Starting phenix.real_space_refine on Sat Mar 16 14:18:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipr_35641/03_2024/8ipr_35641_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipr_35641/03_2024/8ipr_35641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipr_35641/03_2024/8ipr_35641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipr_35641/03_2024/8ipr_35641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipr_35641/03_2024/8ipr_35641_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipr_35641/03_2024/8ipr_35641_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 58 5.16 5 C 9412 2.51 5 N 2692 2.21 5 O 2716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 377": "OE1" <-> "OE2" Residue "A ASP 500": "OD1" <-> "OD2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 377": "OE1" <-> "OE2" Residue "E GLU 202": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14894 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3639 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 31, 'TRANS': 472} Chain: "C" Number of atoms: 3744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3744 Classifications: {'peptide': 515} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 482} Chain: "D" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3639 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 31, 'TRANS': 472} Chain: "E" Number of atoms: 3744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3744 Classifications: {'peptide': 515} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 482} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.95, per 1000 atoms: 0.53 Number of scatterers: 14894 At special positions: 0 Unit cell: (92.352, 120.64, 133.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 12 15.00 Mg 4 11.99 O 2716 8.00 N 2692 7.00 C 9412 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 - 3.50 Amino acid : False - 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: 6.91 Conformation dependent library (CDL) restraints added in 3.2 seconds 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3720 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 6 sheets defined 65.7% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.987A pdb=" N SER A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 107 Processing helix chain 'A' and resid 110 through 113 No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 127 through 160 Proline residue: A 142 - end of helix removed outlier: 4.267A pdb=" N VAL A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 201 removed outlier: 3.659A pdb=" N VAL A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 4.440A pdb=" N ALA A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 210 removed outlier: 5.925A pdb=" N ALA A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 221 through 269 Proline residue: A 245 - end of helix Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 277 through 318 removed outlier: 4.374A pdb=" N LEU A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Proline residue: A 287 - end of helix removed outlier: 3.574A pdb=" N PHE A 291 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Proline residue: A 298 - end of helix removed outlier: 3.566A pdb=" N SER A 307 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 386 through 392 Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 429 through 432 Processing helix chain 'A' and resid 435 through 448 Processing helix chain 'A' and resid 465 through 476 removed outlier: 4.785A pdb=" N ARG A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'C' and resid -4 through 23 Processing helix chain 'C' and resid 36 through 79 removed outlier: 3.822A pdb=" N VAL C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 102 through 109 removed outlier: 3.629A pdb=" N ARG C 106 " --> pdb=" O ASP C 103 " (cutoff:3.500A) Proline residue: C 107 - end of helix Processing helix chain 'C' and resid 113 through 133 removed outlier: 3.544A pdb=" N THR C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 135 through 143 removed outlier: 4.098A pdb=" N ILE C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 182 Proline residue: C 149 - end of helix removed outlier: 5.078A pdb=" N GLU C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ARG C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 190 Processing helix chain 'C' and resid 196 through 245 removed outlier: 3.741A pdb=" N VAL C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 292 Proline residue: C 262 - end of helix removed outlier: 3.845A pdb=" N PHE C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Proline residue: C 267 - end of helix removed outlier: 3.997A pdb=" N HIS C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP C 280 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 344 