Starting phenix.real_space_refine on Sat Aug 23 03:32:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j0j_35904/08_2025/8j0j_35904_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j0j_35904/08_2025/8j0j_35904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j0j_35904/08_2025/8j0j_35904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j0j_35904/08_2025/8j0j_35904.map" model { file = "/net/cci-nas-00/data/ceres_data/8j0j_35904/08_2025/8j0j_35904_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j0j_35904/08_2025/8j0j_35904_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.059 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 Cl 3 4.86 5 C 6174 2.51 5 N 1419 2.21 5 O 1494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9138 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3010 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' CL': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' CL': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' CL': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C Time building chain proxies: 2.56, per 1000 atoms: 0.28 Number of scatterers: 9138 At special positions: 0 Unit cell: (104.676, 100.386, 77.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 3 17.00 S 48 16.00 O 1494 8.00 N 1419 7.00 C 6174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 283.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 76.1% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.577A pdb=" N TYR A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 189 through 192 removed outlier: 3.601A pdb=" N CYS A 192 " --> pdb=" O PRO A 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 192' Processing helix chain 'A' and resid 193 through 210 removed outlier: 3.934A pdb=" N GLN A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.555A pdb=" N ASN A 216 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 250 removed outlier: 3.679A pdb=" N LEU A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.824A pdb=" N VAL A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.540A pdb=" N ASN A 265 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.662A pdb=" N VAL A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N CYS A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 293 through 316 removed outlier: 4.378A pdb=" N TRP A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Proline residue: A 303 - end of helix removed outlier: 3.621A pdb=" N LYS A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.773A pdb=" N HIS A 332 " --> pdb=" O PRO A 329 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 334 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.254A pdb=" N PHE A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 343 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 344 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 372 removed outlier: 3.682A pdb=" N LEU A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 372 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 393 Processing helix chain 'A' and resid 394 through 409 Processing helix chain 'A' and resid 412 through 431 removed outlier: 3.622A pdb=" N THR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 442 through 448 Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.530A pdb=" N ALA A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 499 removed outlier: 3.627A pdb=" N LEU A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 489 " --> pdb=" O MET A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 removed outlier: 3.791A pdb=" N ILE A 510 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.577A pdb=" N TYR B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 189 through 192 removed outlier: 3.602A pdb=" N CYS B 192 " --> pdb=" O PRO B 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 189 through 192' Processing helix chain 'B' and resid 193 through 210 removed outlier: 3.935A pdb=" N GLN B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 216 removed outlier: 3.554A pdb=" N ASN B 216 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 250 removed outlier: 3.680A pdb=" N LEU B 226 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 removed outlier: 3.824A pdb=" N VAL B 254 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 267 removed outlier: 3.540A pdb=" N ASN B 265 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.662A pdb=" N VAL B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N CYS B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 293 through 316 removed outlier: 4.378A pdb=" N TRP B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.622A pdb=" N LYS B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.774A pdb=" N HIS B 332 " --> pdb=" O PRO B 329 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 334 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 348 removed outlier: 4.253A pdb=" N PHE B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 343 " --> pdb=" O PHE B 339 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 