Starting phenix.real_space_refine on Wed Jun 11 08:11:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo5_43364/06_2025/8vo5_43364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo5_43364/06_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_43364/06_2025/8vo5_43364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo5_43364/06_2025/8vo5_43364.map" model { file = "/net/cci-nas-00/data/ceres_data/8vo5_43364/06_2025/8vo5_43364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo5_43364/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.63, per 1000 atoms: 0.68 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: 2.86 Conformation dependent library (CDL) restraints added in 1.6 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: 1.79 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: 4.38 Time building geometry restraints manager: 3.41 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: 7.740 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.010 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.860 ------------------------------------------------------------------------------- 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 : 1.517 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 1.4052 time to fit residues: 207.4620 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 : 1.475 ------------------------------------------------------------------------------- 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 = 0.124316 restraints weight = 16642.175| |-----------------------------------------------------------------------------| 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: 3.52 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 7.449 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 0.04565 ( 516) hydrogen bonds : angle 5.95914 ( 1311) covalent geometry : bond 0.00416 (12897) covalent geometry : angle 0.60317 (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 : 1.605 Fit side-chains revert: symmetry clash REVERT: C 288 ASP cc_start: 0.6628 (m-30) cc_final: 0.6393 (m-30) REVERT: C 325 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6170 (ptm) REVERT: D 82 MET cc_start: 0.9035 (tpt) cc_final: 0.8686 (tpt) outliers start: 20 outliers final: 7 residues processed: 128 average time/residue: 1.3433 time to fit residues: 187.6561 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 : 1.435 ------------------------------------------------------------------------------- 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: 0.0570 chunk 82 optimal weight: 0.0040 chunk 25 optimal weight: 0.0870 chunk 147 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.2266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN C 59 GLN C 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.152273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.127750 restraints weight = 16652.847| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.62 r_work: 0.3434 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12897 Z= 0.092 Angle : 0.523 6.999 17487 Z= 0.262 Chirality : 0.043 0.165 1922 Planarity : 0.004 0.046 2258 Dihedral : 6.937 103.686 1791 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.79 % Allowed : 9.00 % Favored : 89.21 % 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: 0.31 (0.22), residues: 1587 helix: 0.73 (0.25), residues: 480 sheet: 0.04 (0.29), residues: 331 loop : 0.09 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 171 HIS 0.003 0.001 HIS D 87 PHE 0.016 0.001 PHE A 216 TYR 0.021 0.001 TYR A 111 ARG 0.009 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 516) hydrogen bonds : angle 5.35182 ( 1311) covalent geometry : bond 0.00205 (12897) covalent geometry : angle 0.52289 (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 146 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.559 Fit side-chains revert: symmetry clash REVERT: B 47 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7400 (mmm) REVERT: C 288 ASP cc_start: 0.6443 (OUTLIER) cc_final: 0.6234 (m-30) REVERT: D 82 MET cc_start: 0.8948 (tpt) cc_final: 0.8704 (tpt) outliers start: 24 outliers final: 5 residues processed: 135 average time/residue: 1.2867 time to fit residues: 189.8338 Evaluate side-chains 110 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 324 THR 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: 0.7980 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 162 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 = 0.3840 r_free = 0.3840 target = 0.147250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122357 restraints weight = 16721.142| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.47 r_work: 0.3361 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1430 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= 0.257 Angle : 0.650 10.292 17487 Z= 0.329 Chirality : 0.050 0.165 1922 Planarity : 0.005 0.052 2258 Dihedral : 7.523 111.329 1791 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.31 % Allowed : 11.61 % Favored : 86.09 % 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: -0.08 (0.21), residues: 