Starting phenix.real_space_refine on Tue Feb 13 20:32:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gw7_34304/02_2024/8gw7_34304_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gw7_34304/02_2024/8gw7_34304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gw7_34304/02_2024/8gw7_34304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gw7_34304/02_2024/8gw7_34304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gw7_34304/02_2024/8gw7_34304_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gw7_34304/02_2024/8gw7_34304_trim.pdb" } resolution = 3.3 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= 0.002 sd= 0.027 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 39 5.16 5 Cl 6 4.86 5 C 5169 2.51 5 N 1128 2.21 5 O 1182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7524 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2471 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 20, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2471 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 20, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2471 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 20, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' CL': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' CL': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' CL': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.69, per 1000 atoms: 0.62 Number of scatterers: 7524 At special positions: 0 Unit cell: (106.68, 97.44, 66.36, 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 6 17.00 S 39 16.00 O 1182 8.00 N 1128 7.00 C 5169 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: 2.86 Conformation dependent library (CDL) restraints added in 1.4 seconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1806 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 81.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 192 through 212 removed outlier: 4.310A pdb=" N CYS A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 219 removed outlier: 3.752A pdb=" N LEU A 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 250 removed outlier: 3.842A pdb=" N LEU A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 260 removed outlier: 3.757A pdb=" N PHE A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 removed outlier: 3.526A pdb=" N VAL A 264 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN A 265 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A 266 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 removed outlier: 3.743A pdb=" N CYS A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 275 " --> pdb=" O TRP A 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 318 removed outlier: 4.377A pdb=" N TRP A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Proline residue: A 303 - end of helix removed outlier: 3.687A pdb=" N TRP A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 349 removed outlier: 3.892A pdb=" N PHE A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 343 " --> pdb=" O PHE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 375 removed outlier: 4.079A pdb=" N VAL A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.666A pdb=" N SER A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 409 Processing helix chain 'A' and resid 412 through 433 removed outlier: 3.622A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 466 removed outlier: 3.916A pdb=" N TYR A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 449 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A 450 " --> pdb=" O TRP A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.548A pdb=" N LYS A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 499 removed outlier: 3.842A pdb=" N ALA A 497 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' Processing helix chain 'C' and resid 192 through 212 removed outlier: 4.309A pdb=" N CYS C 196 " --> pdb=" O CYS C 192 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 204 " --> pdb=" O SER C 200 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.752A pdb=" N LEU C 218 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 250 removed outlier: 3.843A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 260 removed outlier: 3.756A pdb=" N PHE C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 267 removed outlier: 3.527A pdb=" N VAL C 264 " --> pdb=" O PRO C 261 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN C 