344 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 372 removed outlier: 3.682A pdb=" N LEU B 366 " --> pdb=" O PHE B 362 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 372 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 393 Processing helix chain 'B' and resid 394 through 409 Processing helix chain 'B' and resid 412 through 431 removed outlier: 3.622A pdb=" N THR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 442 through 448 Processing helix chain 'B' and resid 449 through 466 removed outlier: 3.530A pdb=" N ALA B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 457 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 499 removed outlier: 3.626A pdb=" N LEU B 474 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 489 " --> pdb=" O MET B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 511 removed outlier: 3.790A pdb=" N ILE B 510 " --> pdb=" O ASP B 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.577A pdb=" N TYR C 156 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 189 through 192 removed outlier: 3.601A pdb=" N CYS C 192 " --> pdb=" O PRO C 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 192' Processing helix chain 'C' and resid 193 through 210 removed outlier: 3.935A pdb=" N GLN C 202 " --> pdb=" O GLY C 198 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 204 " --> pdb=" O SER C 200 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.555A pdb=" N ASN C 216 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 250 removed outlier: 3.680A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 removed outlier: 3.824A pdb=" N VAL C 254 " --> pdb=" O TYR C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 267 removed outlier: 3.540A pdb=" N ASN C 265 " --> pdb=" O VAL C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 279 removed outlier: 3.663A pdb=" N VAL C 272 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N CYS C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 293 through 316 removed outlier: 4.378A pdb=" N TRP C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Proline residue: C 303 - end of helix removed outlier: 3.622A pdb=" N LYS C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.774A pdb=" N HIS C 332 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER C 334 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 4.254A pdb=" N PHE C 339 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 343 " --> pdb=" O PHE C 339 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 344 " --> pdb=" O VAL C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 372 removed outlier: 3.682A pdb=" N LEU C 366 " --> pdb=" O PHE C 362 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 367 " --> pdb=" O ALA C 363 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 372 " --> pdb=" O VAL C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 393 Processing helix chain 'C' and resid 394 through 409 Processing helix chain 'C' and resid 412 through 431 removed outlier: 3.623A pdb=" N THR C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 449 through 466 removed outlier: 3.530A pdb=" N ALA C 455 " --> pdb=" O PRO C 451 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 457 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 465 " --> pdb=" O LYS C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 499 removed outlier: 3.627A pdb=" N LEU C 474 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 489 " --> pdb=" O MET C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 511 removed outlier: 3.791A pdb=" N ILE C 510 " --> pdb=" O ASP C 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 removed outlier: 3.583A pdb=" N GLU A 167 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 161 removed outlier: 3.584A pdb=" N GLU B 167 " --> pdb=" O ARG B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.583A pdb=" N GLU C 167 " --> pdb=" O ARG C 161 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1377 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: 1.20 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1601 1.33 - 1.45: 2648 1.45 - 1.57: 5138 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 9456 Sorted by residual: bond pdb=" CBD Y01 A 902 " pdb=" CBF Y01 A 902 " ideal model delta sigma weight residual 1.536 1.404 0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" CBD Y01 B 901 " pdb=" CBF Y01 B 901 " ideal model delta sigma weight residual 1.536 1.404 0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" CBD Y01 C 901 " pdb=" CBF Y01 C 901 " ideal model delta sigma weight residual 1.536 1.404 0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" CAV Y01 B 901 " pdb=" CBC Y01 B 901 " ideal model delta sigma weight residual 1.523 1.434 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" CAV Y01 C 901 " pdb=" CBC Y01 C 901 " ideal model delta sigma weight residual 1.523 1.434 0.089 2.00e-02 2.50e+03 1.99e+01 ... (remaining 9451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 12816 2.94 - 5.89: 74 5.89 - 8.83: 