1587 helix: 0.30 (0.24), residues: 483 sheet: -0.07 (0.29), residues: 330 loop : -0.13 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 340 HIS 0.006 0.002 HIS B 161 PHE 0.013 0.002 PHE D 31 TYR 0.009 0.002 TYR C 133 ARG 0.008 0.001 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.04845 ( 516) hydrogen bonds : angle 5.52066 ( 1311) covalent geometry : bond 0.00635 (12897) covalent geometry : angle 0.64975 (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 143 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 1.389 Fit side-chains REVERT: B 47 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7431 (mmm) REVERT: B 65 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8608 (pp) REVERT: C 28 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.8072 (tpp80) REVERT: C 122 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8219 (mp) REVERT: C 211 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8273 (m-30) REVERT: C 288 ASP cc_start: 0.6797 (OUTLIER) cc_final: 0.6563 (m-30) REVERT: C 328 LYS cc_start: 0.8911 (ttpp) cc_final: 0.8614 (tttm) REVERT: D 82 MET cc_start: 0.9078 (tpt) cc_final: 0.8628 (tpt) outliers start: 31 outliers final: 13 residues processed: 134 average time/residue: 1.2370 time to fit residues: 181.1419 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 : 1.450 ------------------------------------------------------------------------------- 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 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 276 GLU Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 69 optimal weight: 0.5980 chunk 152 optimal weight: 0.5980 chunk 112 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.148712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125013 restraints weight = 16605.295| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.42 r_work: 0.3439 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12897 Z= 0.129 Angle : 0.551 9.260 17487 Z= 0.276 Chirality : 0.045 0.165 1922 Planarity : 0.004 0.047 2258 Dihedral : 7.205 107.448 1791 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.08 % Allowed : 13.69 % Favored : 84.23 % 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 (0.22), residues: 1587 helix: 0.52 (0.24), residues: 483 sheet: -0.01 (0.29), residues: 329 loop : -0.02 (0.23), residues: 775 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 0.012 0.001 PHE A 216 TYR 0.008 0.001 TYR A 458 ARG 0.007 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 516) hydrogen bonds : angle 5.25706 ( 1311) covalent geometry : bond 0.00310 (12897) covalent geometry : angle 0.55147 (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 135 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 1.437 Fit side-chains REVERT: B 47 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7459 (mmm) REVERT: B 65 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8548 (pp) REVERT: C 28 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.7988 (tpp80) REVERT: C 122 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8132 (mp) REVERT: C 211 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8167 (m-30) REVERT: C 288 ASP cc_start: 0.6482 (OUTLIER) cc_final: 0.6255 (m-30) REVERT: D 82 MET cc_start: 0.8987 (tpt) cc_final: 0.8536 (tpt) REVERT: D 225 ASN cc_start: 0.8220 (m110) cc_final: 0.7961 (m110) outliers start: 28 outliers final: 8 residues processed: 124 average time/residue: 1.3084 time to fit residues: 177.2814 Evaluate side-chains 118 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 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 122 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 123 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.144671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120542 restraints weight = 16892.898| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.43 r_work: 0.3387 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12897 Z= 0.250 Angle : 0.636 9.428 17487 Z= 0.322 Chirality : 0.049 0.167 1922 Planarity : 0.005 0.053 2258 Dihedral : 7.601 112.601 1791 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.12 % Allowed : 13.62 % Favored : 83.26 % 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: -0.19 (0.21), residues: 1587 helix: 0.23 (0.24), residues: 483 sheet: -0.10 (0.29), residues: 330 loop : -0.23 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 340 HIS 0.006 0.001 HIS B 161 PHE 0.014 0.002 PHE D 31 TYR 0.013 0.001 TYR A 111 ARG 0.006 0.001 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 516) hydrogen bonds : angle 5.43293 ( 1311) covalent geometry : bond 0.00623 (12897) covalent geometry : angle 0.63558 (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 150 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 1.389 Fit side-chains REVERT: A 151 ARG cc_start: 0.7515 (mtt90) cc_final: 0.7212 (mtt180) REVERT: B 47 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7444 (mmm) REVERT: B 65 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8582 (pp) REVERT: C 28 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.8061 (tpp80) REVERT: C 122 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8191 (mp) outliers start: 42 outliers final: 20 residues processed: 136 average time/residue: 1.2504 time to fit residues: 185.4477 Evaluate side-chains 128 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 169 VAL 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 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 326 LYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 178 LEU 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: 0.8980 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 99 optimal weight: 0.0870 chunk 89 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.149809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124864 restraints weight = 16758.976| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.57 r_work: 0.3388 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1631 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= 0.124 Angle : 0.552 9.172 17487 Z= 0.276 Chirality : 0.045 0.167 1922 Planarity : 0.004 0.045 2258 Dihedral : 7.202 106.150 1791 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.93 % Allowed : 15.55 % 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 (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: 0.07 (0.22), residues: 1587 helix: 0.52 (0.25), residues: 483 sheet: -0.02 (0.29), residues: 329 loop : -0.09 (0.23), residues: 775 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 0.013 0.001 PHE A 216 TYR 0.009 0.001 TYR A 458 ARG 0.012 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 516) hydrogen bonds : angle 5.18836 ( 1311) covalent geometry : bond 0.00298 (12897) covalent geometry : angle 0.55156 (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 133 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 1.540 Fit side-chains REVERT: B 47 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7465 (mmm) REVERT: B 65 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8610 (pp) REVERT: C 28 ARG cc_start: 0.8361 (ttm-80) cc_final: 0.8034 (tpp80) REVERT: C 122 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8168 (mp) REVERT: C 288 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.6403 (m-30) REVERT: D 82 MET cc_start: 0.9023 (tpt) cc_final: 0.8683 (tpt) outliers start: 26 outliers final: 10 residues processed: 125 average time/residue: 1.5118 time to fit residues: 205.7673 Evaluate side-chains 117 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 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 190 MET 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 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: 2.9990 chunk 25 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 99 optimal weight: 0.3980 chunk 115 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 111 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.150733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.125864 restraints weight = 16900.707| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.56 r_work: 0.3419 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1696 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= 0.120 Angle : 0.547 9.003 17487 Z= 0.273 Chirality : 0.044 0.169 1922 Planarity : 0.004 0.043 2258 Dihedral : 7.077 104.275 1791 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.71 % Allowed : 16.07 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1587 helix: 0.56 (0.25), residues: 483 sheet: 0.09 (0.28), residues: 342 loop : -0.02 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 340 HIS 0.003 0.001 HIS D 161 PHE 0.010 0.001 PHE D 31 TYR 0.008 0.001 TYR A 458 ARG 0.009 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 516) hydrogen bonds : angle 5.11905 ( 1311) covalent geometry : bond 0.00288 (12897) covalent geometry : angle 0.54698 (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 133 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.772 Fit side-chains revert: symmetry clash REVERT: B 47 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7915 (mmt) REVERT: B 65 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8599 (pp) REVERT: C 28 ARG cc_start: 0.8408 (ttm-80) cc_final: 0.8064 (tpp80) REVERT: C 122 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8170 (mp) REVERT: C 288 ASP cc_start: 0.6473 (OUTLIER) cc_final: 0.6200 (m-30) REVERT: D 47 MET cc_start: 0.2508 (tmm) cc_final: 0.2190 (tmm) REVERT: D 82 MET cc_start: 0.9030 (tpt) cc_final: 0.8701 (tpt) outliers start: 23 outliers final: 13 residues processed: 126 average time/residue: 1.3153 time to fit residues: 181.4566 Evaluate side-chains 122 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 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: 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 = 0.3872 r_free = 0.3872 target = 0.150045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125177 restraints weight = 16857.358| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.55 r_work: 0.3408 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1715 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= 0.139 Angle : 0.562 