Starting phenix.real_space_refine on Wed Feb 4 07:20:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j0j_35904/02_2026/8j0j_35904_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j0j_35904/02_2026/8j0j_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j0j_35904/02_2026/8j0j_35904_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j0j_35904/02_2026/8j0j_35904_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j0j_35904/02_2026/8j0j_35904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j0j_35904/02_2026/8j0j_35904.map" } 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9138 Number of models: 1 Model: "" Number of chains: 6 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: "B" 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: "C" 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} Time building chain proxies: 2.09, per 1000 atoms: 0.23 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: 0.75 Conformation dependent library (CDL) restraints added in 284.4 milliseconds 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: 0.26 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: 1.01 Time building geometry restraints manager: 1.00 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: 1.860 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.650 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- 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 are 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 : 0.285 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: 0.4055 time to fit residues: 45.0370 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 : 0.369 ------------------------------------------------------------------------------- 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 = 8697.544| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.95 r_work: 0.2909 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 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 are 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 : 0.343 Fit side-chains REVERT: A 166 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7549 (t70) REVERT: A 180 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6740 (pt0) REVERT: A 322 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7727 (ptp-170) REVERT: A 333 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8353 (tt) REVERT: A 450 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.6593 (t80) REVERT: B 322 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7596 (ptp-170) REVERT: B 382 LEU cc_start: 0.7183 (tp) cc_final: 0.6885 (mt) REVERT: B 410 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7927 (pm20) REVERT: C 161 ARG cc_start: 0.8188 (ptt90) cc_final: 0.7905 (ptt-90) REVERT: C 166 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7262 (t70) REVERT: C 216 ASN cc_start: 0.8031 (t0) cc_final: 0.7572 (t0) REVERT: C 322 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7791 (ptm160) REVERT: C 450 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.6646 (t80) REVERT: C 452 MET cc_start: 0.8115 (mtp) cc_final: 0.7886 (mtt) REVERT: C 514 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7574 (tttm) outliers start: 32 outliers final: 6 residues processed: 115 average time/residue: 0.4917 time to fit residues: 60.8434 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 : 0.256 ------------------------------------------------------------------------------- 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: 3.9990 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 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: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.138044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.114913 restraints weight = 8605.352| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 0.93 r_work: 0.2878 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2268 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= 0.162 Angle : 0.642 6.757 12930 Z= 0.325 Chirality : 0.043 0.179 1455 Planarity : 0.006 0.051 1563 Dihedral : 6.977 57.105 1431 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.13 % Allowed : 16.72 % Favored : 80.15 % 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 are not related in a simple way. whole: 0.91 (0.25), residues: 1119 helix: 1.10 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.08 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 472 TYR 0.011 0.002 TYR B 408 PHE 0.022 0.002 PHE C 450 TRP 0.017 0.002 TRP A 229 HIS 0.009 0.002 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9456) covalent geometry : angle 0.64165 (12930) hydrogen bonds : bond 0.08753 ( 513) hydrogen bonds : angle 4.03407 ( 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 108 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.343 Fit side-chains REVERT: A 322 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7615 (ptp-170) REVERT: B 180 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6598 (pt0) REVERT: B 190 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8076 (tp) REVERT: B 322 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7488 (ptp-170) REVERT: B 410 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: B 450 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7034 (t80) REVERT: C 161 ARG cc_start: 0.8215 (ptt90) cc_final: 0.7929 (ptt-90) REVERT: C 216 ASN cc_start: 0.8085 (t0) cc_final: 0.7641 (t0) REVERT: C 322 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7746 (ptm160) REVERT: C 450 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.6936 (t80) REVERT: C 452 MET cc_start: 0.8233 (mtp) cc_final: 0.7930 (mtt) REVERT: C 514 LYS cc_start: 0.8251 (ttpt) cc_final: 0.7686 (tttm) outliers start: 30 outliers final: 15 residues processed: 101 average time/residue: 0.4835 time to fit residues: 52.5304 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 : 0.341 ------------------------------------------------------------------------------- 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 410 GLN 