265 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE C 266 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 281 removed outlier: 3.744A pdb=" N CYS C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET C 275 " --> pdb=" O TRP C 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 318 removed outlier: 4.377A pdb=" N TRP C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE C 300 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Proline residue: C 303 - end of helix removed outlier: 3.687A pdb=" N TRP C 315 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 316 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 349 removed outlier: 3.892A pdb=" N PHE C 339 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C 343 " --> pdb=" O PHE C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 375 removed outlier: 4.079A pdb=" N VAL C 367 " --> pdb=" O ALA C 363 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 392 removed outlier: 3.666A pdb=" N SER C 391 " --> pdb=" O HIS C 387 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 409 Processing helix chain 'C' and resid 412 through 433 removed outlier: 3.622A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL C 430 " --> pdb=" O TYR C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 466 removed outlier: 3.916A pdb=" N TYR C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 449 " --> pdb=" O TRP C 445 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE C 450 " --> pdb=" O TRP C 446 " (cutoff:3.500A) Proline residue: C 451 - end of helix removed outlier: 3.548A pdb=" N LYS C 461 " --> pdb=" O VAL C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 499 removed outlier: 3.842A pdb=" N ALA C 497 " --> pdb=" O THR C 493 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 498 " --> pdb=" O LEU C 494 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 192 through 212 removed outlier: 4.310A pdb=" N CYS B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 removed outlier: 3.752A pdb=" N LEU B 218 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 250 removed outlier: 3.842A pdb=" N LEU B 226 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 260 removed outlier: 3.757A pdb=" N PHE B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 267 removed outlier: 3.525A pdb=" N VAL B 264 " --> pdb=" O PRO B 261 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN B 265 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE B 266 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 281 removed outlier: 3.744A pdb=" N CYS B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET B 275 " --> pdb=" O TRP B 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 318 removed outlier: 4.377A pdb=" N TRP B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.687A pdb=" N TRP B 315 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 316 " --> pdb=" O TYR B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 349 removed outlier: 3.893A pdb=" N PHE B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 343 " --> pdb=" O PHE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 375 removed outlier: 4.079A pdb=" N VAL B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 392 removed outlier: 3.667A pdb=" N SER B 391 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 409 Processing helix chain 'B' and resid 412 through 433 removed outlier: 3.623A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 430 " --> pdb=" O TYR B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 466 removed outlier: 3.915A pdb=" N TYR B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 449 " --> pdb=" O TRP B 445 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE B 450 " --> pdb=" O TRP B 446 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.547A pdb=" N LYS B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 499 removed outlier: 3.841A pdb=" N ALA B 497 " --> pdb=" O THR B 493 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 3.02 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: 1185 1.33 - 1.45: 2368 1.45 - 1.57: 4211 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 7818 Sorted by residual: bond pdb=" CBD Y01 B 903 " pdb=" CBF Y01 B 903 " ideal model delta sigma weight residual 1.536 1.463 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CBD Y01 C 903 " pdb=" CBF Y01 C 903 " ideal model delta sigma weight residual 1.536 1.463 