Starting phenix.real_space_refine on Sat Jun 14 14:34:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dx7_47282/06_2025/9dx7_47282.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dx7_47282/06_2025/9dx7_47282.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/cci-nas-00/data/ceres_data/9dx7_47282/06_2025/9dx7_47282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dx7_47282/06_2025/9dx7_47282.map" model { file = "/net/cci-nas-00/data/ceres_data/9dx7_47282/06_2025/9dx7_47282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dx7_47282/06_2025/9dx7_47282.cif" } 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= 0.001 sd= 0.026 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 P 9 5.49 5 S 103 5.16 5 C 10817 2.51 5 N 2510 2.21 5 O 2799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16238 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2658 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "A" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2654 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain breaks: 2 Chain: "B" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2658 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "D" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2600 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 2 Chain: "E" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2580 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain breaks: 2 Chain: "F" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2580 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain breaks: 2 Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 11.26, per 1000 atoms: 0.69 Number of scatterers: 16238 At special positions: 0 Unit cell: (108.992, 102.704, 132.048, 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) S 103 16.00 P 9 15.00 O 2799 8.00 N 2510 7.00 C 10817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 355 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 340 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 355 " distance=2.03 Simple disulfide: pdb=" SG CYS F 154 " - pdb=" SG CYS F 340 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.8 seconds 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 9 sheets defined 77.1% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'C' and resid 15 through 21 removed outlier: 3.987A pdb=" N ARG C 18 " --> pdb=" O PRO C 15 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 50 removed outlier: 3.861A pdb=" N ASP C 50 " --> pdb=" O GLN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 5.114A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.984A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 258 through 285 removed outlier: 4.041A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 346 removed outlier: 4.035A pdb=" N ARG C 346 " --> pdb=" O TRP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 370 through 383 Processing helix chain 'C' and resid 383 through 391 removed outlier: 3.956A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 395 through 411 removed outlier: 3.559A pdb=" N GLU C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP C 411 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 21 removed outlier: 3.837A pdb=" N ARG A 18 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 50 removed outlier: 3.880A pdb=" N ASP A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.554A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 141 Processing helix chain 'A' and resid 146 through 165 Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.856A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 258 through 285 removed outlier: 3.582A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 346 removed outlier: 4.331A pdb=" N ARG A 346 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 370 through 383 Processing helix chain 'A' and resid 383 through 391 removed outlier: 4.092A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 411 removed outlier: 3.555A pdb=" N GLU A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.589A pdb=" N ARG B 18 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 146 removed outlier: 5.148A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.971A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.948A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 258 through 285 removed outlier: 4.130A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 289 removed outlier: 3.641A pdb=" N ILE B 289 " --> pdb=" O VAL B 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 289' Processing helix chain 'B' and resid 314 through 346 removed outlier: 4.169A pdb=" N ARG B 346 " --> pdb=" O TRP B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 370 through 383 Processing helix chain 'B' and resid 383 through 391 removed outlier: 4.247A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 removed outlier: 3.540A pdb=" N GLU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 21 removed outlier: 4.211A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 124 through 141 removed outlier: 3.583A pdb=" N LEU D 128 " --> pdb=" O TYR D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 3.837A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 4.389A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 258 through 285 removed outlier: 4.030A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 346 removed outlier: 4.162A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 370 through 383 Processing helix chain 'D' and resid 383 through 391 removed outlier: 3.958A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 395 through 411 removed outlier: 3.620A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 20 removed outlier: 4.139A pdb=" N ILE E 19 " --> pdb=" O THR E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 143 through 158 Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 165 through 182 removed outlier: 3.566A pdb=" N ASN E 182 " --> pdb=" O MET E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 186 Processing helix chain 'E' and resid 187 through 206 Processing helix chain 'E' and resid 207 through 216 removed outlier: 4.017A