Starting phenix.real_space_refine on Fri Nov 15 18:58:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0j_35904/11_2024/8j0j_35904_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0j_35904/11_2024/8j0j_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0j_35904/11_2024/8j0j_35904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0j_35904/11_2024/8j0j_35904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0j_35904/11_2024/8j0j_35904_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0j_35904/11_2024/8j0j_35904_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} 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: 5.94, per 1000 atoms: 0.65 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: 2.32 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.91 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: 2.48 Time building geometry restraints manager: 2.67 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: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.990 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- 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= 0.334 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.001 TRP B 404 HIS 0.009 0.001 HIS C 387 PHE 0.010 0.001 PHE B 217 TYR 0.012 0.001 TYR A 365 ARG 0.002 0.000 ARG B 472 *********************** 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 : 1.042 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: 0.9690 time to fit residues: 107.9230 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 : 1.105 ------------------------------------------------------------------------------- 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 93 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.0060 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9456 Z= 0.197 Angle : 0.655 7.627 12930 Z= 0.331 Chirality : 0.043 0.180 1455 Planarity : 0.006 0.047 1563 Dihedral : 8.019 59.965 1435 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.45 % Allowed : 16.72 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.25), residues: 1119 helix: 0.26 (0.20), residues: 711 sheet: None (None), residues: 0 loop : -0.24 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 229 HIS 0.007 0.001 HIS C 387 PHE 0.020 0.002 PHE C 450 TYR 0.013 0.002 TYR B 408 ARG 0.005 0.001 ARG C 472 *********************** 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 124 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.809 Fit side-chains REVERT: A 166 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7359 (t70) REVERT: A 180 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6822 (pt0) REVERT: A 322 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7757 (ptp-170) REVERT: A 333 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8444 (tt) REVERT: A 450 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.6616 (t80) REVERT: B 322 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7651 (ptp-170) REVERT: B 382 LEU cc_start: 0.7310 (tp) cc_final: 0.7023 (mt) REVERT: B 410 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7781 (pm20) REVERT: C 161 ARG cc_start: 0.8122 (ptt90) cc_final: 0.7862 (ptt-90) REVERT: C 166 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7121 (t70) REVERT: C 216 ASN cc_start: 0.7976 (t0) cc_final: 0.7705 (t0) REVERT: C 322 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7879 (ptm160) REVERT: C 450 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.6672 (t80) REVERT: C 452 MET cc_start: 0.8134 (mtp) cc_final: 0.7908 (mtt) outliers start: 33 outliers final: 8 residues processed: 116 average time/residue: 0.8734 time to fit residues: 108.8863 Evaluate side-chains 92 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 111 THR 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 333 LEU 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 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9456 Z= 0.266 Angle : 0.728 7.857 12930 Z= 0.370 Chirality : 0.047 0.192 1455 Planarity : 0.007 0.050 1563 Dihedral : 7.370 54.718 1431 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.55 % Allowed : 16.09 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1119 helix: 0.83 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.21 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 206 HIS 0.009 0.002 HIS C 387 PHE 0.020 0.002 PHE B 450 TYR 0.014 0.002 TYR B 408 ARG 0.003 0.001 ARG A 472 *********************** 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 113 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.972 Fit side-chains REVERT: A 322 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7637 (ptp-170) REVERT: B 190 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8269 (tp) REVERT: B 322 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7515 (ptp-170) REVERT: B 429 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8099 (tp) REVERT: B 450 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7190 (t80) REVERT: C 161 ARG cc_start: 0.8168 (ptt90) cc_final: 0.7887 (ptt-90) REVERT: C 180 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7151 (pt0) REVERT: C 216 ASN cc_start: 0.8089 (t0) cc_final: 0.7838 (t0) REVERT: C 322 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7510 (ptp-170) REVERT: C 325 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8015 (mtpp) REVERT: C 452 MET cc_start: 0.8399 (mtp) cc_final: 0.8123 (mtm) outliers start: 34 outliers final: 18 residues processed: 106 average time/residue: 1.0626 time to fit residues: 121.8787 Evaluate side-chains 102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 218 LEU 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 429 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 322 ARG 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 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 75 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS C 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 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= 0.162 Angle : 0.578 6.393 12930 Z= 0.292 Chirality : 0.041 0.175 1455 Planarity : 0.006 0.052 1563 Dihedral : 6.613 50.497 1431 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.13 % Allowed : 16.20 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1119 helix: 1.22 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -0.03 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 229 HIS 0.008 0.001 HIS C 387 PHE 0.021 0.001 PHE B 450 TYR 