25 8.83 - 11.77: 12 11.77 - 14.71: 3 Bond angle restraints: 12930 Sorted by residual: angle pdb=" CAR Y01 B 901 " pdb=" CBC Y01 B 901 " pdb=" OAW Y01 B 901 " ideal model delta sigma weight residual 107.47 122.18 -14.71 3.00e+00 1.11e-01 2.41e+01 angle pdb=" CAR Y01 A 902 " pdb=" CBC Y01 A 902 " pdb=" OAW Y01 A 902 " ideal model delta sigma weight residual 107.47 122.18 -14.71 3.00e+00 1.11e-01 2.41e+01 angle pdb=" CAR Y01 C 901 " pdb=" CBC Y01 C 901 " pdb=" OAW Y01 C 901 " ideal model delta sigma weight residual 107.47 122.15 -14.68 3.00e+00 1.11e-01 2.40e+01 angle pdb=" CAR Y01 A 902 " pdb=" CBC Y01 A 902 " pdb=" CAV Y01 A 902 " ideal model delta sigma weight residual 110.42 99.65 10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" CAK Y01 C 901 " pdb=" CAI Y01 C 901 " pdb=" CAZ Y01 C 901 " ideal model delta sigma weight residual 124.96 114.21 10.75 3.00e+00 1.11e-01 1.28e+01 ... (remaining 12925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 4830 17.59 - 35.19: 516 35.19 - 52.78: 168 52.78 - 70.38: 18 70.38 - 87.97: 6 Dihedral angle restraints: 5538 sinusoidal: 2208 harmonic: 3330 Sorted by residual: dihedral pdb=" CB GLU C 257 " pdb=" CG GLU C 257 " pdb=" CD GLU C 257 " pdb=" OE1 GLU C 257 " ideal model delta sinusoidal sigma weight residual 0.00 87.97 -87.97 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " pdb=" CD GLU A 257 " pdb=" OE1 GLU A 257 " ideal model delta sinusoidal sigma weight residual 0.00 87.95 -87.95 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU B 257 " pdb=" CG GLU B 257 " pdb=" CD GLU B 257 " pdb=" OE1 GLU B 257 " ideal model delta sinusoidal sigma weight residual 0.00 87.95 -87.95 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 5535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1440 0.127 - 0.253: 0 0.253 - 0.380: 6 0.380 - 0.506: 3 0.506 - 0.633: 6 Chirality restraints: 1455 Sorted by residual: chirality pdb=" CBF Y01 A 902 " pdb=" CAS Y01 A 902 " pdb=" CBD Y01 A 902 " pdb=" CBH Y01 A 902 " both_signs ideal model delta sigma weight residual False -2.45 -1.81 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CBF Y01 C 901 " pdb=" CAS Y01 C 901 " pdb=" CBD Y01 C 901 " pdb=" CBH Y01 C 901 " both_signs ideal model delta sigma weight residual False -2.45 -1.81 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CBF Y01 B 901 " pdb=" CAS Y01 B 901 " pdb=" CBD Y01 B 901 " pdb=" CBH Y01 B 901 " both_signs ideal model delta sigma weight residual False -2.45 -1.82 -0.63 2.00e-01 2.50e+01 9.91e+00 ... (remaining 1452 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 469 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO C 470 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 470 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 470 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 469 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO B 470 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 469 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO A 470 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 470 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 470 " -0.031 5.00e-02 4.00e+02 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1897 2.77 - 3.30: 8034 3.30 - 3.84: 14001 3.84 - 4.37: 17824 4.37 - 4.90: 29815 Nonbonded interactions: 71571 Sorted by model distance: nonbonded pdb=" OE2 GLU C 164 " pdb=" OH TYR C 448 " model vdw 2.238 3.040 nonbonded pdb=" OE2 GLU B 164 " pdb=" OH TYR B 448 " model vdw 2.238 3.040 nonbonded pdb=" OE2 GLU A 164 " pdb=" OH TYR A 448 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASP A 166 " pdb=" NH2 ARG A 263 " model vdw 2.264 3.120 nonbonded pdb=" OD1 ASP C 166 " pdb=" NH2 ARG C 263 " model vdw 2.264 3.120 ... (remaining 71566 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 105 through 516) selection = (chain 'B' and resid 105 through 516) selection = (chain 'C' and resid 105 through 516) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.690 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.005 0.132 9456 Z= 0.235 Angle : 0.700 14.713 12930 Z= 0.281 Chirality : 0.059 0.633 1455 Planarity : 0.005 0.056 1563 Dihedral : 16.091 87.973 3378 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.25 % Allowed : 21.94 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.23), residues: 1119 helix: -1.73 (0.17), residues: 705 sheet: None (None), residues: 0 loop : -0.53 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 472 TYR 0.012 0.001 TYR A 365 PHE 0.010 0.001 PHE B 217 TRP 0.018 0.001 TRP B 404 HIS 0.009 0.001 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 9456) covalent geometry : angle 0.70039 (12930) hydrogen bonds : bond 0.33696 ( 513) hydrogen bonds : angle 7.36185 ( 1377) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.371 Fit side-chains REVERT: A 366 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8173 (mt) REVERT: B 168 VAL cc_start: 0.8493 (t) cc_final: 0.8282 (m) REVERT: B 450 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7467 (t80) REVERT: C 216 