pdb=" N THR E 211 " --> pdb=" O SER E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 300 removed outlier: 3.541A pdb=" N ALA E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 329 removed outlier: 3.999A pdb=" N ASN E 329 " --> pdb=" O CYS E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 391 removed outlier: 3.543A pdb=" N ILE E 391 " --> pdb=" O TRP E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 405 Processing helix chain 'E' and resid 415 through 428 Processing helix chain 'E' and resid 428 through 439 removed outlier: 4.225A pdb=" N SER E 432 " --> pdb=" O ASP E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 456 Processing helix chain 'F' and resid 16 through 20 removed outlier: 3.820A pdb=" N ILE F 19 " --> pdb=" O THR F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 46 Processing helix chain 'F' and resid 143 through 157 Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 165 through 181 Processing helix chain 'F' and resid 187 through 207 Processing helix chain 'F' and resid 207 through 216 removed outlier: 3.960A pdb=" N THR F 211 " --> pdb=" O SER F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 300 Processing helix chain 'F' and resid 303 through 328 Processing helix chain 'F' and resid 329 through 331 No H-bonds generated for 'chain 'F' and resid 329 through 331' Processing helix chain 'F' and resid 344 through 349 Processing helix chain 'F' and resid 360 through 391 removed outlier: 3.913A pdb=" N ILE F 391 " --> pdb=" O TRP F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 405 Processing helix chain 'F' and resid 415 through 428 removed outlier: 3.586A pdb=" N LEU F 421 " --> pdb=" O PHE F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 440 removed outlier: 3.512A pdb=" N SER F 432 " --> pdb=" O ASP F 428 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU F 439 " --> pdb=" O PHE F 435 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER F 440 " --> pdb=" O GLY F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 456 removed outlier: 3.556A pdb=" N GLU F 444 " --> pdb=" O SER F 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'E' and resid 52 through 56 removed outlier: 3.512A pdb=" N VAL E 53 " --> pdb=" O THR E 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 395 through 396 Processing sheet with id=AA8, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AA9, first strand: chain 'F' and resid 395 through 396 1087 hydrogen bonds defined for protein. 3183 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: 4.39 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2600 1.32 - 1.45: 4720 1.45 - 1.57: 9193 1.57 - 1.69: 18 1.69 - 1.81: 149 Bond restraints: 16680 Sorted by residual: bond pdb=" C18 PEE E 901 " pdb=" C19 PEE E 901 " ideal model delta sigma weight residual 1.523 1.306 0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C18 PEE C 902 " pdb=" C19 PEE C 902 " ideal model delta sigma weight residual 1.523 1.306 0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C38 PEE A 901 " pdb=" C39 PEE A 901 " ideal model delta sigma weight residual 1.523 1.307 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C18 PEE C 904 " pdb=" C19 PEE C 904 " ideal model delta sigma weight residual 1.523 1.307 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C18 PEE B 902 " pdb=" C19 PEE B 902 " ideal model delta sigma weight residual 1.523 1.307 0.216 2.00e-02 2.50e+03 1.17e+02 ... (remaining 16675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 22353 3.24 - 6.49: 44 6.49 - 9.73: 3 9.73 - 12.98: 42 12.98 - 16.22: 17 Bond angle restraints: 22459 Sorted by residual: angle pdb=" C38 PEE A 901 " pdb=" C39 PEE A 901 " pdb=" C40 PEE A 901 " ideal model delta sigma weight residual 112.47 128.69 -16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" C38 PEE C 901 " pdb=" C39 PEE C 901 " pdb=" C40 PEE C 901 " ideal model delta sigma weight residual 112.47 127.40 -14.93 3.00e+00 1.11e-01 2.48e+01 angle pdb=" C37 PEE A 901 " pdb=" C38 PEE A 901 " pdb=" C39 PEE A 901 " ideal model delta sigma weight residual 114.27 128.63 -14.36 3.00e+00 1.11e-01 2.29e+01 angle pdb=" O3P PEE F 901 " pdb=" P PEE F 901 " pdb=" O4P PEE F 901 " ideal model delta sigma weight residual 92.91 107.00 -14.09 3.00e+00 1.11e-01 2.21e+01 angle pdb=" C38 PEE F 901 " pdb=" C39 PEE F 901 " pdb=" C40 PEE F 901 " ideal model delta sigma weight residual 112.47 126.07 -13.60 3.00e+00 1.11e-01 2.06e+01 ... (remaining 22454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.62: 9757 31.62 - 63.24: 177 63.24 - 94.86: 8 94.86 - 126.48: 12 126.48 - 158.10: 3 Dihedral angle restraints: 9957 sinusoidal: 4320 harmonic: 5637 Sorted by residual: dihedral pdb=" C12 PEE A 903 " pdb=" C10 PEE A 903 " pdb=" C11 PEE A 903 " pdb=" O4 PEE A 903 " ideal model delta sinusoidal sigma weight residual -19.47 -177.57 158.10 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C32 PEE A 901 " pdb=" C30 PEE A 901 " pdb=" C31 PEE A 901 " pdb=" O3 PEE A 901 " ideal model delta sinusoidal sigma weight residual 161.16 6.70 154.46 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C4 PEE A 901 " pdb=" O4P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sinusoidal sigma weight residual -75.78 76.75 -152.53 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 9954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1706 0.035 - 0.069: 564 0.069 - 0.104: 93 0.104 - 0.138: 41 0.138 - 0.173: 4 Chirality restraints: 2408 Sorted by residual: chirality pdb=" C2 PEE A 901 " pdb=" C1 PEE A 901 " pdb=" C3 PEE A 901 " pdb=" O2 PEE A 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.50 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" C2 PEE D 902 " pdb=" C1 PEE D 902 " pdb=" C3 PEE D 902 " pdb=" O2 PEE D 902 " both_signs ideal model delta sigma weight residual False -2.33 -2.49 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" C2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C3 PEE C 901 " pdb=" O2 PEE C 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.49 0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 2405 not shown) Planarity restraints: 2676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PEE