0.011 0.001 TYR B 408 ARG 0.004 0.000 ARG A 472 *********************** 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 111 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.955 Fit side-chains REVERT: A 333 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8428 (tt) REVERT: B 180 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6915 (pt0) REVERT: B 190 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8263 (tp) REVERT: B 410 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: B 416 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8804 (mtt180) REVERT: C 161 ARG cc_start: 0.8156 (ptt90) cc_final: 0.7892 (ptt-90) REVERT: C 216 ASN cc_start: 0.8049 (t0) cc_final: 0.7772 (t0) REVERT: C 392 MET cc_start: 0.8678 (mmm) cc_final: 0.8462 (mmt) REVERT: C 452 MET cc_start: 0.8123 (mtp) cc_final: 0.7854 (mtt) outliers start: 30 outliers final: 10 residues processed: 104 average time/residue: 1.1924 time to fit residues: 133.2637 Evaluate side-chains 90 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 166 ASP Chi-restraints excluded: chain B residue 180 GLU 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 366 LEU Chi-restraints excluded: chain C residue 428 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2456 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= 0.202 Angle : 0.626 6.622 12930 Z= 0.318 Chirality : 0.043 0.179 1455 Planarity : 0.006 0.051 1563 Dihedral : 6.307 49.689 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 : 2.82 % Allowed : 16.09 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1119 helix: 1.47 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.08 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 206 HIS 0.008 0.002 HIS B 387 PHE 0.020 0.002 PHE B 450 TYR 0.012 0.002 TYR B 408 ARG 0.003 0.000 ARG C 110 *********************** 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 104 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.987 Fit side-chains REVERT: A 180 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6892 (pt0) REVERT: A 333 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8422 (tt) REVERT: B 180 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6967 (pt0) REVERT: B 190 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8256 (tp) REVERT: B 416 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8903 (mtt180) REVERT: C 161 ARG cc_start: 0.8171 (ptt90) cc_final: 0.7915 (ptt-90) REVERT: C 216 ASN cc_start: 0.8144 (t0) cc_final: 0.7875 (t0) REVERT: C 392 MET cc_start: 0.8700 (mmm) cc_final: 0.8467 (mmt) REVERT: C 452 MET cc_start: 0.8293 (mtp) cc_final: 0.7981 (mtt) outliers start: 27 outliers final: 16 residues processed: 97 average time/residue: 1.0752 time to fit residues: 113.7179 Evaluate side-chains 100 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 410 GLN Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 0.0980 chunk 103 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 0.022 9456 Z= 0.176 Angle : 0.586 6.440 12930 Z= 0.298 Chirality : 0.042 0.178 1455 Planarity : 0.006 0.051 1563 Dihedral : 6.128 48.264 1423 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.82 % Allowed : 16.09 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.26), residues: 1119 helix: 1.43 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -0.01 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 206 HIS 0.008 0.001 HIS B 387 PHE 0.019 0.001 PHE A 450 TYR 0.012 0.002 TYR B 408 ARG 0.003 0.000 ARG A 472 *********************** 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: 27 poor density : 81 time to evaluate : 1.096 Fit side-chains REVERT: A 180 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6913 (pt0) REVERT: A 333 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8431 (tt) REVERT: B 180 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6956 (pt0) REVERT: B 190 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8261 (tp) REVERT: B 416 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8837 (mtt180) REVERT: C 161 ARG cc_start: 0.8194 (ptt90) cc_final: 0.7934 (ptt-90) REVERT: C 216 ASN cc_start: 0.8138 (t0) cc_final: 0.7861 (t0) REVERT: C 392 MET cc_start: 0.8668 (mmm) cc_final: 0.8454 (mmt) REVERT: C 452 MET cc_start: 0.8205 (mtp) cc_final: 0.7925 (mtt) outliers start: 27 outliers final: 16 residues processed: 101 average time/residue: 1.0888 time to fit residues: 119.1809 Evaluate side-chains 97 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 333 LEU 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 201 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9456 Z= 0.253 Angle : 0.680 7.021 12930 Z= 0.348 Chirality : 0.046 0.186 1455 Planarity : 0.006 0.051 1563 Dihedral : 6.200 47.832 1421 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.72 % Allowed : 15.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1119 helix: 1.37 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.14 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 206 HIS 0.009 0.002 HIS B 387 PHE 0.020 0.002 PHE B 450 TYR 0.014 0.002 TYR B 408 ARG 0.003 0.000 ARG A 110 *********************** 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 106 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 1.104 Fit side-chains REVERT: A 180 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6985 (pt0) REVERT: B 180 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7018 (pt0) REVERT: B 190 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8293 (tp) REVERT: B 416 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8941 (mtt180) REVERT: C 161 ARG cc_start: 0.8183 (ptt90) cc_final: 0.7907 (ptt-90) REVERT: C 180 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7296 (pt0) REVERT: C 216 ASN cc_start: 0.8116 (t0) cc_final: 0.7861 (t0) REVERT: C 452 MET cc_start: 0.8335 (mtp) cc_final: 0.8035 (mtt) outliers start: 26 outliers final: 17 residues processed: 101 average time/residue: 1.0415 time to fit residues: 114.2018 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 : 0.987 ------------------------------------------------------------------------------- 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 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 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 410 GLN 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 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 68 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2543 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= 0.212 Angle : 0.632 6.588 12930 Z= 0.324 Chirality : 0.044 0.187 1455 Planarity : 0.006 0.053 1563 Dihedral : 6.050 46.334 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 : 2.61 % Allowed : 16.