ASN cc_start: 0.7809 (t0) cc_final: 0.7501 (t0) REVERT: C 366 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8142 (mt) REVERT: C 405 ASN cc_start: 0.8770 (t0) cc_final: 0.8474 (t160) outliers start: 12 outliers final: 5 residues processed: 101 average time/residue: 0.4307 time to fit residues: 47.7219 Evaluate side-chains 95 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS C 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.140451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.116127 restraints weight = 8697.539| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 0.95 r_work: 0.2913 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9456 Z= 0.163 Angle : 0.650 7.414 12930 Z= 0.329 Chirality : 0.043 0.178 1455 Planarity : 0.006 0.047 1563 Dihedral : 7.981 59.801 1435 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.34 % Allowed : 16.93 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.25), residues: 1119 helix: 0.28 (0.20), residues: 711 sheet: None (None), residues: 0 loop : -0.23 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 472 TYR 0.013 0.002 TYR B 408 PHE 0.020 0.002 PHE B 450 TRP 0.022 0.002 TRP A 229 HIS 0.007 0.001 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9456) covalent geometry : angle 0.64965 (12930) hydrogen bonds : bond 0.08808 ( 513) hydrogen bonds : angle 4.18575 ( 1377) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.368 Fit side-chains REVERT: A 166 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7530 (t70) REVERT: A 180 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6733 (pt0) REVERT: A 322 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7729 (ptp-170) REVERT: A 333 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8352 (tt) REVERT: A 450 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.6592 (t80) REVERT: B 322 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7598 (ptp-170) REVERT: B 382 LEU cc_start: 0.7175 (tp) cc_final: 0.6882 (mt) REVERT: B 410 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: C 161 ARG cc_start: 0.8186 (ptt90) cc_final: 0.7903 (ptt-90) REVERT: C 166 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7241 (t70) REVERT: C 216 ASN cc_start: 0.8025 (t0) cc_final: 0.7566 (t0) REVERT: C 322 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7794 (ptm160) REVERT: C 450 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.6647 (t80) REVERT: C 452 MET cc_start: 0.8113 (mtp) cc_final: 0.7884 (mtt) REVERT: C 514 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7563 (tttm) outliers start: 32 outliers final: 6 residues processed: 115 average time/residue: 0.5074 time to fit residues: 62.5969 Evaluate side-chains 90 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS C 314 GLN C 387 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.136906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.111684 restraints weight = 8609.224| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.11 r_work: 0.2831 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9456 Z= 0.174 Angle : 0.664 6.973 12930 Z= 0.337 Chirality : 0.044 0.184 1455 Planarity : 0.006 0.051 1563 Dihedral : 7.059 56.586 1431 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.34 % Allowed : 16.61 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.25), residues: 1119 helix: 1.04 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.11 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 472 TYR 0.012 0.002 TYR B 408 PHE 0.021 0.002 PHE C 450 TRP 0.018 0.002 TRP A 229 HIS 0.009 0.002 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9456) covalent geometry : angle 0.66364 (12930) hydrogen bonds : bond 0.09243 ( 513) hydrogen bonds : angle 4.07808 ( 1377) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.385 Fit side-chains REVERT: A 322 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7598 (ptp-170) REVERT: B 180 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6528 (pt0) REVERT: B 190 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8067 (tp) REVERT: B 322 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7441 (ptp-170) REVERT: B 450 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7088 (t80) REVERT: C 161 ARG cc_start: 0.8208 (ptt90) cc_final: 0.7910 (ptt-90) REVERT: C 216 ASN cc_start: 0.7990 (t0) cc_final: 0.7517 (t0) REVERT: C 322 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7685 (ptm160) REVERT: C 450 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.6980 (t80) REVERT: C 452 MET cc_start: 0.8290 (mtp) cc_final: 0.8014 (mtt) REVERT: C 514 LYS cc_start: 0.8251 (ttpt) cc_final: 0.7599 (tttm) outliers start: 32 outliers final: 16 residues processed: 102 average time/residue: 0.4948 time to fit residues: 54.5455 Evaluate side-chains 98 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS C 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.141243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.116512 restraints weight = 8786.686| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.12 