Processing helix chain 'C' and resid 366 through 372 removed outlier: 3.551A pdb=" N GLY C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG C 372 " --> pdb=" O ALA C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 400 through 407 Processing helix chain 'C' and resid 410 through 415 removed outlier: 3.816A pdb=" N GLU C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 445 Processing helix chain 'C' and resid 463 through 478 Processing helix chain 'C' and resid 490 through 495 removed outlier: 3.735A pdb=" N ALA C 495 " --> pdb=" O PRO C 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 16 Processing helix chain 'D' and resid 21 through 40 removed outlier: 3.962A pdb=" N SER D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 107 Processing helix chain 'D' and resid 110 through 113 No H-bonds generated for 'chain 'D' and resid 110 through 113' Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 127 through 160 Proline residue: D 142 - end of helix removed outlier: 4.265A pdb=" N VAL D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 201 removed outlier: 3.654A pdb=" N VAL D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) Proline residue: D 180 - end of helix removed outlier: 4.409A pdb=" N ALA D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 210 removed outlier: 5.919A pdb=" N ALA D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU D 209 " --> pdb=" O GLY D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 221 through 269 Proline residue: D 245 - end of helix Proline residue: D 253 - end of helix Processing helix chain 'D' and resid 277 through 318 removed outlier: 4.391A pdb=" N LEU D 286 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Proline residue: D 287 - end of helix removed outlier: 3.561A pdb=" N PHE D 291 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 3.551A pdb=" N SER D 307 " --> pdb=" O LEU D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 362 Processing helix chain 'D' and resid 386 through 392 Processing helix chain 'D' and resid 399 through 408 Processing helix chain 'D' and resid 412 through 416 Processing helix chain 'D' and resid 421 through 423 No H-bonds generated for 'chain 'D' and resid 421 through 423' Processing helix chain 'D' and resid 429 through 432 Processing helix chain 'D' and resid 435 through 448 Processing helix chain 'D' and resid 465 through 476 removed outlier: 4.799A pdb=" N ARG D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLN D 470 " --> pdb=" O GLY D 466 " (cutoff:3.500A) Processing helix chain 'E' and resid -4 through 23 Processing helix chain 'E' and resid 36 through 79 removed outlier: 3.853A pdb=" N VAL E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA E 41 " --> pdb=" O PRO E 37 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 90 Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 102 through 109 removed outlier: 3.623A pdb=" N ARG E 106 " --> pdb=" O ASP E 103 " (cutoff:3.500A) Proline residue: E 107 - end of helix Processing helix chain 'E' and resid 113 through 133 removed outlier: 3.547A pdb=" N THR E 123 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 135 through 143 removed outlier: 4.027A pdb=" N ILE E 143 " --> pdb=" O ALA E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 182 Proline residue: E 149 - end of helix removed outlier: 5.036A pdb=" N GLU E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARG E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 Processing helix chain 'E' and resid 196 through 245 removed outlier: 3.740A pdb=" N VAL E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 292 Proline residue: E 262 - end of helix removed outlier: 3.829A pdb=" N PHE E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Proline residue: E 267 - end of helix removed outlier: 3.997A pdb=" N HIS E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 277 " --> pdb=" O ALA E 273 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP E 280 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 344 Processing helix chain 'E' and resid 366 through 372 removed outlier: 3.647A pdb=" N GLY E 371 " --> pdb=" O SER E 367 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG E 372 " --> pdb=" O ALA E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 400 through 407 Processing helix chain 'E' and resid 410 through 415 removed outlier: 3.822A pdb=" N GLU E 415 " --> pdb=" O GLU E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 445 Processing helix chain 'E' and resid 463 through 478 Processing helix chain 'E' and resid 490 through 495 removed outlier: 3.733A pdb=" N ALA E 495 " --> pdb=" O PRO E 491 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 372 through 375 removed outlier: 6.919A pdb=" N VAL A 453 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE A 375 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU A 455 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR A 487 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU A 456 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 489 " --> pdb=" O LEU A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 318 through 320 Processing sheet with id= C, first strand: chain 'C' and resid 498 through 500 removed outlier: 6.390A pdb=" N VAL C 483 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU C 328 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET C 485 " --> pdb=" O LEU C 328 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 372 through 375 removed outlier: 6.919A pdb=" N VAL D 453 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE D 375 " --> pdb=" O VAL D 453 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU D 455 " --> pdb=" O PHE D 375 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR D 487 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU D 456 " --> pdb=" O THR D 487 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 489 " --> pdb=" O LEU D 456 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'E' and resid 318 through 320 Processing sheet with id= F, first strand: chain 'E' and resid 498 through 500 removed outlier: 6.387A pdb=" N VAL E 483 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU E 328 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N MET E 485 " --> pdb=" O LEU E 328 " (cutoff:3.500A) 937 hydrogen bonds defined for protein. 2601 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 7.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2440 1.31 - 1.44: 3548 1.44 - 1.57: 9046 1.57 - 1.69: 20 1.69 - 1.82: 98 Bond restraints: 15152 Sorted by residual: bond pdb=" CA PRO A 56 " pdb=" C PRO A 56 " ideal model delta sigma weight residual 1.514 1.534 -0.020 5.50e-03 3.31e+04 1.31e+01 bond pdb=" N PHE E 55 " pdb=" CA PHE E 55 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.30e-02 5.92e+03 1.02e+01 bond pdb=" C ASP C 455 " pdb=" O ASP C 455 " ideal model delta sigma weight residual 1.231 1.187 0.044 1.41e-02 5.03e+03 9.96e+00 bond pdb=" O2B ATP D 602 " pdb=" PB ATP D 602 " ideal model delta sigma weight residual 1.529 1.460 0.069 2.20e-02 2.07e+03 9.81e+00 bond pdb=" O2B ATP A 602 " pdb=" PB ATP A 602 " ideal model delta sigma weight residual 1.529 1.460 0.069 2.20e-02 2.07e+03 9.76e+00 ... (remaining 15147 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.99: 492 105.99 - 113.76: 9096 113.76 - 121.52: 7791 121.52 - 129.29: 3260 129.29 - 137.06: 131 Bond angle restraints: 20770 Sorted by residual: angle pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " pdb=" O3G ATP E 602 " ideal model delta sigma weight residual 104.48 111.44 -6.96 1.14e+00 7.76e-01 3.76e+01 angle pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " pdb=" O3G ATP C 602 " ideal model delta sigma weight residual 104.48 111.44 -6.96 1.14e+00 7.76e-01 3.76e+01 angle pdb=" N GLN E 56 " pdb=" CA GLN E 56 " pdb=" C GLN E 56 " ideal model delta sigma weight residual 111.82 105.55 6.27 1.16e+00 7.43e-01 2.92e+01 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 134.55 5.32 1.00e+00 1.00e+00 2.83e+01 angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 134.55 5.32 1.00e+00 1.00e+00 2.83e+01 ... (remaining 20765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 7950 17.85 - 35.71: 938 35.71 - 53.56: 247 53.56 - 71.42: 53 71.42 - 89.27: 18 Dihedral angle restraints: 9206 sinusoidal: 3440 harmonic: 5766 Sorted by residual: dihedral pdb=" CA GLY D 205 " pdb=" C GLY D 205 " pdb=" N MET D 206 " pdb=" CA MET D 206 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA GLY A 205 " pdb=" C GLY A 205 " pdb=" N MET A 206 " pdb=" CA MET A 206 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA SER D 199 " pdb=" C SER D 199 " pdb=" N GLN D 200 " pdb=" CA GLN D 200 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 9203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2189 0.058 - 0.116: 368 0.116 - 0.174: 27 0.174 - 0.232: 6 0.232 - 0.290: 2 Chirality restraints: 2592 Sorted by residual: chirality pdb=" CA LEU A 17 " pdb=" N LEU A 17 " pdb=" C LEU A 17 " pdb=" CB LEU A 17 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB VAL C 141 " pdb=" CA VAL C 141 " pdb=" CG1 VAL C 141 " pdb=" CG2 VAL C 141 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB VAL D 135 " pdb=" CA VAL D 135 " pdb=" CG1 VAL D 135 " pdb=" CG2 VAL D 135 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2589 not shown) Planarity restraints: 2656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 252 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO A 253 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 136 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C