F 901 " -0.045 2.00e-02 2.50e+03 2.60e-02 6.74e+00 pdb=" C11 PEE F 901 " 0.012 2.00e-02 2.50e+03 pdb=" O2 PEE F 901 " 0.014 2.00e-02 2.50e+03 pdb=" O4 PEE F 901 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PEE A 901 " -0.020 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C11 PEE A 901 " 0.006 2.00e-02 2.50e+03 pdb=" O2 PEE A 901 " 0.006 2.00e-02 2.50e+03 pdb=" O4 PEE A 901 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PEE C 904 " -0.019 2.00e-02 2.50e+03 1.10e-02 1.21e+00 pdb=" C11 PEE C 904 " 0.005 2.00e-02 2.50e+03 pdb=" O2 PEE C 904 " 0.006 2.00e-02 2.50e+03 pdb=" O4 PEE C 904 " 0.008 2.00e-02 2.50e+03 ... (remaining 2673 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3507 2.78 - 3.31: 15304 3.31 - 3.84: 27745 3.84 - 4.37: 31087 4.37 - 4.90: 55435 Nonbonded interactions: 133078 Sorted by model distance: nonbonded pdb=" OG1 THR B 303 " pdb=" OH TYR B 308 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR D 351 " pdb=" OD2 ASP D 380 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR F 396 " pdb=" OD2 ASP F 425 " model vdw 2.306 3.040 nonbonded pdb=" O VAL C 47 " pdb=" NE2 GLN D 49 " model vdw 2.319 3.120 nonbonded pdb=" OD2 ASP C 50 " pdb=" OH TYR C 114 " model vdw 2.323 3.040 ... (remaining 133073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 60 or resid 94 through 411 or (resid 901 and (n \ ame C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name O2 or name O \ 4 )) or (resid 902 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ O2 or name O4 )))) selection = (chain 'B' and (resid 15 through 60 or resid 94 through 411 or resid 901 through \ 902)) selection = (chain 'C' and (resid 15 through 60 or resid 94 through 411 or (resid 901 and (n \ ame C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C20 or name C21 or name O2 or name O \ 4 )) or (resid 902 and (name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ O2 or name O4 )))) selection = (chain 'D' and (resid 15 through 60 or resid 94 through 411 or resid 901 or (res \ id 902 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C18 or name C19 or name C20 or name O2 or name \ O4 )))) } ncs_group { reference = (chain 'E' and (resid 15 through 456 or resid 901 or (resid 902 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name O2 or name O4 )))) selection = (chain 'F' and (resid 15 through 456 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C20 or name C21 or name O2 or name O4 )) or resid 902)) } 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: 4.380 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: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.100 Set scattering table: 0.170 Process input model: 36.150 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.010 0.217 16695 Z= 0.480 Angle : 0.792 16.224 22489 Z= 0.327 Chirality : 0.037 0.173 2408 Planarity : 0.003 0.027 2676 Dihedral : 12.833 158.096 6256 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.17 % Allowed : 3.21 % Favored : 96.62 % 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: 1.85 (0.19), residues: 1837 helix: 1.85 (0.14), residues: 1314 sheet: 0.86 (0.54), residues: 103 loop : -0.64 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 24 HIS 0.004 0.001 HIS F 196 PHE 0.013 0.001 PHE F 417 TYR 0.011 0.001 TYR B 332 ARG 0.002 0.000 ARG D 403 Details of bonding type rmsd hydrogen bonds : bond 0.12053 ( 1087) hydrogen bonds : angle 4.63589 ( 3183) SS BOND : bond 0.00139 ( 15) SS BOND : angle 0.54685 ( 30) covalent geometry : bond 0.00954 (16680) covalent geometry : angle 0.79213 (22459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 485 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASP cc_start: 0.8297 (m-30) cc_final: 0.8026 (p0) REVERT: C 245 GLU cc_start: 0.8615 (tp30) cc_final: 0.8336 (mt-10) REVERT: C 252 THR cc_start: 0.8533 (t) cc_final: 0.8058 (p) REVERT: C 255 GLU cc_start: 0.7839 (tt0) cc_final: 0.7474 (tt0) REVERT: A 154 GLU cc_start: 0.8365 (tp30) cc_final: 0.7886 (tp30) REVERT: A 250 PHE cc_start: 0.8211 (t80) cc_final: 0.7727 (t80) REVERT: A 350 LYS cc_start: 0.7387 (mttt) cc_final: 0.7090 (mmtt) REVERT: A 404 GLN cc_start: 0.8518 (tp40) cc_final: 0.8231 (tp-100) REVERT: B 51 LYS cc_start: 0.8936 (ptpt) cc_final: 0.8669 (ptpp) REVERT: B 243 LEU cc_start: 0.8919 (tp) cc_final: 0.8709 (tp) REVERT: B 292 ASP cc_start: 0.8622 (p0) cc_final: 0.8333 (p0) REVERT: D 249 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8480 (mmmt) REVERT: D 371 ASP cc_start: 0.6825 (m-30) cc_final: 0.6547 (t0) REVERT: D 375 MET cc_start: 0.7690 (mtm) cc_final: 0.7192 (mtm) REVERT: E 40 ILE cc_start: 0.8572 (mt) cc_final: 0.8371 (mt) REVERT: E 196 HIS cc_start: 0.7981 (t-170) cc_final: 0.7648 (t70) REVERT: E 296 ARG cc_start: 0.8541 (ttp-170) cc_final: 0.8015 (ttp-170) REVERT: E 377 TYR cc_start: 0.7685 (t80) cc_final: 0.7409 (t80) REVERT: E 425 ASP cc_start: 0.8416 (t70) cc_final: 0.8141 (t0) REVERT: E 447 LEU cc_start: 0.8418 (tp) cc_final: 0.8155 (pp) REVERT: F 29 ASP cc_start: 0.7993 (t0) cc_final: 0.7527 (m-30) REVERT: F 46 GLN cc_start: 0.8895 (tp40) cc_final: 0.8688 (tp40) REVERT: F 47 LEU cc_start: 0.8940 (mt) cc_final: 0.8704 (mp) REVERT: F 51 GLN cc_start: 0.8327 (pt0) cc_final: 0.7929 (pm20) REVERT: F 185 PHE cc_start: 0.7200 (p90) cc_final: 0.6915 (p90) REVERT: F 284 GLN cc_start: 0.7984 (mt0) cc_final: 0.7645 (mm110) REVERT: F 291 LYS cc_start: 0.8821 (tppt) cc_final: 0.8406 (tppt) REVERT: F 296 ARG cc_start: 0.7250 (ttm-80) cc_final: 0.6871 (ttm170) REVERT: F 307 LYS cc_start: 0.6447 (tttt) cc_final: 0.6099 (mttm) REVERT: F 323 ILE cc_start: 0.8258 (mt) cc_final: 0.7986 (tt) REVERT: F 359 MET cc_start: 0.8130 (ttt) cc_final: 0.7879 (ttt) REVERT: F 379 PHE cc_start: 0.8150 (m-10) cc_final: 0.7920 (t80) REVERT: F 400 LYS cc_start: 0.8814 (mttt) cc_final: 0.8587 (tmmt) outliers start: 3 outliers final: 2 residues processed: 485 average time/residue: 0.2863 time to fit residues: 203.1027 Evaluate side-chains 296 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 294 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 435 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 2.9990 chunk 138 