564 11.185 17487 Z= 0.281 Chirality : 0.045 0.165 1922 Planarity : 0.004 0.041 2258 Dihedral : 7.023 102.539 1791 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.86 % Allowed : 16.89 % Favored : 81.25 % 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: 0.13 (0.21), residues: 1587 helix: 0.54 (0.25), residues: 483 sheet: 0.04 (0.28), residues: 342 loop : -0.04 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 340 HIS 0.004 0.001 HIS D 161 PHE 0.010 0.001 PHE D 31 TYR 0.007 0.001 TYR B 306 ARG 0.010 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 516) hydrogen bonds : angle 5.09384 ( 1311) covalent geometry : bond 0.00305 (12897) covalent geometry : angle 0.56376 (17487) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7754.40 seconds wall clock time: 134 minutes 48.46 seconds (8088.46 seconds total)