LEU A 136 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU A 136 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 137 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 506 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C LEU C 506 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU C 506 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL C 507 " -0.012 2.00e-02 2.50e+03 ... (remaining 2653 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 125 2.56 - 3.15: 11768 3.15 - 3.73: 24182 3.73 - 4.32: 31434 4.32 - 4.90: 53249 Nonbonded interactions: 120758 Sorted by model distance: nonbonded pdb=" OG SER C 337 " pdb="MG MG C 601 " model vdw 1.978 2.170 nonbonded pdb=" OG SER E 337 " pdb="MG MG E 601 " model vdw 1.978 2.170 nonbonded pdb=" OG1 THR D 351 " pdb="MG MG D 601 " model vdw 2.053 2.170 nonbonded pdb=" OG1 THR A 351 " pdb="MG MG A 601 " model vdw 2.054 2.170 nonbonded pdb=" O ASP E 497 " pdb=" OD1 ASP E 497 " model vdw 2.160 3.040 ... (remaining 120753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' } 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: 4.040 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: 12.200 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 43.830 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.110 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:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.004 0.072 15152 Z= 0.294 Angle : 0.707 8.768 20770 Z= 0.395 Chirality : 0.043 0.290 2592 Planarity : 0.005 0.074 2656 Dihedral : 16.937 89.274 5486 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.99 % Rotamer: Outliers : 0.13 % Allowed : 24.43 % Favored : 75.43 % 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: 1.55 (0.20), residues: 2030 helix: 2.28 (0.14), residues: 1356 sheet: 0.28 (0.50), residues: 132 loop : -2.19 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 369 HIS 0.003 0.001 HIS C 460 PHE 0.006 0.001 PHE D 291 TYR 0.006 0.001 TYR D 102 ARG 0.014 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ASN cc_start: 0.7952 (m-40) cc_final: 0.7679 (m-40) REVERT: E 24 ASN cc_start: 0.7987 (m-40) cc_final: 0.7751 (m-40) outliers start: 2 outliers final: 2 residues processed: 193 average time/residue: 1.0880 time to fit residues: 235.0735 Evaluate side-chains 111 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain E residue 55 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 0.2980 chunk 153 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN C 53 GLN E 53 GLN E 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15152 Z= 0.190 Angle : 0.616 9.303 20770 Z= 0.297 Chirality : 0.039 0.148 2592 Planarity : 0.005 0.045 2656 Dihedral : 8.071 86.636 2342 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.67 % Allowed : 25.83 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.20), residues: 2030 helix: 2.37 (0.14), residues: 1356 sheet: 0.37 (0.50), residues: 132 loop : -2.04 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 54 HIS 0.002 0.001 HIS D 87 PHE 0.025 0.002 PHE C 151 TYR 0.011 0.002 TYR E 133 ARG 0.006 0.000 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 119 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ASN cc_start: 0.8022 (m-40) cc_final: 0.7749 (m-40) REVERT: E 24 ASN cc_start: 0.7993 (m-40) cc_final: 0.7741 (m-40) outliers start: 55 outliers final: 17 residues processed: 158 average time/residue: 0.8020 time to fit residues: 147.1866 Evaluate side-chains 125 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 HIS Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 301 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN C 0 ASN E 0 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15152 Z= 0.234 Angle : 0.599 8.651 20770 Z= 0.289 Chirality : 0.038 0.131 2592 Planarity : 0.004 0.036 2656 Dihedral : 7.431 81.906 2338 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.54 % Allowed : 25.37 % Favored : 71.09 % 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: 1.75 (0.20), residues: 2030 helix: 2.38 (0.14), residues: 1366 sheet: 0.33 (0.49), residues: 132 loop : -2.05 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 54 HIS 0.003 0.001 HIS D 87 PHE 0.017 0.001 PHE E 55 TYR 0.010 0.002 TYR E 133 ARG 0.004 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 106 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7674 (tmm) cc_final: 0.7462 (tmm) REVERT: C 24 ASN cc_start: 0.8004 (m-40) cc_final: 0.7739 (m-40) REVERT: E 24 ASN cc_start: 0.8046 (m-40) cc_final: 0.7793 (m-40) outliers start: 53 outliers final: 24 residues processed: 146 average time/residue: 0.7776 time to fit residues: 132.4046 Evaluate side-chains 127 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 HIS Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 301 