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" CBD Y01 A 903 " pdb=" CBF Y01 A 903 " ideal model delta sigma weight residual 1.536 1.463 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" CAK Y01 A 903 " pdb=" CBD Y01 A 903 " ideal model delta sigma weight residual 1.525 1.467 0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" CAK Y01 B 903 " pdb=" CBD Y01 B 903 " ideal model delta sigma weight residual 1.525 1.467 0.058 2.00e-02 2.50e+03 8.45e+00 ... (remaining 7813 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.37: 234 105.37 - 112.55: 4034 112.55 - 119.72: 2326 119.72 - 126.89: 3974 126.89 - 134.06: 181 Bond angle restraints: 10749 Sorted by residual: angle pdb=" CAK Y01 A 903 " pdb=" CAI Y01 A 903 " pdb=" CAZ Y01 A 903 " ideal model delta sigma weight residual 124.96 113.15 11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CAK Y01 C 903 " pdb=" CAI Y01 C 903 " pdb=" CAZ Y01 C 903 " ideal model delta sigma weight residual 124.96 113.21 11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CAK Y01 B 903 " pdb=" CAI Y01 B 903 " pdb=" CAZ Y01 B 903 " ideal model delta sigma weight residual 124.96 113.25 11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CAD Y01 A 903 " pdb=" CBH Y01 A 903 " pdb=" CAZ Y01 A 903 " ideal model delta sigma weight residual 108.53 98.20 10.33 3.00e+00 1.11e-01 1.19e+01 angle pdb=" CAD Y01 B 903 " pdb=" CBH Y01 B 903 " pdb=" CAZ Y01 B 903 " ideal model delta sigma weight residual 108.53 98.23 10.30 3.00e+00 1.11e-01 1.18e+01 ... (remaining 10744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 4030 17.05 - 34.10: 350 34.10 - 51.16: 87 51.16 - 68.21: 15 68.21 - 85.26: 6 Dihedral angle restraints: 4488 sinusoidal: 1701 harmonic: 2787 Sorted by residual: dihedral pdb=" CB GLU C 308 " pdb=" CG GLU C 308 " pdb=" CD GLU C 308 " pdb=" OE1 GLU C 308 " ideal model delta sinusoidal sigma weight residual 0.00 -85.26 85.26 1 3.00e+01 1.11e-03 9.79e+00 dihedral pdb=" CB GLU B 308 " pdb=" CG GLU B 308 " pdb=" CD GLU B 308 " pdb=" OE1 GLU B 308 " ideal model delta sinusoidal sigma weight residual 0.00 -85.26 85.26 1 3.00e+01 1.11e-03 9.79e+00 dihedral pdb=" CB GLU A 308 " pdb=" CG GLU A 308 " pdb=" CD GLU A 308 " pdb=" OE1 GLU A 308 " ideal model delta sinusoidal sigma weight residual 0.00 -85.24 85.24 1 3.00e+01 1.11e-03 9.78e+00 ... (remaining 4485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 1212 0.144 - 0.288: 6 0.288 - 0.431: 9 0.431 - 0.575: 0 0.575 - 0.719: 3 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CBH Y01 A 903 " pdb=" CAT Y01 A 903 " pdb=" CAZ Y01 A 903 " pdb=" CBF Y01 A 903 " both_signs ideal model delta sigma weight residual False -2.85 -2.13 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CBH Y01 B 903 " pdb=" CAT Y01 B 903 " pdb=" CAZ Y01 B 903 " pdb=" CBF Y01 B 903 " both_signs ideal model delta sigma weight residual False -2.85 -2.13 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CBH Y01 C 903 " pdb=" CAT Y01 C 903 " pdb=" CAZ Y01 C 903 " pdb=" CBF Y01 C 903 " both_signs ideal model delta sigma weight residual False -2.85 -2.14 -0.72 2.00e-01 2.50e+01 1.28e+01 ... (remaining 1227 not shown) Planarity restraints: 1269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 286 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO B 287 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 286 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A 287 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 286 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO C 287 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 287 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 287 " -0.030 5.00e-02 4.00e+02 ... (remaining 1266 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 970 2.76 - 3.29: 7878 3.29 - 3.83: 11781 3.83 - 4.36: 13144 4.36 - 4.90: 22551 Nonbonded interactions: 56324 Sorted by model distance: nonbonded pdb=" OE1 GLN B 202 " pdb=" OG1 THR B 453 " model vdw 2.220 2.440 nonbonded pdb=" OE1 GLN A 202 " pdb=" OG1 THR A 453 " model vdw 2.220 2.440 nonbonded pdb=" OE1 GLN C 202 " pdb=" OG1 THR C 453 " model vdw 2.221 2.440 nonbonded pdb=" O PHE A 498 " pdb=" NE2 GLN A 501 " model vdw 2.288 2.520 nonbonded pdb=" O PHE C 498 " pdb=" NE2 GLN C 501 " model vdw 2.288 2.520 ... (remaining 56319 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 'B' selection = chain 'C' } 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: 0.700 