8.925 17487 Z= 0.282 Chirality : 0.045 0.170 1922 Planarity : 0.004 0.044 2258 Dihedral : 7.089 103.584 1791 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.71 % Allowed : 16.52 % Favored : 81.77 % 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 (0.22), residues: 1587 helix: 0.52 (0.25), residues: 483 sheet: -0.01 (0.29), residues: 339 loop : -0.02 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 340 HIS 0.004 0.001 HIS D 161 PHE 0.014 0.001 PHE A 216 TYR 0.008 0.001 TYR B 306 ARG 0.009 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 516) hydrogen bonds : angle 5.12252 ( 1311) covalent geometry : bond 0.00340 (12897) covalent geometry : angle 0.56214 (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 131 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.235 Fit side-chains REVERT: B 47 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7477 (mmm) REVERT: B 65 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8606 (pp) REVERT: B 334 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6901 (pp20) REVERT: C 28 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8072 (tpp80) REVERT: C 122 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8172 (mp) REVERT: C 288 ASP cc_start: 0.6520 (OUTLIER) cc_final: 0.6245 (m-30) REVERT: D 47 MET cc_start: 0.2545 (tmm) cc_final: 0.2211 (tmm) REVERT: D 82 MET cc_start: 0.9052 (tpt) cc_final: 0.8726 (tpt) outliers start: 23 outliers final: 13 residues processed: 126 average time/residue: 1.3649 time to fit residues: 188.3009 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 : 1.454 ------------------------------------------------------------------------------- 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 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 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 80 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.147775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123931 restraints weight = 16580.504| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.45 r_work: 0.3422 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12897 Z= 0.157 Angle : 0.574 8.943 17487 Z= 0.289 Chirality : 0.046 0.170 1922 Planarity : 0.004 0.043 2258 Dihedral : 7.146 104.095 1791 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.56 % Allowed : 16.82 % Favored : 81.62 % 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 (0.22), residues: 1587 helix: 0.50 (0.24), residues: 483 sheet: -0.04 (0.29), 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 0.005 0.001 HIS D 161 PHE 0.011 0.001 PHE D 31 TYR 0.009 0.001 TYR A 458 ARG 0.008 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 516) hydrogen bonds : angle 5.17972 ( 1311) covalent geometry : bond 0.00386 (12897) covalent geometry : angle 0.57422 (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 128 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.410 Fit side-chains REVERT: B 47 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7468 (mmm) REVERT: B 65 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8573 (pp) REVERT: B 334 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6867 (pp20) REVERT: C 28 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.8001 (tpp80) REVERT: C 122 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8157 (mp) REVERT: C 288 ASP cc_start: 0.6545 (OUTLIER) cc_final: 0.6308 (m-30) REVERT: D 47 MET cc_start: 0.2515 (tmm) cc_final: 0.2170 (tmm) REVERT: D 82 MET cc_start: 0.9002 (tpt) cc_final: 0.8720 (tpt) outliers start: 21 outliers final: 14 residues processed: 123 average time/residue: 1.6153 time to fit residues: 217.3590 Evaluate side-chains 124 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 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 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 75 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 147 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.147577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123709 restraints weight = 16605.091| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.45 r_work: 0.3410 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1762 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= 0.151 Angle : 0.571 8.940 17487 Z= 0.287 Chirality : 0.046 0.167 1922 Planarity : 0.004 0.042 2258 Dihedral : 7.132 103.897 1791 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.56 % Allowed : 16.74 % 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 (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: 0.05 (0.21), residues: 1587 helix: 0.45 (0.24), residues: 483 sheet: -0.03 (0.29), residues: 339 loop : -0.06 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 340 HIS 0.005 0.001 HIS D 161 PHE 0.013 0.001 PHE A 216 TYR 0.009 0.001 TYR A 111 ARG 0.008 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 516) hydrogen bonds : angle 5.16395 ( 1311) covalent geometry : bond 0.00371 (12897) covalent geometry : angle 0.57078 (17487) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8924.51 seconds wall clock time: 156 minutes 48.80 seconds (9408.80 seconds total)