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 0.0470 chunk 106 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 HIS A 253 HIS B 404 GLN D 46 GLN D 104 HIS D 409 ASN E 46 GLN E 151 ASN E 298 HIS F 196 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.154935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117364 restraints weight = 23903.067| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.10 r_work: 0.3409 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16695 Z= 0.126 Angle : 0.475 7.579 22489 Z= 0.252 Chirality : 0.038 0.164 2408 Planarity : 0.003 0.050 2676 Dihedral : 12.185 165.985 2488 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.29 % Allowed : 11.01 % Favored : 86.70 % 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: 2.22 (0.19), residues: 1837 helix: 2.12 (0.14), residues: 1323 sheet: 1.12 (0.51), residues: 103 loop : -0.58 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 184 HIS 0.010 0.001 HIS A 253 PHE 0.024 0.001 PHE E 185 TYR 0.019 0.001 TYR F 187 ARG 0.004 0.000 ARG E 402 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 1087) hydrogen bonds : angle 3.61027 ( 3183) SS BOND : bond 0.00280 ( 15) SS BOND : angle 0.70733 ( 30) covalent geometry : bond 0.00281 (16680) covalent geometry : angle 0.47492 (22459) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 312 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 THR cc_start: 0.8778 (m) cc_final: 0.8533 (p) REVERT: C 153 LEU cc_start: 0.9081 (mt) cc_final: 0.8796 (mp) REVERT: C 165 ASP cc_start: 0.8510 (m-30) cc_final: 0.8120 (p0) REVERT: C 252 THR cc_start: 0.8767 (t) cc_final: 0.8442 (p) REVERT: C 411 TRP cc_start: 0.5228 (t-100) cc_final: 0.3276 (p-90) REVERT: A 127 TYR cc_start: 0.8855 (m-10) cc_final: 0.8204 (m-80) REVERT: D 153 LEU cc_start: 0.8669 (mt) cc_final: 0.8361 (mt) REVERT: D 249 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8492 (mmmt) REVERT: D 371 ASP cc_start: 0.6649 (m-30) cc_final: 0.5879 (t0) REVERT: D 375 MET cc_start: 0.7896 (mtm) cc_final: 0.7243 (mtm) REVERT: E 184 TRP cc_start: 0.8070 (p-90) cc_final: 0.7805 (p-90) REVERT: E 195 GLU cc_start: 0.8571 (pt0) cc_final: 0.8286 (tp30) REVERT: E 196 HIS cc_start: 0.8122 (t-170) cc_final: 0.7518 (t70) REVERT: E 295 PHE cc_start: 0.7398 (t80) cc_final: 0.7018 (t80) REVERT: E 425 ASP cc_start: 0.8607 (t70) cc_final: 0.8158 (t0) REVERT: E 447 LEU cc_start: 0.8417 (tp) cc_final: 0.8140 (pp) REVERT: F 29 ASP cc_start: 0.7967 (t0) cc_final: 0.7509 (m-30) REVERT: F 46 GLN cc_start: 0.8687 (tp40) cc_final: 0.8328 (tp40) REVERT: F 51 GLN cc_start: 0.8478 (pt0) cc_final: 0.8022 (pm20) REVERT: F 359 MET cc_start: 0.8005 (ttt) cc_final: 0.7565 (ttt) REVERT: F 379 PHE cc_start: 0.8215 (m-10) cc_final: 0.7943 (t80) REVERT: F 382 LEU cc_start: 0.8516 (mt) cc_final: 0.8271 (tt) REVERT: F 400 LYS cc_start: 0.8724 (mttt) cc_final: 0.8437 (tttm) outliers start: 40 outliers final: 26 residues processed: 339 average time/residue: 0.2831 time to fit residues: 143.5532 Evaluate side-chains 289 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 263 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 384 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 93 optimal weight: 4.9990 chunk 171 optimal weight: 0.2980 chunk 139 optimal weight: 1.9990 chunk 34 optimal weight: 0.0570 chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 HIS A 253 HIS A 404 GLN B 404 GLN D 104 HIS D 400 ASN E 151 ASN E 284 GLN E 298 HIS F 445 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.150759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111339 restraints weight = 24245.704| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.38 r_work: 0.3303 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16695 Z= 0.123 Angle : 0.461 8.964 22489 Z= 0.246 Chirality : 0.038 0.171 2408 Planarity : 0.003 0.031 2676 Dihedral : 11.135 171.732 2486 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.52 % Allowed : 12.04 % Favored : 85.44 % 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: 2.36 (0.19), residues: 1837 helix: 2.22 (0.14), residues: 1325 sheet: 1.12 (0.48), residues: 105 loop : -0.54 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 184 HIS 0.011 0.001 HIS A 253 PHE 0.026 0.001 PHE D 393 TYR 0.017 0.001 TYR E 377 ARG 0.003 0.000 ARG E 448 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 1087) hydrogen bonds : angle 3.54684 ( 3183) SS BOND : bond 0.00352 ( 15) SS BOND : angle 0.80213 ( 30) covalent geometry : bond 0.00278 (16680) covalent geometry : angle 0.46001 (22459) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 THR cc_start: 0.8935 (m) cc_final: 0.8471 (p) REVERT: C 165 ASP cc_start: 0.8551 (m-30) cc_final: 0.8120 (p0) REVERT: C 252 THR cc_start: 0.8758 (t) cc_final: 0.8368 (p) REVERT: C 343 MET cc_start: 0.8256 (mtm) cc_final: 0.8032 (mtm) REVERT: C 411 TRP cc_start: 0.5074 (t-100) cc_final: 0.3204 (p-90) REVERT: A 36 LEU cc_start: 0.8844 (tp) cc_final: 0.8563 (mt) REVERT: A 127 TYR cc_start: 0.8848 (m-10) cc_final: 0.8192 (m-80) REVERT: A 379 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7470 (tp) REVERT: B 245 GLU cc_start: 0.8108 (tp30) cc_final: 0.7845 (tp30) REVERT: D 239 GLN cc_start: 0.7307 (pp30) cc_final: 0.7022 (pp30) REVERT: D 371 ASP cc_start: 0.6547 (m-30) cc_final: 0.5809 (t0) REVERT: D 375 MET cc_start: 0.7706 (mtm) cc_final: 0.7033 (mtm) REVERT: E 40 ILE cc_start: 0.8480 (mt) cc_final: 0.8157 (mt) REVERT: E 184 TRP cc_start: 0.8222 (p-90) cc_final: 0.7885 (p-90) REVERT: E 196 HIS cc_start: 0.8225 (t-170) cc_final: 0.7745 (t70) REVERT: E 447 LEU cc_start: 0.8354 (tp) cc_final: 0.8090 (pp) REVERT: F 29 ASP cc_start: 0.7865 (t0) cc_final: 0.7358 (m-30) REVERT: F 37 MET cc_start: 0.8211 (mmt) cc_final: 0.7907 (mmm) REVERT: F 46 GLN cc_start: 0.8446 (tp40) cc_final: 0.8064 (tp40) REVERT: F 51 GLN cc_start: 0.8234 (pt0) cc_final: 0.7647 (pm20) REVERT: F 379 PHE cc_start: 0.8145 (m-10) cc_final: 0.7611 (t80) REVERT: F 382 LEU cc_start: 0.8449 (mt) cc_final: 0.8227 (tt) REVERT: F 400 LYS cc_start: 0.8813 (mttt) cc_final: 0.8511 (tmmt) REVERT: F 438 PHE cc_start: 0.5770 (OUTLIER) cc_final: 0.5059 (t80) outliers start: 44 