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: 3.240 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.260 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 0.073 7818 Z= 0.255 Angle : 0.789 11.813 10749 Z= 0.331 Chirality : 0.060 0.719 1230 Planarity : 0.006 0.055 1269 Dihedral : 13.998 85.261 2682 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.39 % Allowed : 1.96 % Favored : 97.65 % 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: 1.51 (0.25), residues: 933 helix: 1.58 (0.18), residues: 651 sheet: None (None), residues: 0 loop : -0.26 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 446 HIS 0.004 0.001 HIS B 387 PHE 0.006 0.001 PHE A 217 TYR 0.012 0.001 TYR B 390 ARG 0.002 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 185 time to evaluate : 0.829 Fit side-chains REVERT: A 195 ILE cc_start: 0.8634 (tt) cc_final: 0.8266 (pt) REVERT: A 255 LYS cc_start: 0.8077 (tttm) cc_final: 0.7750 (ttpp) REVERT: A 469 TYR cc_start: 0.7262 (m-80) cc_final: 0.6965 (m-80) REVERT: C 195 ILE cc_start: 0.8831 (tt) cc_final: 0.8412 (pt) REVERT: C 469 TYR cc_start: 0.7321 (m-80) cc_final: 0.7109 (m-80) REVERT: B 195 ILE cc_start: 0.8778 (tt) cc_final: 0.8445 (pt) REVERT: B 469 TYR cc_start: 0.7266 (m-80) cc_final: 0.6989 (m-80) outliers start: 3 outliers final: 0 residues processed: 188 average time/residue: 0.1665 time to fit residues: 43.3639 Evaluate side-chains 149 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 265 ASN A 405 ASN C 219 HIS C 405 ASN B 219 HIS B 405 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7818 Z= 0.192 Angle : 0.619 8.897 10749 Z= 0.306 Chirality : 0.042 0.144 1230 Planarity : 0.006 0.045 1269 Dihedral : 7.686 43.839 1212 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.01 % Allowed : 11.76 % Favored : 85.23 % 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: 2.56 (0.28), residues: 933 helix: 2.32 (0.20), residues: 675 sheet: None (None), residues: 0 loop : 0.06 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 206 HIS 0.003 0.001 HIS B 387 PHE 0.020 0.001 PHE B 184 TYR 0.016 0.002 TYR C 365 ARG 0.002 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 0.799 Fit side-chains REVERT: A 255 LYS cc_start: 0.7995 (tttm) cc_final: 0.7786 (ttpp) REVERT: A 277 LEU cc_start: 0.8194 (mp) cc_final: 0.7980 (mp) REVERT: A 314 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8248 (tm-30) REVERT: C 314 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8347 (tm-30) REVERT: B 255 LYS cc_start: 0.8215 (tttm) cc_final: 0.7654 (mttm) outliers start: 23 outliers final: 20 residues processed: 185 average time/residue: 0.1844 time to fit residues: 46.3406 Evaluate side-chains 165 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 393 PHE Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 483 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 HIS C 219 HIS B 219 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7818 Z= 0.177 Angle : 0.577 8.214 10749 Z= 0.281 Chirality : 0.041 0.149 1230 Planarity : 0.005 0.038 1269 Dihedral : 7.331 41.198 1212 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.88 % Allowed : 15.82 % Favored : 81.31 % 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: 2.70 (0.28), residues: 933 helix: 2.51 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -0.20 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 446 HIS 0.003 0.001 HIS C 387 PHE 0.019 0.001 PHE A 441 TYR 0.008 0.001 TYR C 365 ARG 0.001 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 0.824 Fit side-chains REVERT: A 375 ARG cc_start: 0.7347 (ptp-170) cc_final: 0.7114 (ptp90) REVERT: C 255 LYS cc_start: 0.8046 (tttm) cc_final: 0.7784 (ttpp) REVERT: C 314 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8400 (tm-30) REVERT: C 411 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.6226 (m-10) REVERT: B 187 ARG cc_start: 0.8389 (ptp-110) cc_final: 0.8147 (ptp-110) REVERT: B 255 LYS cc_start: 0.8224 (tttm) cc_final: 0.7639 (mttm) REVERT: B 314 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8264 (tm-30) outliers start: 22 outliers final: 14 residues processed: 170 average time/residue: 0.1870 time to fit residues: 43.1185 Evaluate side-chains 152 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 414 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 0.0970 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 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 