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS A 458 GLN C 0 ASN D 231 HIS D 458 GLN E 0 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15152 Z= 0.325 Angle : 0.628 9.482 20770 Z= 0.307 Chirality : 0.040 0.162 2592 Planarity : 0.004 0.035 2656 Dihedral : 7.201 85.079 2338 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.34 % Allowed : 24.17 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.74 (0.20), residues: 2030 helix: 2.40 (0.14), residues: 1366 sheet: 0.12 (0.47), residues: 138 loop : -2.08 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 54 HIS 0.003 0.001 HIS E 460 PHE 0.015 0.001 PHE C 275 TYR 0.010 0.002 TYR E 133 ARG 0.005 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 107 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7710 (tmm) cc_final: 0.7458 (tmm) REVERT: C 24 ASN cc_start: 0.8117 (m-40) cc_final: 0.7845 (m-40) outliers start: 65 outliers final: 27 residues processed: 157 average time/residue: 0.8350 time to fit residues: 152.4324 Evaluate side-chains 125 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 HIS Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 504 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 166 optimal weight: 0.0270 chunk 134 optimal weight: 10.0000 chunk 0 optimal weight: 10.9990 chunk 99 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN C 0 ASN E 0 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15152 Z= 0.263 Angle : 0.623 10.733 20770 Z= 0.298 Chirality : 0.039 0.155 2592 Planarity : 0.004 0.037 2656 Dihedral : 6.948 88.632 2338 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.94 % Allowed : 25.30 % Favored : 70.76 % 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: 1.78 (0.20), residues: 2030 helix: 2.42 (0.14), residues: 1366 sheet: 0.16 (0.47), residues: 138 loop : -2.05 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 135 HIS 0.003 0.001 HIS D 87 PHE 0.013 0.001 PHE C 275 TYR 0.009 0.002 TYR C -4 ARG 0.006 0.000 ARG D 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 101 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7786 (tmm) cc_final: 0.7468 (tmm) outliers start: 59 outliers final: 27 residues processed: 143 average time/residue: 0.9610 time to fit residues: 156.2828 Evaluate side-chains 124 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 HIS Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 504 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 0.0070 chunk 175 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN C 0 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN E 0 ASN E 56 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15152 Z= 0.254 Angle : 0.617 12.126 20770 Z= 0.296 Chirality : 0.039 0.133 2592 Planarity : 0.004 0.034 2656 Dihedral : 6.763 85.552 2338 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.74 % Allowed : 25.77 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.20), residues: 2030 helix: 2.50 (0.14), residues: 1360 sheet: 0.24 (0.47), residues: 138 loop : -1.97 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 135 HIS 0.002 0.001 HIS D 87 PHE 0.018 0.001 PHE C 151 TYR 0.009 0.001 TYR C -4 ARG 0.007 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 100 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7796 (tmm) cc_final: 0.7550 (tmm) outliers start: 56 outliers final: 32 residues processed: 138 average time/residue: 0.8603 time to fit residues: 136.6361 Evaluate side-chains 125 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 93 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 301 HIS Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 301 HIS Chi-restraints excluded: chain E residue 504 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN C 0 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN E 0 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15152 Z= 0.185 Angle : 0.604 12.367 20770 Z= 0.289 Chirality : 0.038 0.134 2592 Planarity : 0.004 0.035 2656 Dihedral : 6.456 82.444 2338 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.07 % Allowed : 26.03 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.20), residues: 2030 helix: 2.53 (0.14), residues: 1360 sheet: 0.40 (0.48), residues: 138 loop : -1.90 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 369 HIS 0.002 0.000 HIS C 488 PHE 0.019 0.001 PHE E 151 TYR 0.013 0.002 TYR E -4 ARG 0.007 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 103 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7785 (tmm) cc_final: 0.7561 (tmm) REVERT: C 502 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8410 (ttt) outliers start: 46 outliers final: 26 residues processed: 132 average time/residue: 0.8744 time to fit residues: 133.9785 Evaluate side-chains 124 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 504 