outliers final: 33 residues processed: 319 average time/residue: 0.2622 time to fit residues: 127.9798 Evaluate side-chains 293 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 438 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 150 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 HIS C 312 HIS A 253 HIS B 49 GLN D 104 HIS E 46 GLN E 151 ASN E 298 HIS E 454 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.149395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109955 restraints weight = 24259.069| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.38 r_work: 0.3284 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16695 Z= 0.138 Angle : 0.471 7.456 22489 Z= 0.250 Chirality : 0.039 0.178 2408 Planarity : 0.003 0.029 2676 Dihedral : 10.700 174.554 2486 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.56 % Allowed : 12.27 % Favored : 84.17 % 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: 2.39 (0.19), residues: 1837 helix: 2.24 (0.14), residues: 1322 sheet: 1.23 (0.48), residues: 104 loop : -0.54 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 184 HIS 0.011 0.001 HIS A 253 PHE 0.026 0.001 PHE F 185 TYR 0.017 0.001 TYR E 377 ARG 0.006 0.000 ARG F 434 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 1087) hydrogen bonds : angle 3.51925 ( 3183) SS BOND : bond 0.00349 ( 15) SS BOND : angle 0.90986 ( 30) covalent geometry : bond 0.00317 (16680) covalent geometry : angle 0.47032 (22459) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 277 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 THR cc_start: 0.8974 (m) cc_final: 0.8504 (p) REVERT: C 165 ASP cc_start: 0.8512 (m-30) cc_final: 0.8125 (p0) REVERT: C 252 THR cc_start: 0.8857 (t) cc_final: 0.8483 (p) REVERT: C 411 TRP cc_start: 0.5042 (t-100) cc_final: 0.3506 (p90) REVERT: A 36 LEU cc_start: 0.8819 (tp) cc_final: 0.8488 (mt) REVERT: A 127 TYR cc_start: 0.8888 (m-10) cc_final: 0.8223 (m-80) REVERT: A 404 GLN cc_start: 0.8580 (tp40) cc_final: 0.8321 (tp40) REVERT: B 245 GLU cc_start: 0.8134 (tp30) cc_final: 0.7704 (tp30) REVERT: D 153 LEU cc_start: 0.8569 (mt) cc_final: 0.8275 (tt) REVERT: D 245 GLU cc_start: 0.8544 (tp30) cc_final: 0.8302 (tp30) REVERT: D 249 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8653 (pttt) REVERT: D 371 ASP cc_start: 0.6623 (m-30) cc_final: 0.5789 (t0) REVERT: D 375 MET cc_start: 0.7690 (mtm) cc_final: 0.6932 (mtm) REVERT: E 40 ILE cc_start: 0.8432 (mt) cc_final: 0.8229 (mt) REVERT: E 184 TRP cc_start: 0.8179 (p-90) cc_final: 0.7968 (p-90) REVERT: E 196 HIS cc_start: 0.8280 (t-170) cc_final: 0.7754 (t70) REVERT: E 447 LEU cc_start: 0.8324 (tp) cc_final: 0.8040 (pp) REVERT: F 29 ASP cc_start: 0.7964 (t0) cc_final: 0.7415 (m-30) REVERT: F 37 MET cc_start: 0.8185 (mmt) cc_final: 0.7876 (mmm) REVERT: F 46 GLN cc_start: 0.8565 (tp40) cc_final: 0.8134 (tp40) REVERT: F 51 GLN cc_start: 0.8213 (pt0) cc_final: 0.7628 (pm20) REVERT: F 359 MET cc_start: 0.8017 (ttt) cc_final: 0.7227 (ttt) REVERT: F 379 PHE cc_start: 0.8235 (m-10) cc_final: 0.7630 (t80) REVERT: F 382 LEU cc_start: 0.8474 (mt) cc_final: 0.8221 (tt) REVERT: F 400 LYS cc_start: 0.8789 (mttt) cc_final: 0.8464 (tttm) outliers start: 62 outliers final: 46 residues processed: 318 average time/residue: 0.2630 time to fit residues: 127.2769 Evaluate side-chains 300 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 254 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 384 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 107 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 HIS A 239 GLN A 253 HIS B 49 GLN D 267 GLN D 400 ASN E 151 ASN E 298 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.148586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108625 restraints weight = 24915.323| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.43 r_work: 0.3270 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16695 Z= 0.149 Angle : 0.477 8.652 22489 Z= 0.254 Chirality : 0.039 0.185 2408 Planarity : 0.003 0.029 2676 Dihedral : 10.532 175.339 2486 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.61 % Allowed : 13.19 % Favored : 83.20 % 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: 2.36 (0.19), residues: 1837 helix: 2.22 (0.14), residues: 1322 sheet: 1.29 (0.49), residues: 104 loop : -0.56 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 184 HIS 0.011 0.001 HIS A 253 PHE 0.026 0.001 PHE F 185 TYR 0.020 0.001 TYR E 155 ARG 0.002 0.000 ARG B 346 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 1087) hydrogen bonds : angle 3.53149 ( 3183) SS BOND : bond 0.00399 ( 15) SS BOND : angle 0.92510 ( 30) covalent geometry : bond 0.00346 (16680) covalent geometry : angle 0.47635 (22459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 258 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 THR cc_start: 0.8940 (m) cc_final: 0.8456 (p) REVERT: C 165 ASP cc_start: 0.8476 (m-30) cc_final: 0.8102 (p0) REVERT: C 252 THR cc_start: 0.8884 (t) cc_final: 0.8508 (p) REVERT: C 411 TRP cc_start: 0.5020 (t-100) cc_final: 0.3550 (p90) REVERT: A 36 LEU cc_start: 0.8828 (tp) cc_final: 0.8491 (mt) REVERT: A 127 TYR cc_start: 0.8882 (m-80) cc_final: 0.8244 (m-80) REVERT: D 153 LEU cc_start: 0.8737 (mt) cc_final: 0.8519 (mt) REVERT: D 245 GLU cc_start: 0.8580 (tp30) cc_final: 0.8123 (tp30) REVERT: D 371 ASP cc_start: 0.6690 (m-30) cc_final: 0.5860 (t0) REVERT: D 375 MET cc_start: 0.7649 (mtm) cc_final: 0.6888 (mtm) REVERT: E 40 ILE cc_start: 0.8452 (mt) cc_final: 0.8242 (mt) REVERT: E 184 TRP cc_start: 0.8173 (p-90) cc_final: 0.7965 (p-90) REVERT: E 196 HIS cc_start: 0.8183 (t-170) cc_final: 0.7679 (t70) REVERT: E 447 LEU cc_start: 0.8305 (tp) cc_final: 0.8023 (pp) REVERT: F 29 ASP cc_start: 0.7965 (t0) cc_final: 0.7444 (m-30) REVERT: F 37 MET cc_start: 0.8179 (mmt) cc_final: 0.7870 (mmm) REVERT: F 46 GLN cc_start: 0.8543 (tp40) cc_final: 0.8050 (tp40) REVERT: F 51 GLN cc_start: 0.8163 (pt0) cc_final: 0.7600 (pm20) REVERT: F 359 MET cc_start: 0.7915 (ttt) cc_final: 0.7053 (ttt) REVERT: F 379 PHE cc_start: 0.8278 (m-10) cc_final: 0.7618 (t80) REVERT: F 382 LEU cc_start: 0.8488 (mt) cc_final: 0.8221 (tt) REVERT: F 400 LYS cc_start: 0.8800 (mttt) cc_final: 0.8473 (tttm) REVERT: F 438 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5139 (t80) outliers start: 63 outliers final: 51 residues processed: 304 average time/residue: 0.2780 time to fit residues: 129.5511 Evaluate side-chains 298 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 246 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 438 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 144 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 15 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: C 155 HIS A 253 HIS B 49 GLN D 267 GLN E 46 GLN E 151 ASN E 298 HIS E 332 ASN E 445 ASN F 284 GLN F 445 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.146792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107004 restraints weight = 24687.315| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.40 r_work: 0.3240 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16695 Z= 0.194 Angle : 0.516 9.767 22489 Z= 0.274 Chirality : 0.040 0.191 2408 Planarity : 0.003 0.028 2676 Dihedral : 10.780 175.355 2486 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.01 % Allowed : 13.36 % Favored : 82.63 % 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: 2.17 (0.19), residues: 1837 helix: 2.09 (0.14), residues: 1321 sheet: 1.23 (0.50), residues: 105 loop : -0.68 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 184 HIS 0.012 0.001 HIS A 253 PHE 0.027 0.002 PHE D 250 TYR 0.019 0.001 TYR E 377 ARG 0.002 0.000 ARG B 346 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 1087) hydrogen bonds : angle 3.63148 ( 3183) SS BOND : bond 0.00444 ( 15) SS BOND : angle 0.98893 ( 30) covalent geometry : bond 0.00455 (16680) covalent geometry : angle 0.51478 (22459) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 250 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8563 (pm20) REVERT: C 165 ASP cc_start: 0.8539 (m-30) cc_final: 0.8157 (p0) REVERT: C 252 THR cc_start: 0.8868 (t) cc_final: 0.8523 (p) REVERT: C 411 TRP cc_start: 0.5045 (t-100) cc_final: 0.3540 (p90) REVERT: B 245 GLU cc_start: 0.8196 (tp30) cc_final: 0.7816 (tp30) REVERT: D 245 GLU cc_start: 0.8635 (tp30) cc_final: 0.8342 (tp30) REVERT: D 249 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8556 (pttt) REVERT: D 371 ASP cc_start: 0.6825 (m-30) cc_final: 0.5927 (t0) REVERT: D 375 MET cc_start: 0.7733 (mtm) cc_final: 0.6939 (mtm) REVERT: D 411 TRP cc_start: 0.1966 (OUTLIER) cc_final: 0.1245 (p-90) REVERT: E 40 ILE cc_start: 0.8538 (mt) cc_final: 0.8292 (mt) REVERT: E 184 TRP cc_start: 0.8277 (p-90) cc_final: 0.8075 (p-90) REVERT: E 196 HIS cc_start: 0.8193 (t-170) cc_final: 0.7697 (t70) REVERT: E 294 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8645 (mttt) REVERT: F 29 ASP cc_start: 0.8047 (t0) cc_final: 0.7606 (m-30) REVERT: F 46 GLN cc_start: 0.8441 (tp40) cc_final: 0.7927 (tp40) REVERT: F 51 GLN cc_start: 0.8420 (pt0) cc_final: 0.7731 (pm20) REVERT: F 379 PHE cc_start: 0.8306 (m-10) cc_final: 0.7649 (t80) REVERT: F 382 LEU cc_start: 0.8478 (mt) cc_final: 0.8212 (tt) REVERT: F 400 LYS cc_start: 0.8829 (mttt) cc_final: 0.8486 (tttm) REVERT: F 438 PHE cc_start: 0.5952 (OUTLIER) cc_final: 0.5174 (t80) outliers start: 70 outliers final: 56 residues processed: 300 average time/residue: 0.2667 time to fit residues: 122.8278 Evaluate side-chains 297 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 237 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 411 TRP Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 294 LYS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 438 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 55 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 HIS A 253 HIS B 49 GLN D 49 GLN E 151 ASN E 298 HIS F 445 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.148403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.108725 restraints weight = 24582.550| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.41 r_work: 0.3267 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16695 Z= 0.140 Angle : 0.487 11.187 22489 Z= 0.260 Chirality : 0.040 0.237 2408 Planarity : 0.003 0.029 2676 Dihedral : 10.560 175.155 2486 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.38 % Allowed : 14.97 % Favored : 81.65 % 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: 2.22 (0.19), residues: 1837 helix: 2.12 (0.14), residues: 1325 sheet: 1.32 (0.50), residues: 105 loop : -0.66 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 184 HIS 0.012 0.001 HIS A 253 PHE 0.028 0.001 PHE F 185 TYR 0.021 0.001 TYR E 155 ARG 0.003 0.000 ARG E 402 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 1087) hydrogen bonds : angle 3.60343 ( 3183) SS BOND : bond 0.00341 ( 15) SS BOND : angle 0.84649 ( 30) covalent geometry : bond 0.00323 (16680) covalent geometry : angle 0.48626 (22459) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 254 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8438 (mp10) REVERT: C 165 ASP cc_start: 0.8447 (m-30) cc_final: 0.8075 (p0) REVERT: C 252 THR cc_start: 0.8797 (t) cc_final: 0.8430 (p) REVERT: C 411 TRP cc_start: 0.4962 (t-100) cc_final: 0.3473 (p-90) REVERT: B 245 GLU cc_start: 0.8068 (tp30) cc_final: 0.7803 (tp30) REVERT: D 153 LEU cc_start: 0.8767 (mt) cc_final: 0.8431 (tt) REVERT: D 245 GLU cc_start: 0.8612 (tp30) cc_final: 0.8311 (tp30) REVERT: D 249 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8628 (pttt) REVERT: D 371 ASP cc_start: 0.6668 (m-30) cc_final: 0.5845 (t0) REVERT: D 375 MET cc_start: 0.7561 (mtm) cc_final: 0.6767 (mtm) REVERT: D 411 TRP cc_start: 0.1938 (OUTLIER) cc_final: 0.1180 (p-90) REVERT: E 40 ILE cc_start: 0.8495 (mt) cc_final: 0.8243 (mt) REVERT: E 196 HIS cc_start: 0.8172 (t-170) cc_final: 0.7673 (t70) REVERT: E 294 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8727 (mttt) REVERT: F 29 ASP cc_start: 0.7972 (t0) cc_final: 0.7509 (m-30) REVERT: F 37 MET cc_start: 0.8097 (mmt) cc_final: 0.7797 (mmm) REVERT: F 46 GLN cc_start: 0.8393 (tp40) cc_final: 0.7889 (tp40) REVERT: F 51 GLN cc_start: 0.8145 (pt0) cc_final: 0.7569 (pm20) REVERT: F 379 PHE cc_start: 0.8232 (m-10) cc_final: 0.7612 (t80) REVERT: F 382 LEU cc_start: 0.8473 (mt) cc_final: 0.8220 (tt) REVERT: F 400 LYS cc_start: 0.8831 (mttt) cc_final: 0.8499 (tttm) REVERT: F 438 PHE cc_start: 0.5882 (OUTLIER) cc_final: 0.5106 (t80) outliers start: 59 outliers final: 46 residues processed: 299 average time/residue: 0.2540 time to fit residues: 115.7957 Evaluate side-chains 288 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 411 TRP Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 294 LYS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 438 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 25 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 145 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS A 253 HIS B 49 GLN D 49 GLN D 400 ASN E 151 ASN E 298 HIS ** F 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.148286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108625 restraints weight = 24580.655| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.41 r_work: 0.3269 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16695 Z= 0.135 Angle : 0.503 14.185 22489 Z= 0.263 Chirality : 0.040 0.198 2408 Planarity : 0.003 0.030 2676 Dihedral : 10.415 174.839 2486 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.67 % Allowed : 14.85 % Favored : 81.48 % 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: 2.23 (0.19), residues: 1837 helix: 2.11 (0.14), residues: 1326 sheet: 1.30 (0.50), residues: 105 loop : -0.62 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 184 HIS 0.013 0.001 HIS A 253 PHE 0.027 0.001 PHE F 185 TYR 0.017 0.001 TYR E 377 ARG 0.004 0.000 ARG E 402 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 1087) hydrogen bonds : angle 3.59640 ( 3183) SS BOND : bond 0.00323 ( 15) SS BOND : angle 0.80784 ( 30) covalent geometry : bond 0.00311 (16680) covalent geometry : angle 0.50262 (22459) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 252 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASP cc_start: 0.8446 (m-30) cc_final: 0.8087 (p0) REVERT: C 252 THR cc_start: 0.8813 (t) cc_final: 0.8449 (p) REVERT: C 411 TRP cc_start: 0.4950 (t-100) cc_final: 0.3454 (p-90) REVERT: A 265 MET cc_start: 0.7850 (tpt) cc_final: 0.7611 (tpp) REVERT: B 245 GLU cc_start: 0.8107 (tp30) cc_final: 0.7833 (tp30) REVERT: D 153 LEU cc_start: 0.8888 (mt) cc_final: 0.8545 (tt) REVERT: D 245 GLU cc_start: 0.8600 (tp30) cc_final: 0.8306 (tp30) REVERT: D 249 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8674 (pttt) REVERT: D 371 ASP cc_start: 0.6640 (m-30) cc_final: 0.5826 (t0) REVERT: D 375 MET cc_start: 0.7532 (mtm) cc_final: 0.6757 (mtm) REVERT: D 411 TRP cc_start: 0.1869 (OUTLIER) cc_final: 0.1130 (p-90) REVERT: E 40 ILE cc_start: 0.8504 (mt) cc_final: 0.8258 (mt) REVERT: E 196 HIS cc_start: 0.8197 (t-170) cc_final: 0.7656 (t70) REVERT: E 294 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8672 (mttm) REVERT: E 324 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7158 (mm) REVERT: F 29 ASP cc_start: 0.7931 (t0) cc_final: 0.7466 (m-30) REVERT: F 37 MET cc_start: 0.8044 (mmt) cc_final: 0.7754 (mmm) REVERT: F 46 GLN cc_start: 0.8328 (tp40) cc_final: 0.7736 (tp40) REVERT: F 51 GLN cc_start: 0.8138 (pt0) cc_final: 0.7566 (pm20) REVERT: F 379 PHE cc_start: 0.8234 (m-10) cc_final: 0.7597 (t80) REVERT: F 382 LEU cc_start: 0.8472 (mt) cc_final: 0.8226 (tt) REVERT: F 400 LYS cc_start: 0.8830 (mttt) cc_final: 0.8494 (tttm) REVERT: F 434 ARG cc_start: 0.7562 (ttm-80) cc_final: 0.7145 (ttp80) REVERT: F 438 PHE cc_start: 0.5770 (OUTLIER) cc_final: 0.5012 (t80) outliers start: 64 outliers final: 52 residues processed: 300 average time/residue: 0.2545 time to fit residues: 116.9462 Evaluate side-chains 293 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 237 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 411 TRP Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 294 LYS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 438 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 166 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 0.0970 chunk 116 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 130 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS A 253 HIS D 49 GLN E 46 GLN E 151 ASN E 298 HIS E 445 ASN E 454 HIS ** F 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.148979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109576 restraints weight = 24750.886| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.42 r_work: 0.3277 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16695 Z= 0.127 Angle : 0.509 12.908 22489 Z= 0.267 Chirality : 0.040 0.199 2408 Planarity : 0.003 0.029 2676 Dihedral : 10.275 174.746 2486 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.50 % Allowed : 15.14 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.19), residues: 1837 helix: 2.13 (0.14), residues: 1326 sheet: 1.40 (0.51), residues: 105 loop : -0.62 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 184 HIS 0.013 0.001 HIS A 253 PHE 0.028 0.001 PHE F 185 TYR 0.020 0.001 TYR E 155 ARG 0.007 0.000 ARG E 402 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 1087) hydrogen bonds : angle 3.59227 ( 3183) SS BOND : bond 0.00306 ( 15) SS BOND : angle 0.80578 ( 30) covalent geometry : bond 0.00291 (16680) covalent geometry : angle 0.50829 (22459) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 243 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASP cc_start: 0.8448 (m-30) cc_final: 0.8094 (p0) REVERT: C 252 THR cc_start: 0.8816 (t) cc_final: 0.8451 (p) REVERT: C 411 TRP cc_start: 0.4940 (t-100) cc_final: 0.3433 (p-90) REVERT: B 245 GLU cc_start: 0.8095 (tp30) cc_final: 0.7807 (tp30) REVERT: D 153 LEU cc_start: 0.8861 (mt) cc_final: 0.8474 (tt) REVERT: D 245 GLU cc_start: 0.8595 (tp30) cc_final: 0.8303 (tp30) REVERT: D 249 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8687 (pttt) REVERT: D 371 ASP cc_start: 0.6616 (m-30) cc_final: 0.5962 (t0) REVERT: D 375 MET cc_start: 0.7526 (mtm) cc_final: 0.6853 (mtm) REVERT: D 411 TRP cc_start: 0.1780 (OUTLIER) cc_final: 0.1023 (p-90) REVERT: E 40 ILE cc_start: 0.8490 (mt) cc_final: 0.8234 (mt) REVERT: E 184 TRP cc_start: 0.8142 (p-90) cc_final: 0.7900 (p-90) REVERT: E 196 HIS