r_work: 0.2892 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9456 Z= 0.136 Angle : 0.577 6.333 12930 Z= 0.291 Chirality : 0.041 0.176 1455 Planarity : 0.006 0.053 1563 Dihedral : 6.492 54.031 1429 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.72 % Allowed : 16.41 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.26), residues: 1119 helix: 1.30 (0.20), residues: 708 sheet: None (None), residues: 0 loop : 0.01 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.011 0.001 TYR B 408 PHE 0.022 0.001 PHE C 450 TRP 0.016 0.001 TRP A 229 HIS 0.007 0.001 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9456) covalent geometry : angle 0.57694 (12930) hydrogen bonds : bond 0.07164 ( 513) hydrogen bonds : angle 3.85371 ( 1377) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.306 Fit side-chains REVERT: A 322 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7540 (ptp-170) REVERT: B 180 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6554 (pt0) REVERT: B 190 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8036 (tp) REVERT: B 416 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8728 (mtt180) REVERT: B 452 MET cc_start: 0.8190 (mtp) cc_final: 0.7989 (mtt) REVERT: C 161 ARG cc_start: 0.8201 (ptt90) cc_final: 0.7916 (ptt-90) REVERT: C 216 ASN cc_start: 0.8028 (t0) cc_final: 0.7537 (t0) REVERT: C 333 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8366 (tt) REVERT: C 392 MET cc_start: 0.8635 (mmm) cc_final: 0.8375 (mmt) REVERT: C 450 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.6610 (t80) REVERT: C 452 MET cc_start: 0.8120 (mtp) cc_final: 0.7852 (mtt) outliers start: 26 outliers final: 11 residues processed: 103 average time/residue: 0.5309 time to fit residues: 58.6277 Evaluate side-chains 92 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS C 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.140748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.118147 restraints weight = 8636.527| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 0.82 r_work: 0.2954 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9456 Z= 0.142 Angle : 0.581 6.388 12930 Z= 0.295 Chirality : 0.042 0.176 1455 Planarity : 0.006 0.052 1563 Dihedral : 6.359 54.527 1425 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.30 % Allowed : 16.72 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.26), residues: 1119 helix: 1.44 (0.20), residues: 708 sheet: None (None), residues: 0 loop : 0.04 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.011 0.001 TYR B 408 PHE 0.022 0.001 PHE C 450 TRP 0.014 0.001 TRP A 229 HIS 0.008 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9456) covalent geometry : angle 0.58141 (12930) hydrogen bonds : bond 0.07501 ( 513) hydrogen bonds : angle 3.84532 ( 1377) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.369 Fit side-chains REVERT: A 180 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6669 (pt0) REVERT: A 322 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7618 (ptp-170) REVERT: A 333 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8370 (tt) REVERT: B 180 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6545 (pt0) REVERT: B 190 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8057 (tp) REVERT: B 452 MET cc_start: 0.8292 (mtp) cc_final: 0.8055 (mtt) REVERT: C 161 ARG cc_start: 0.8292 (ptt90) cc_final: 0.8044 (ptt-90) REVERT: C 216 ASN cc_start: 0.8114 (t0) cc_final: 0.7628 (t0) REVERT: C 333 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8403 (tt) REVERT: C 392 MET cc_start: 0.8689 (mmm) cc_final: 0.8458 (mmt) REVERT: C 450 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.6772 (t80) REVERT: C 452 MET cc_start: 0.8214 (mtp) cc_final: 0.7919 (mtt) outliers start: 22 outliers final: 13 residues processed: 97 average time/residue: 0.4504 time to fit residues: 47.3868 Evaluate side-chains 96 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 76 optimal weight: 0.0870 chunk 49 optimal weight: 0.0170 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS C 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.144955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.123511 restraints weight = 8744.426| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 0.81 r_work: 0.3016 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9456 Z= 0.121 Angle : 0.532 6.176 12930 Z= 0.269 Chirality : 0.040 0.178 1455 Planarity : 0.006 0.051 1563 Dihedral : 6.224 53.892 1425 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.72 % Allowed : 15.46 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.26), residues: 1119 helix: 1.69 (0.21), residues: 708 sheet: None (None), residues: 0 loop : 0.14 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.010 0.001 TYR B 408 PHE 0.022 0.001 PHE C 450 TRP 0.013 0.001 TRP A 229 HIS 0.008 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9456) covalent geometry : angle 0.53225 (12930) hydrogen bonds : bond 0.06165 ( 513) hydrogen bonds : angle 3.70595 ( 1377) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.361 