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN C 0 ASN D 54 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 0 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15152 Z= 0.304 Angle : 0.645 13.549 20770 Z= 0.309 Chirality : 0.040 0.138 2592 Planarity : 0.004 0.034 2656 Dihedral : 6.611 85.410 2338 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.54 % Allowed : 26.17 % Favored : 70.29 % 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: 1.97 (0.20), residues: 2030 helix: 2.54 (0.14), residues: 1360 sheet: 0.37 (0.48), residues: 138 loop : -1.89 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 375 HIS 0.003 0.001 HIS D 87 PHE 0.016 0.002 PHE C 151 TYR 0.009 0.002 TYR D 102 ARG 0.005 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 97 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7852 (tmm) cc_final: 0.7628 (tmm) REVERT: C 502 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8540 (ttt) outliers start: 53 outliers final: 28 residues processed: 131 average time/residue: 0.8896 time to fit residues: 134.1221 Evaluate side-chains 124 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 504 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 170 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN C 0 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 0 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15152 Z= 0.189 Angle : 0.634 14.171 20770 Z= 0.298 Chirality : 0.038 0.166 2592 Planarity : 0.004 0.034 2656 Dihedral : 6.355 81.974 2338 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.47 % Allowed : 27.30 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.20), residues: 2030 helix: 2.55 (0.14), residues: 1348 sheet: 0.51 (0.49), residues: 138 loop : -1.76 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 46 HIS 0.001 0.000 HIS C 16 PHE 0.016 0.001 PHE E 151 TYR 0.009 0.001 TYR C -4 ARG 0.006 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 94 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7862 (tmm) cc_final: 0.7660 (tmm) REVERT: C 502 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8435 (ttt) outliers start: 37 outliers final: 23 residues processed: 120 average time/residue: 0.9419 time to fit residues: 129.4797 Evaluate side-chains 115 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 504 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 201 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 16 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN C 0 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN E 0 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.003 0.039 15152 Z= 0.200 Angle : 0.642 14.648 20770 Z= 0.300 Chirality : 0.038 0.179 2592 Planarity : 0.004 0.035 2656 Dihedral : 6.260 81.281 2338 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.20 % Allowed : 27.57 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.20), residues: 2030 helix: 2.59 (0.14), residues: 1348 sheet: 0.59 (0.49), residues: 138 loop : -1.76 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 369 HIS 0.002 0.000 HIS A 87 PHE 0.017 0.001 PHE E 151 TYR 0.008 0.001 TYR C -4 ARG 0.005 0.000 ARG A 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 502 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8441 (ttt) outliers start: 33 outliers final: 24 residues processed: 123 average time/residue: 0.8903 time to fit residues: 126.5000 Evaluate side-chains 120 residues out of total 1498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 6 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 504 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 30.0000 chunk 170 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 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 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN C 0 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN E 0 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.069467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.050111 restraints weight = 52375.918| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.62 r_work: 0.2689 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15152 Z= 0.220 Angle : 0.658 16.070 20770 Z= 0.306 Chirality : 0.039 0.178 2592 Planarity : 0.004 0.035 2656 Dihedral : 6.280 81.835 2338 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.07 % Allowed : 27.64 % Favored : 70.29 % 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: 2.03 (0.20), residues: 2030 helix: 2.57 (0.14), residues: 1348 sheet: 0.58 (0.49), residues: 138 loop : -1.77 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 369 HIS 0.002 0.000 HIS D 87 PHE 0.010 0.001 PHE C 151 TYR 0.008 0.001 TYR C -4 ARG 0.005 0.000 ARG A 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3598.71 seconds wall clock time: 65 minutes 58.64 seconds (3958.64 seconds total)