cc_start: 0.8194 (t-170) cc_final: 0.7674 (t70) REVERT: E 294 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8737 (mttm) REVERT: E 296 ARG cc_start: 0.8340 (ttp-170) cc_final: 0.7986 (ttp-110) REVERT: E 324 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7093 (mm) REVERT: F 29 ASP cc_start: 0.7921 (t0) cc_final: 0.7336 (m-30) REVERT: F 37 MET cc_start: 0.8026 (mmt) cc_final: 0.7733 (mmm) REVERT: F 51 GLN cc_start: 0.8084 (pt0) cc_final: 0.7513 (pm20) REVERT: F 291 LYS cc_start: 0.8277 (mmmt) cc_final: 0.8042 (ptpp) REVERT: F 379 PHE cc_start: 0.8218 (m-10) cc_final: 0.7580 (t80) REVERT: F 382 LEU cc_start: 0.8477 (mt) cc_final: 0.8226 (tt) REVERT: F 400 LYS cc_start: 0.8871 (mttt) cc_final: 0.8533 (tttm) REVERT: F 438 PHE cc_start: 0.5475 (OUTLIER) cc_final: 0.4743 (t80) outliers start: 61 outliers final: 49 residues processed: 291 average time/residue: 0.2906 time to fit residues: 132.2594 Evaluate side-chains 290 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 411 TRP Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LYS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 438 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 39 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 127 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN C 155 HIS A 253 HIS D 49 GLN D 267 GLN E 151 ASN E 298 HIS E 445 ASN E 454 HIS ** F 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.148828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109275 restraints weight = 24826.664| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.40 r_work: 0.3281 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16695 Z= 0.130 Angle : 0.513 12.507 22489 Z= 0.270 Chirality : 0.040 0.202 2408 Planarity : 0.003 0.029 2676 Dihedral : 10.187 174.674 2486 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.56 % Allowed : 15.19 % Favored : 81.25 % 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: 2.25 (0.19), residues: 1837 helix: 2.11 (0.14), residues: 1326 sheet: 1.34 (0.50), residues: 107 loop : -0.57 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 168 HIS 0.014 0.001 HIS A 253 PHE 0.030 0.001 PHE F 185 TYR 0.022 0.001 TYR E 377 ARG 0.006 0.000 ARG E 402 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 1087) hydrogen bonds : angle 3.58986 ( 3183) SS BOND : bond 0.00312 ( 15) SS BOND : angle 0.81858 ( 30) covalent geometry : bond 0.00297 (16680) covalent geometry : angle 0.51265 (22459) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 242 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASP cc_start: 0.8450 (m-30) cc_final: 0.8093 (p0) REVERT: C 252 THR cc_start: 0.8814 (t) cc_final: 0.8445 (p) REVERT: C 411 TRP cc_start: 0.4948 (t-100) cc_final: 0.3436 (p-90) REVERT: A 265 MET cc_start: 0.7799 (tpt) cc_final: 0.7450 (tpt) REVERT: B 245 GLU cc_start: 0.8088 (tp30) cc_final: 0.7808 (tp30) REVERT: D 153 LEU cc_start: 0.8857 (mt) cc_final: 0.8526 (tt) REVERT: D 245 GLU cc_start: 0.8612 (tp30) cc_final: 0.8320 (tp30) REVERT: D 249 LYS cc_start: 0.9029 (mmmt) cc_final: 0.8723 (pttt) REVERT: D 371 ASP cc_start: 0.6626 (m-30) cc_final: 0.5977 (t0) REVERT: D 375 MET cc_start: 0.7552 (mtm) cc_final: 0.6866 (mtm) REVERT: D 411 TRP cc_start: 0.1760 (OUTLIER) cc_final: 0.0997 (p-90) REVERT: E 40 ILE cc_start: 0.8486 (mt) cc_final: 0.8232 (mt) REVERT: E 184 TRP cc_start: 0.8108 (p-90) cc_final: 0.7876 (p-90) REVERT: E 196 HIS cc_start: 0.8188 (t-170) cc_final: 0.7628 (t70) REVERT: E 294 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8750 (mttm) REVERT: E 296 ARG cc_start: 0.8380 (ttp-170) cc_final: 0.8028 (ttp-110) REVERT: E 324 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7057 (mm) REVERT: F 29 ASP cc_start: 0.7966 (t0) cc_final: 0.7390 (m-30) REVERT: F 51 GLN cc_start: 0.8062 (pt0) cc_final: 0.7501 (pm20) REVERT: F 291 LYS cc_start: 0.8324 (mmmt) cc_final: 0.8075 (ptpp) REVERT: F 359 MET cc_start: 0.8055 (ttt) cc_final: 0.7781 (ttt) REVERT: F 379 PHE cc_start: 0.8220 (m-10) cc_final: 0.7584 (t80) REVERT: F 382 LEU cc_start: 0.8490 (mt) cc_final: 0.8218 (tt) REVERT: F 400 LYS cc_start: 0.8851 (mttt) cc_final: 0.8494 (tttm) REVERT: F 438 PHE cc_start: 0.5500 (OUTLIER) cc_final: 0.4785 (t80) outliers start: 62 outliers final: 51 residues processed: 290 average time/residue: 0.2603 time to fit residues: 115.6042 Evaluate side-chains 293 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 238 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 411 TRP Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LYS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 326 TYR Chi-restraints excluded: chain E residue 407 PHE Chi-restraints excluded: chain E residue 435 PHE Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 438 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 0.0060 chunk 167 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS A 253 HIS B 49 GLN D 49 GLN D 400 ASN E 151 ASN E 298 HIS E 454 HIS ** F 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.148506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109079 restraints weight = 24653.174| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.39 r_work: 0.3275 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16695 Z= 0.146 Angle : 0.530 12.702 22489 Z= 0.280 Chirality : 0.040 0.197 2408 Planarity : 0.003 0.059 2676 Dihedral : 10.190 174.383 2486 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.56 % Allowed : 15.42 % Favored : 81.02 % 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: 2.21 (0.19), residues: 1837 helix: 2.08 (0.14), residues: 1324 sheet: 1.36 (0.50), residues: 107 loop : -0.57 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP A 168 HIS 0.013 0.001 HIS A 253 PHE 0.031 0.001 PHE F 185 TYR 0.022 0.001 TYR E 377 ARG 0.006 0.000 ARG E 402 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 1087) hydrogen bonds : angle 3.62750 ( 3183) SS BOND : bond 0.00326 ( 15) SS BOND : angle 0.79658 ( 30) covalent geometry : bond 0.00338 (16680) covalent geometry : angle 0.52916 (22459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8576.61 seconds wall clock time: 148 minutes 34.50 seconds (8914.50 seconds total)