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 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: 0.6980 chunk 24 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 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: 0.6980 chunk 39 optimal weight: 0.3980 chunk 35 optimal weight: 6.9990 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 = 0.3477 r_free = 0.3477 target = 0.140461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.115689 restraints weight = 8791.017| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.13 r_work: 0.2876 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2462 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= 0.141 Angle : 0.588 6.375 12930 Z= 0.297 Chirality : 0.042 0.176 1455 Planarity : 0.006 0.053 1563 Dihedral : 6.501 55.430 1429 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.93 % Allowed : 16.30 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.26), residues: 1119 helix: 1.27 (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 0.004 0.000 ARG A 472 TYR 0.011 0.001 TYR B 408 PHE 0.022 0.001 PHE C 450 TRP 0.016 0.002 TRP A 229 HIS 0.007 0.001 HIS C 387 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9456) covalent geometry : angle 0.58791 (12930) hydrogen bonds : bond 0.07469 ( 513) hydrogen bonds : angle 3.87156 ( 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: 28 poor density : 81 time to evaluate : 0.336 Fit side-chains REVERT: A 322 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7532 (ptp-170) REVERT: B 180 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6593 (pt0) REVERT: B 190 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.8016 (tp) REVERT: B 322 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7493 (ptp-170) REVERT: B 410 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7766 (pm20) REVERT: B 416 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8749 (mtt180) REVERT: B 452 MET cc_start: 0.8237 (mtp) cc_final: 0.8002 (mtt) REVERT: C 161 ARG cc_start: 0.8218 (ptt90) cc_final: 0.7929 (ptt-90) REVERT: C 216 ASN cc_start: 0.8031 (t0) cc_final: 0.7537 (t0) REVERT: C 392 MET cc_start: 0.8666 (mmm) cc_final: 0.8411 (mmt) REVERT: C 450 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.6799 (t80) REVERT: C 452 MET cc_start: 0.8141 (mtp) cc_final: 0.7872 (mtt) outliers start: 28 outliers final: 15 residues processed: 103 average time/residue: 0.4850 time to fit residues: 53.6988 Evaluate side-chains 97 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 410 GLN 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 429 LEU 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: 3.9990 chunk 44 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.134919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.106461 restraints weight = 8848.279| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.11 r_work: 0.2853 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9456 Z= 0.184 Angle : 0.668 6.988 12930 Z= 0.341 Chirality : 0.045 0.181 1455 Planarity : 0.006 0.052 1563 Dihedral : 6.531 54.920 1425 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.93 % Allowed : 16.09 % 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 are not related in a simple way. whole: 1.13 (0.25), residues: 1119 helix: 1.33 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.09 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 161 TYR 0.013 0.002 TYR B 408 PHE 0.022 0.002 PHE C 450 TRP 0.017 0.002 TRP C 206 HIS 0.007 0.002 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9456) covalent geometry : angle 0.66823 (12930) hydrogen bonds : bond 0.09540 ( 513) hydrogen bonds : angle 4.02111 ( 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 106 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.340 Fit side-chains REVERT: A 180 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6906 (pt0) REVERT: A 322 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7580 (ptp-170) REVERT: B 190 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8124 (tp) REVERT: B 322 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7504 (ptp-170) REVERT: B 416 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8876 (mtt180) REVERT: B 429 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8070 (tp) REVERT: B 450 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7084 (t80) REVERT: C 161 ARG cc_start: 0.8342 (ptt90) cc_final: 0.8089 (ptt-90) REVERT: C 180 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7144 (pt0) REVERT: C 216 ASN cc_start: 0.8151 (t0) cc_final: 0.7687 (t0) REVERT: C 452 MET cc_start: 0.8376 (mtp) cc_final: 0.8076 (mtt) REVERT: C 514 LYS cc_start: 0.8391 (ttpt) cc_final: 0.7737 (tttm) outliers start: 28 outliers final: 16 residues processed: 99 average time/residue: 0.4495 time to fit residues: 48.1093 Evaluate side-chains 100 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 190 ILE Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 429 LEU 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 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: 0.9980 chunk 40 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.142540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.119492 restraints weight = 8753.813| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 0.83 r_work: 0.2987 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2636 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= 0.128 Angle : 0.551 6.311 12930 Z= 0.279 Chirality : 0.041 0.179 1455 Planarity : 0.006 0.053 1563 Dihedral : 6.200 52.084 1425 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.61 % Allowed : 15.99 % 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 are not related in a simple way. whole: 1.43 (0.26), residues: 1119 helix: 1.52 (0.21), residues: 708 sheet: None (None), residues: 0 loop : 0.07 (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 0.007 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9456) covalent geometry : angle 0.55080 (12930) hydrogen bonds : bond 0.06638 ( 513) hydrogen bonds : angle 3.79851 ( 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 108 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.224 Fit side-chains REVERT: A 333 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8381 (tt) REVERT: B 190 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8053 (tp) REVERT: B 410 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7766 (pm20) REVERT: B 416 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8729 (mtt180) REVERT: B 452 MET cc_start: 0.8171 (mtp) cc_final: 0.7956 (mtt) REVERT: C 161 ARG cc_start: 0.8283 (ptt90) cc_final: 0.8033 (ptt-90) REVERT: C 180 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6997 (pt0) REVERT: C 216 ASN cc_start: 0.8087 (t0) cc_final: 0.7601 (t0) REVERT: C 333 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8397 (tt) REVERT: C 392 MET cc_start: 0.8664 (mmm) cc_final: 0.8459 (mmt) REVERT: C 452 MET cc_start: 0.8123 (mtp) cc_final: 0.7856 (mtt) outliers start: 25 outliers final: 12 residues processed: 101 average time/residue: 0.4592 time to fit residues: 50.1025 Evaluate side-chains 93 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 410 GLN 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 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=2.50 ------------------------------------------------------------------------------- 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: 1.9990 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.133241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.105361 restraints weight = 8797.614| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.15 r_work: 0.2836 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9456 Z= 0.205 Angle : 0.709 10.311 12930 Z= 0.362 Chirality : 0.047 0.189 1455 Planarity : 0.007 0.051 1563 Dihedral : 6.393 51.474 1423 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.03 % Allowed : 15.46 % 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 are not related in a simple way. whole: 1.11 (0.25), residues: 1119 helix: 1.33 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.13 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.014 0.002 TYR B 408 PHE 0.019 0.002 PHE B 450 TRP 0.017 0.002 TRP C 206 HIS 0.009 0.002 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9456) covalent geometry : angle 0.70914 (12930) hydrogen bonds : bond 0.10214 ( 513) hydrogen bonds : angle 4.03513 ( 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 109 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.348 Fit side-chains REVERT: A 180 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6918 (pt0) REVERT: A 333 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8356 (tt) REVERT: B 180 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6783 (pt0) REVERT: B 190 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8208 (tp) REVERT: B 416 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8893 (mtt180) REVERT: C 161 ARG cc_start: 0.8339 (ptt90) cc_final: 0.8078 (ptt-90) REVERT: C 180 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7149 (pt0) REVERT: C 216 ASN cc_start: 0.8126 (t0) cc_final: 0.7657 (t0) REVERT: C 325 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7944 (mtpp) REVERT: C 452 MET cc_start: 0.8399 (mtp) cc_final: 0.8132 (mtt) outliers start: 29 outliers final: 17 residues processed: 103 average time/residue: 0.4654 time to fit residues: 51.8519 Evaluate side-chains 102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 201 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 410 GLN 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 325 LYS 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: 1.9990 chunk 92 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.140178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.116705 restraints weight = 8672.257| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 0.87 r_work: 0.2945 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2647 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= 0.138 Angle : 0.577 8.689 12930 Z= 0.293 Chirality : 0.042 0.183 1455 Planarity : 0.006 0.053 1563 Dihedral : 6.027 49.280 1423 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 : 2.40 % Allowed : 16.41 % Favored : 81.19 % 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 are not related in a simple way. whole: 1.36 (0.26), residues: 1119 helix: 1.46 (0.20), residues: 708 sheet: None (None), residues: 0 loop : 0.03 (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 0.021 0.001 PHE B 450 TRP 0.014 0.001 TRP B 206 HIS 0.010 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9456) covalent geometry : angle 0.57691 (12930) hydrogen bonds : bond 0.07259 ( 513) hydrogen bonds : angle 3.84603 ( 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: 23 poor density : 78 time to evaluate : 0.343 Fit side-chains REVERT: A 301 MET cc_start: 0.8479 (tpt) cc_final: 0.8276 (mmt) REVERT: B 112 LYS cc_start: 0.7767 (mttp) cc_final: 0.6632 (mmtt) REVERT: B 161 ARG cc_start: 0.8537 (ptt90) cc_final: 0.8322 (ptt90) REVERT: B 180 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6565 (pt0) REVERT: B 190 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8089 (tp) REVERT: B 410 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7878 (pm20) REVERT: B 416 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8758 (mtt180) REVERT: C 161 ARG cc_start: 0.8306 (ptt90) cc_final: 0.8055 (ptt-90) REVERT: C 180 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.7005 (pt0) REVERT: C 216 ASN cc_start: 0.8150 (t0) cc_final: 0.7682 (t0) REVERT: C 392 MET cc_start: 0.8679 (mmm) cc_final: 0.8449 (mmt) REVERT: C 452 MET cc_start: 0.8181 (mtp) cc_final: 0.7875 (mtt) outliers start: 23 outliers final: 15 residues processed: 96 average time/residue: 0.4739 time to fit residues: 49.2358 Evaluate side-chains 97 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 180 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 410 GLN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 97 