Fit side-chains REVERT: A 333 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8378 (tt) REVERT: A 514 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7640 (tttm) REVERT: B 112 LYS cc_start: 0.7739 (mttp) cc_final: 0.6619 (mmtt) REVERT: B 180 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6461 (pt0) REVERT: B 190 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8080 (tp) REVERT: B 416 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8698 (mtt180) REVERT: B 452 MET cc_start: 0.8163 (mtp) cc_final: 0.7937 (mtt) REVERT: C 161 ARG cc_start: 0.8278 (ptt90) cc_final: 0.8027 (ptt-90) REVERT: C 216 ASN cc_start: 0.8057 (t0) cc_final: 0.7551 (t0) REVERT: C 392 MET cc_start: 0.8624 (mmm) cc_final: 0.8390 (mmt) REVERT: C 450 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.6658 (t80) REVERT: C 452 MET cc_start: 0.8088 (mtp) cc_final: 0.7832 (mtt) outliers start: 26 outliers final: 10 residues processed: 107 average time/residue: 0.4410 time to fit residues: 51.0563 Evaluate side-chains 94 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS C 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.135430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.106166 restraints weight = 8784.331| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.28 r_work: 0.2874 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 9456 Z= 0.175 Angle : 0.650 9.850 12930 Z= 0.330 Chirality : 0.044 0.181 1455 Planarity : 0.006 0.049 1563 Dihedral : 6.244 54.516 1423 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.51 % Allowed : 15.88 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.25), residues: 1119 helix: 1.59 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.01 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.012 0.002 TYR B 408 PHE 0.022 0.002 PHE C 450 TRP 0.015 0.002 TRP C 206 HIS 0.009 0.002 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9456) covalent geometry : angle 0.64965 (12930) hydrogen bonds : bond 0.09034 ( 513) hydrogen bonds : angle 3.93012 ( 1377) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.343 Fit side-chains REVERT: A 180 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6856 (pt0) REVERT: A 333 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8351 (tt) REVERT: B 190 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8114 (tp) REVERT: B 416 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8825 (mtt180) REVERT: B 450 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.6974 (t80) REVERT: C 161 ARG cc_start: 0.8310 (ptt90) cc_final: 0.8049 (ptt-90) REVERT: C 216 ASN cc_start: 0.8128 (t0) cc_final: 0.7667 (t0) REVERT: C 392 MET cc_start: 0.8696 (mmm) cc_final: 0.8470 (mmt) REVERT: C 452 MET cc_start: 0.8302 (mtp) cc_final: 0.8004 (mtt) outliers start: 24 outliers final: 12 residues processed: 96 average time/residue: 0.4304 time to fit residues: 44.8587 Evaluate side-chains 92 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 24 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.134857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.106390 restraints weight = 8726.736| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.15 r_work: 0.2861 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9456 Z= 0.177 Angle : 0.654 9.102 12930 Z= 0.333 Chirality : 0.044 0.188 1455 Planarity : 0.006 0.050 1563 Dihedral : 6.212 50.993 1423 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.51 % Allowed : 16.20 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.25), residues: 1119 helix: 1.49 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.07 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.013 0.002 TYR B 408 PHE 0.021 0.002 PHE A 450 TRP 0.015 0.002 TRP C 206 HIS 0.010 0.002 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9456) covalent geometry : angle 0.65376 (12930) hydrogen bonds : bond 0.09125 ( 513) hydrogen bonds : angle 3.95943 ( 1377) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.439 Fit side-chains REVERT: A 166 ASP cc_start: 0.8150 (t70) cc_final: 0.7766 (m-30) REVERT: A 180 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6906 (pt0) REVERT: A 333 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8347 (tt) REVERT: B 190 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8151 (tp) REVERT: B 416 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8814 (mtt180) REVERT: C 161 ARG cc_start: 0.8352 (ptt90) cc_final: 0.8096 (ptt-90) REVERT: C 180 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7155 (pt0) REVERT: C 216 ASN cc_start: 0.8160 (t0) cc_final: 0.7702 (t0) REVERT: C 392 MET cc_start: 0.8734 (mmm) cc_final: 0.8512 (mmt) REVERT: C 452 MET cc_start: 0.8327 (mtp) cc_final: 0.8047 (mtt) outliers start: 24 outliers final: 16 residues processed: 97 average time/residue: 0.4900 time to fit residues: 51.8015 Evaluate side-chains 98 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 97 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 36 optimal weight: 0.0470 chunk 38 