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1119 helix: 1.46 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.12 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 206 HIS 0.010 0.002 HIS B 387 PHE 0.021 0.002 PHE B 450 TYR 0.013 0.002 TYR B 408 ARG 0.003 0.000 ARG A 110 *********************** 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 103 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 1.157 Fit side-chains REVERT: A 180 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6956 (pt0) REVERT: B 112 LYS cc_start: 0.8062 (mttp) cc_final: 0.7240 (mmtt) REVERT: B 180 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6996 (pt0) REVERT: B 190 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8280 (tp) REVERT: B 416 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8904 (mtt180) REVERT: C 161 ARG cc_start: 0.8178 (ptt90) cc_final: 0.7907 (ptt-90) REVERT: C 180 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7273 (pt0) REVERT: C 216 ASN cc_start: 0.8124 (t0) cc_final: 0.7864 (t0) REVERT: C 392 MET cc_start: 0.8679 (mmm) cc_final: 0.8463 (mmt) REVERT: C 452 MET cc_start: 0.8282 (mtp) cc_final: 0.7990 (mtt) outliers start: 25 outliers final: 16 residues processed: 98 average time/residue: 1.0649 time to fit residues: 113.2040 Evaluate side-chains 100 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 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 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 410 GLN 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 102 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2567 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= 0.210 Angle : 0.630 6.573 12930 Z= 0.323 Chirality : 0.044 0.187 1455 Planarity : 0.006 0.053 1563 Dihedral : 6.034 46.281 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 : 2.40 % Allowed : 16.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1119 helix: 1.27 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -0.12 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 206 HIS 0.012 0.002 HIS B 387 PHE 0.019 0.002 PHE B 450 TYR 0.012 0.002 TYR B 408 ARG 0.003 0.000 ARG A 110 *********************** 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: 23 poor density : 79 time to evaluate : 0.988 Fit side-chains REVERT: A 180 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6951 (pt0) REVERT: B 112 LYS cc_start: 0.8057 (mttp) cc_final: 0.7236 (mmtt) REVERT: B 180 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6991 (pt0) REVERT: B 190 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8280 (tp) REVERT: C 161 ARG cc_start: 0.8177 (ptt90) cc_final: 0.7907 (ptt-90) REVERT: C 180 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7255 (pt0) REVERT: C 216 ASN cc_start: 0.8127 (t0) cc_final: 0.7868 (t0) REVERT: C 392 MET cc_start: 0.8677 (mmm) cc_final: 0.8464 (mmt) REVERT: C 452 MET cc_start: 0.8272 (mtp) cc_final: 0.7979 (mtt) outliers start: 23 outliers final: 16 residues processed: 96 average time/residue: 1.0313 time to fit residues: 107.5292 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 : 0.976 ------------------------------------------------------------------------------- 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 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 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 410 GLN 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 50 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.0010 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2720 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= 0.154 Angle : 0.554 6.375 12930 Z= 0.283 Chirality : 0.041 0.182 1455 Planarity : 0.006 0.053 1563 Dihedral : 5.804 45.068 1421 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.19 % Allowed : 16.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1119 helix: 1.56 (0.20), residues: 708 sheet: None (None), residues: 0 loop : 0.06 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 229 HIS 0.011 0.001 HIS B 387 PHE 0.019 0.001 PHE B 450 TYR 0.010 0.001 TYR A 243 ARG 0.004 0.000 ARG A 110 ********************** 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 105 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 1.043 Fit side-chains REVERT: A 180 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6867 (pt0) REVERT: A 333 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8469 (tt) REVERT: B 112 LYS cc_start: 0.8060 (mttp) cc_final: 0.7238 (mmtt) REVERT: B 180 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6893 (pt0) REVERT: B 190 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8251 (tp) REVERT: C 161 ARG cc_start: 0.8192 (ptt90) cc_final: 0.7931 (ptt-90) REVERT: C 180 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7192 (pt0) REVERT: C 216 ASN cc_start: 0.8129 (t0) cc_final: 0.7830 (t0) REVERT: C 333 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8505 (tt) REVERT: C 392 MET cc_start: 0.8627 (mmm) cc_final: 0.8397 (mmt) REVERT: C 452 MET cc_start: 0.8084 (mtp) cc_final: 0.7837 (mtt) outliers start: 21 outliers final: 13 residues processed: 99 average time/residue: 1.0263 time to fit residues: 110.8464 Evaluate side-chains 98 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 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 428 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.133330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.105812 restraints weight = 8710.228| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.14 r_work: 0.2865 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9456 Z= 0.269 Angle : 0.701 10.391 12930 Z= 0.358 Chirality : 0.047 0.190 1455 Planarity : 0.006 0.051 1563 Dihedral : 6.078 40.401 1419 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.40 % Allowed : 16.51 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1119 helix: 1.36 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.14 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 206 HIS 0.011 0.002 HIS B 387 PHE 0.018 0.002 PHE B 450 TYR 0.014 0.002 TYR B 408 ARG 0.003 0.000 ARG A 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2720.91 seconds wall clock time: 53 minutes 30.70 seconds (3210.70 seconds total)