219 HIS C 219 HIS B 219 HIS ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7818 Z= 0.163 Angle : 0.563 7.885 10749 Z= 0.271 Chirality : 0.040 0.141 1230 Planarity : 0.004 0.033 1269 Dihedral : 6.889 44.322 1212 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.18 % Allowed : 19.35 % Favored : 76.47 % 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: 2.69 (0.28), residues: 933 helix: 2.56 (0.21), residues: 678 sheet: None (None), residues: 0 loop : -0.41 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 206 HIS 0.003 0.001 HIS B 387 PHE 0.015 0.001 PHE A 184 TYR 0.008 0.001 TYR A 258 ARG 0.001 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 0.825 Fit side-chains REVERT: A 277 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8066 (mp) REVERT: A 285 PHE cc_start: 0.7827 (m-10) cc_final: 0.7602 (m-80) REVERT: A 375 ARG cc_start: 0.7225 (ptp-170) cc_final: 0.6948 (ptp90) REVERT: C 199 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6973 (tt) REVERT: C 255 LYS cc_start: 0.8044 (tttm) cc_final: 0.7777 (ttpp) REVERT: B 187 ARG cc_start: 0.8423 (ptp-110) cc_final: 0.8119 (ptp-110) REVERT: B 255 LYS cc_start: 0.8198 (tttm) cc_final: 0.7624 (mttm) REVERT: B 314 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8283 (tm-30) REVERT: B 375 ARG cc_start: 0.7167 (ptp-170) cc_final: 0.6964 (ptp90) outliers start: 32 outliers final: 20 residues processed: 173 average time/residue: 0.1878 time to fit residues: 43.6909 Evaluate side-chains 167 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 414 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.0000 chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 225 ASN A 260 HIS C 219 HIS C 225 ASN B 219 HIS B 225 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7818 Z= 0.182 Angle : 0.585 8.193 10749 Z= 0.280 Chirality : 0.041 0.142 1230 Planarity : 0.004 0.030 1269 Dihedral : 6.763 45.774 1212 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.36 % Allowed : 22.22 % Favored : 72.42 % 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: 2.62 (0.29), residues: 933 helix: 2.52 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -0.56 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 206 HIS 0.003 0.001 HIS C 387 PHE 0.025 0.001 PHE A 441 TYR 0.008 0.001 TYR A 258 ARG 0.001 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 0.837 Fit side-chains REVERT: A 249 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.5788 (m-80) REVERT: A 277 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8085 (mp) REVERT: A 285 PHE cc_start: 0.7908 (m-10) cc_final: 0.7676 (m-80) REVERT: A 375 ARG cc_start: 0.7242 (ptp-170) cc_final: 0.6931 (ptp90) REVERT: C 184 PHE cc_start: 0.7923 (t80) cc_final: 0.7704 (t80) REVERT: C 249 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6092 (m-80) REVERT: C 255 LYS cc_start: 0.8061 (tttm) cc_final: 0.7792 (ttpp) REVERT: B 187 ARG cc_start: 0.8494 (ptp-110) cc_final: 0.8135 (ptp-110) REVERT: B 249 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.5997 (m-80) REVERT: B 255 LYS cc_start: 0.8224 (tttm) cc_final: 0.7616 (mttm) REVERT: B 277 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8028 (mp) REVERT: B 375 ARG cc_start: 0.7224 (ptp-170) cc_final: 0.6994 (ptp90) outliers start: 41 outliers final: 26 residues processed: 183 average time/residue: 0.1837 time to fit residues: 45.6173 Evaluate side-chains 184 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 414 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 89 optimal weight: 0.0170 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS C 219 HIS B 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7818 Z= 0.159 Angle : 0.576 8.291 10749 Z= 0.272 Chirality : 0.040 0.143 1230 Planarity : 0.004 0.027 1269 Dihedral : 6.682 48.673 1212 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.49 % Allowed : 21.44 % Favored : 73.07 % 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: 2.50 (0.29), residues: 933 helix: 2.43 (0.21), residues: 687 sheet: None (None), residues: 0 loop : -0.66 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 206 HIS 0.003 0.001 HIS A 387 PHE 0.021 0.001 PHE A 184 TYR 0.007 0.001 TYR A 258 ARG 0.003 0.000 ARG C 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 0.744 Fit side-chains REVERT: A 249 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.5820 (m-80) REVERT: A 277 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8043 (mp) REVERT: A 301 MET cc_start: 0.7119 (tpt) cc_final: 0.6900 (mmm) REVERT: A 375 ARG cc_start: 0.7146 (ptp-170) cc_final: 0.6815 (ptp90) REVERT: C 199 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6892 (tt) REVERT: C 249 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.6008 (m-80) REVERT: C 255 LYS cc_start: 0.8045 (tttm) cc_final: 0.7770 (ttpp) REVERT: C 285 PHE cc_start: 0.7896 (m-80) cc_final: 0.7494 (m-80) REVERT: B 249 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.5985 (m-80) REVERT: B 255 LYS cc_start: 0.8209 (tttm) cc_final: 0.7610 (mttm) REVERT: B 277 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8029 (mp) REVERT: B 375 ARG cc_start: 0.7091 (ptp-170) cc_final: 0.6862 (ptp90) outliers start: 42 outliers final: 25 residues processed: 182 average time/residue: 0.1897 time to fit residues: 46.4576 Evaluate side-chains 184 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 414 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 7.9990 chunk 10 optimal weight: 0.0270 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS C 219 HIS B 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7818 Z= 0.223 Angle : 0.627 9.533 10749 Z= 0.299 Chirality : 0.042 0.145 1230 Planarity : 0.004 0.027 1269 Dihedral : 6.794 49.220 1212 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.49 % Allowed : 21.83 % Favored : 72.68 % 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: 2.41 (0.29), residues: 933 helix: 2.38 (0.21), residues: 684 sheet: None (None), residues: 0 loop : -0.70 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 446 HIS 0.004 0.001 HIS B 387 PHE 0.021 0.001 PHE B 450 TYR 0.008 0.001 TYR A 258 ARG 0.006 0.000 ARG C 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 0.857 Fit side-chains REVERT: A 249 PHE cc_start: 0.6578 (OUTLIER) cc_final: 0.5766 (m-80) REVERT: A 277 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8106 (mp) REVERT: A 375 ARG cc_start: 0.7358 (ptp-170) cc_final: 0.7002 (ptp90) REVERT: C 249 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6152 (m-80) REVERT: C 255 LYS cc_start: 0.8071 (tttm) cc_final: 0.7799 (ttpp) REVERT: C 285 PHE cc_start: 0.8040 (m-80) cc_final: 0.7619 (m-80) REVERT: C 432 ARG cc_start: 0.7485 (ttt-90) cc_final: 0.7279 (ttt-90) REVERT: B 249 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.6052 (m-80) REVERT: B 277 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8028 (mp) REVERT: B 375 ARG cc_start: 0.7302 (ptp-170) cc_final: 0.7050 (ptp90) outliers start: 42 outliers final: 29 residues processed: 180 average time/residue: 0.1778 time to fit residues: 43.7666 Evaluate side-chains 182 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 414 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.0470 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS C 219 HIS B 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7818 Z= 0.163 Angle : 0.598 9.191 10749 Z= 0.280 Chirality : 0.040 0.143 1230 Planarity : 0.004 0.026 1269 Dihedral : 6.653 53.991 1212 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.84 % Allowed : 22.35 % Favored : 72.81 % 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: 2.37 (0.29), residues: 933 helix: 2.30 (0.21), residues: 690 sheet: None (None), residues: 0 loop : -0.62 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 206 HIS 0.003 0.001 HIS C 387 PHE 0.015 0.001 PHE C 411 TYR 0.006 0.001 TYR A 258 ARG 0.006 0.000 ARG C 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 0.867 Fit side-chains REVERT: A 249 PHE cc_start: 0.6691 (OUTLIER) cc_final: 0.5900 (m-80) REVERT: A 277 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8070 (mp) REVERT: A 375 ARG cc_start: 0.6914 (ptp-170) cc_final: 0.6627 (ptp90) REVERT: C 249 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.6096 (m-80) REVERT: C 255 LYS cc_start: 0.8041 (tttm) cc_final: 0.7763 (ttpp) REVERT: B 249 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.5982 (m-80) REVERT: B 255 LYS cc_start: 0.8198 (tttm) cc_final: 0.7586 (mttm) REVERT: B 277 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8010 (mp) REVERT: B 375 ARG cc_start: 0.7076 (ptp-170) cc_final: 0.6851 (ptp90) outliers start: 37 outliers final: 27 residues processed: 177 average time/residue: 0.1889 time to fit residues: 45.3742 Evaluate side-chains 185 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 414 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS C 219 HIS B 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7818 Z= 0.199 Angle : 0.632 10.146 10749 Z= 0.295 Chirality : 0.042 0.150 1230 Planarity : 0.004 0.027 1269 Dihedral : 6.758 52.709 1212 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.44 % Allowed : 22.61 % Favored : 72.94 % 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: 2.32 (0.29), residues: 933 helix: 2.28 (0.21), residues: 687 sheet: None (None), residues: 0 loop : -0.65 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 206 HIS 0.004 0.001 HIS A 387 PHE 0.024 0.001 PHE A 184 TYR 0.009 0.001 TYR A 258 ARG 0.004 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 0.880 Fit side-chains REVERT: A 249 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.5910 (m-80) REVERT: A 277 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8097 (mp) REVERT: A 375 ARG cc_start: 0.7197 (ptp-170) cc_final: 0.6863 (ptp90) REVERT: C 249 PHE cc_start: 0.6913 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: C 255 LYS cc_start: 0.8049 (tttm) cc_final: 0.7775 (ttpp) REVERT: B 249 PHE cc_start: 0.6826 (OUTLIER) cc_final: 0.6021 (m-80) REVERT: B 277 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7971 (mp) REVERT: B 314 GLN cc_start: 0.8505 (tp40) cc_final: 0.8294 (tm-30) REVERT: B 375 ARG cc_start: 0.7218 (ptp-170) cc_final: 0.6973 (ptp90) outliers start: 34 outliers final: 25 residues processed: 167 average time/residue: 0.1777 time to fit residues: 41.1557 Evaluate side-chains 178 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 414 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS C 219 HIS B 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 7818 Z= 0.382 Angle : 0.758 10.418 10749 Z= 0.368 Chirality : 0.046 0.158 1230 Planarity : 0.005 0.033 1269 Dihedral : 7.267 53.152 1212 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.97 % Allowed : 21.70 % Favored : 73.33 % 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: 1.84 (0.28), residues: 933 helix: 1.97 (0.21), residues: 681 sheet: None (None), residues: 0 loop : -0.88 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 446 HIS 0.006 0.001 HIS B 387 PHE 0.034 0.002 PHE B 450 TYR 0.025 0.002 TYR B 390 ARG 0.004 0.001 ARG B 187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 0.868 Fit side-chains REVERT: A 249 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.5944 (m-10) REVERT: A 277 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8118 (mp) REVERT: A 375 ARG cc_start: 0.7427 (ptp-170) cc_final: 0.7045 (ptp90) REVERT: A 426 TYR cc_start: 0.8645 (t80) cc_final: 0.8407 (t80) REVERT: C 249 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6088 (m-10) REVERT: C 255 LYS cc_start: 0.8070 (tttm) cc_final: 0.7781 (ttpp) REVERT: C 426 TYR cc_start: 0.8652 (t80) cc_final: 0.8407 (t80) REVERT: B 249 PHE cc_start: 0.7011 (OUTLIER) cc_final: 0.6167 (m-80) REVERT: B 255 LYS cc_start: 0.8220 (tttm) cc_final: 0.7923 (ttpp) REVERT: B 375 ARG cc_start: 0.7594 (ptp-170) cc_final: 0.7276 (ptp90) outliers start: 38 outliers final: 27 residues processed: 174 average time/residue: 0.1830 time to fit residues: 43.5091 Evaluate side-chains 176 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 249 PHE Chi-restraints excluded: chain C residue 298 CYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 414 CYS Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 414 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS B 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.161316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140251 restraints weight = 12309.028| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.57 r_work: 0.3579 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7818 Z= 0.185 Angle : 0.633 9.545 10749 Z= 0.299 Chirality : 0.041 0.158 1230 Planarity : 0.004 0.029 1269 Dihedral : 7.141 59.923 1212 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.53 % Allowed : 23.40 % Favored : 73.07 % 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: 2.15 (0.29), residues: 933 helix: 2.22 (0.21), residues: 687 sheet: None (None), residues: 0 loop : -0.94 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 206 HIS 0.004 0.001 HIS C 219 PHE 0.016 0.001 PHE C 411 TYR 0.010 0.001 TYR B 390 ARG 0.003 0.000 ARG B 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1799.22 seconds wall clock time: 33 minutes 9.19 seconds (1989.19 seconds total)