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.135169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.107918 restraints weight = 8764.353| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.09 r_work: 0.2859 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9456 Z= 0.173 Angle : 0.646 9.059 12930 Z= 0.330 Chirality : 0.044 0.189 1455 Planarity : 0.006 0.051 1563 Dihedral : 6.165 51.105 1423 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.30 % Allowed : 16.30 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.25), residues: 1119 helix: 1.27 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -0.08 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.013 0.002 TYR B 408 PHE 0.020 0.002 PHE B 450 TRP 0.015 0.002 TRP C 206 HIS 0.012 0.002 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9456) covalent geometry : angle 0.64621 (12930) hydrogen bonds : bond 0.08976 ( 513) hydrogen bonds : angle 3.95292 ( 1377) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.307 Fit side-chains REVERT: A 166 ASP cc_start: 0.8198 (t70) cc_final: 0.7800 (m-30) REVERT: A 180 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6928 (pt0) REVERT: A 333 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8365 (tt) REVERT: B 112 LYS cc_start: 0.7714 (mttp) cc_final: 0.6575 (mmtt) REVERT: B 190 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8151 (tp) REVERT: B 416 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8818 (mtt180) REVERT: C 161 ARG cc_start: 0.8354 (ptt90) cc_final: 0.8099 (ptt-90) REVERT: C 180 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7155 (pt0) REVERT: C 216 ASN cc_start: 0.8158 (t0) cc_final: 0.7699 (t0) REVERT: C 392 MET cc_start: 0.8730 (mmm) cc_final: 0.8509 (mmt) REVERT: C 452 MET cc_start: 0.8336 (mtp) cc_final: 0.8039 (mtt) outliers start: 22 outliers final: 15 residues processed: 94 average time/residue: 0.4782 time to fit residues: 48.9216 Evaluate side-chains 96 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.142592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.122352 restraints weight = 8729.565| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 0.77 r_work: 0.3005 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9456 Z= 0.129 Angle : 0.558 8.404 12930 Z= 0.283 Chirality : 0.041 0.184 1455 Planarity : 0.006 0.052 1563 Dihedral : 5.879 49.610 1423 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.09 % Allowed : 16.41 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.26), residues: 1119 helix: 1.59 (0.21), residues: 708 sheet: None (None), residues: 0 loop : 0.13 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.010 0.001 TYR A 243 PHE 0.021 0.001 PHE A 450 TRP 0.013 0.001 TRP A 229 HIS 0.011 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9456) covalent geometry : angle 0.55829 (12930) hydrogen bonds : bond 0.06733 ( 513) hydrogen bonds : angle 3.78016 ( 1377) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.348 Fit side-chains REVERT: A 333 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8383 (tt) REVERT: A 514 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7328 (mptt) REVERT: B 112 LYS cc_start: 0.7796 (mttp) cc_final: 0.6656 (mmtt) REVERT: B 190 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8062 (tp) REVERT: B 416 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8726 (mtt180) REVERT: C 161 ARG cc_start: 0.8286 (ptt90) cc_final: 0.8032 (ptt-90) REVERT: C 180 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7052 (pt0) REVERT: C 216 ASN cc_start: 0.8132 (t0) cc_final: 0.7643 (t0) REVERT: C 392 MET cc_start: 0.8649 (mmm) cc_final: 0.8429 (mmt) REVERT: C 452 MET cc_start: 0.8119 (mtp) cc_final: 0.7857 (mtt) REVERT: C 514 LYS cc_start: 0.8159 (ttpt) cc_final: 0.7501 (tttm) outliers start: 20 outliers final: 12 residues processed: 93 average time/residue: 0.4818 time to fit residues: 48.5385 Evaluate side-chains 93 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 428 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.140233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.115938 restraints weight = 8654.836| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 0.94 r_work: 0.2906 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9456 Z= 0.139 Angle : 0.576 8.589 12930 Z= 0.292 Chirality : 0.042 0.182 1455 Planarity : 0.006 0.052 1563 Dihedral : 5.771 48.320 1421 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.19 % Allowed : 16.51 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.26), residues: 1119 helix: 1.57 (0.20), residues: 708 sheet: None (None), residues: 0 loop : 0.14 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.011 0.001 TYR B 408 PHE 0.020 0.001 PHE A 450 TRP 0.015 0.001 TRP C 206 HIS 0.011 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9456) covalent geometry : angle 0.57582 (12930) hydrogen bonds : bond 0.07287 ( 513) hydrogen bonds : angle 3.80412 ( 1377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2535.46 seconds wall clock time: 43 minutes 54.89 seconds (2634.89 seconds total)