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 0.0010 chunk 17 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.136519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.109442 restraints weight = 8763.105| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.09 r_work: 0.2880 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9456 Z= 0.158 Angle : 0.616 9.075 12930 Z= 0.313 Chirality : 0.043 0.184 1455 Planarity : 0.006 0.052 1563 Dihedral : 5.967 48.794 1421 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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 are not related in a simple way. whole: 1.27 (0.26), residues: 1119 helix: 1.39 (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 110 TYR 0.012 0.002 TYR B 408 PHE 0.019 0.002 PHE B 450 TRP 0.015 0.002 TRP C 206 HIS 0.011 0.002 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9456) covalent geometry : angle 0.61629 (12930) hydrogen bonds : bond 0.08299 ( 513) hydrogen bonds : angle 3.90048 ( 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 102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.376 Fit side-chains REVERT: A 333 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8354 (tt) REVERT: B 112 LYS cc_start: 0.7753 (mttp) cc_final: 0.6625 (mmtt) REVERT: B 180 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6714 (pt0) REVERT: B 190 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8133 (tp) REVERT: B 410 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: B 416 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8813 (mtt180) REVERT: C 161 ARG cc_start: 0.8360 (ptt90) cc_final: 0.8104 (ptt-90) REVERT: C 180 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7125 (pt0) REVERT: C 216 ASN cc_start: 0.8180 (t0) cc_final: 0.7720 (t0) REVERT: C 392 MET cc_start: 0.8696 (mmm) cc_final: 0.8480 (mmt) REVERT: C 452 MET cc_start: 0.8307 (mtp) cc_final: 0.7989 (mtt) outliers start: 24 outliers final: 14 residues processed: 96 average time/residue: 0.4867 time to fit residues: 50.6402 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 : 0.357 ------------------------------------------------------------------------------- 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 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 180 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 410 GLN 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 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: 0.8980 chunk 63 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.140388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.115508 restraints weight = 8730.984| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.13 r_work: 0.2902 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2700 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= 0.138 Angle : 0.575 8.666 12930 Z= 0.292 Chirality : 0.042 0.182 1455 Planarity : 0.006 0.052 1563 Dihedral : 5.841 46.239 1421 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.19 % Allowed : 16.61 % Favored : 81.19 % 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 are not related in a simple way. whole: 1.46 (0.26), residues: 1119 helix: 1.53 (0.20), residues: 708 sheet: None (None), residues: 0 loop : 0.09 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.011 0.002 TYR B 408 PHE 0.018 0.001 PHE B 450 TRP 0.014 0.001 TRP B 206 HIS 0.011 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9456) covalent geometry : angle 0.57523 (12930) hydrogen bonds : bond 0.07223 ( 513) hydrogen bonds : angle 3.82263 ( 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 103 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.381 Fit side-chains REVERT: B 112 LYS cc_start: 0.7808 (mttp) cc_final: 0.6663 (mmtt) REVERT: B 161 ARG cc_start: 0.8489 (ptt90) cc_final: 0.8275 (ptt90) REVERT: B 180 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6661 (pt0) REVERT: B 410 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: B 416 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8747 (mtt180) REVERT: C 161 ARG cc_start: 0.8254 (ptt90) cc_final: 0.7985 (ptt-90) REVERT: C 180 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7007 (pt0) REVERT: C 216 ASN cc_start: 0.8055 (t0) cc_final: 0.7577 (t0) REVERT: C 333 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8418 (tt) REVERT: C 392 MET cc_start: 0.8626 (mmm) cc_final: 0.8385 (mmt) REVERT: C 452 MET cc_start: 0.8132 (mtp) cc_final: 0.7843 (mtt) REVERT: C 514 LYS cc_start: 0.8066 (ttpt) cc_final: 0.7397 (tttm) outliers start: 21 outliers final: 13 residues processed: 97 average time/residue: 0.4784 time to fit residues: 50.2964 Evaluate side-chains 98 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 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 180 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 428 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 3 optimal weight: 0.0770 chunk 81 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.146319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.122177 restraints weight = 8680.477| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 0.96 r_work: 0.2998 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9456 Z= 0.112 Angle : 0.517 8.161 12930 Z= 0.260 Chirality : 0.040 0.182 1455 Planarity : 0.006 0.053 1563 Dihedral : 5.557 48.160 1419 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.78 % Allowed : 16.93 % 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 are not related in a simple way. whole: 1.85 (0.26), residues: 1119 helix: 1.80 (0.21), residues: 708 sheet: None (None), residues: 0 loop : 0.33 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 110 TYR 0.009 0.001 TYR A 243 PHE 0.020 0.001 PHE B 450 TRP 0.013 0.001 TRP A 229 HIS 0.012 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 9456) covalent geometry : angle 0.51692 (12930) hydrogen bonds : bond 0.05427 ( 513) hydrogen bonds : angle 3.64471 ( 1377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2465.21 seconds wall clock time: 42 minutes 46.03 seconds (2566.03 seconds total)