Starting phenix.real_space_refine on Tue Jan 21 03:39:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dx7_47282/01_2025/9dx7_47282.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dx7_47282/01_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_47282/01_2025/9dx7_47282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dx7_47282/01_2025/9dx7_47282.map" model { file = "/net/cci-nas-00/data/ceres_data/9dx7_47282/01_2025/9dx7_47282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dx7_47282/01_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-5571/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: 10.32, per 1000 atoms: 0.64 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: 4.01 Conformation dependent library (CDL) restraints added in 1.9 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: 1.60 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: 4.67 Time building geometry restraints manager: 4.65 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: 2.950 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: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.590 Find NCS groups from input model: 0.850 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: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.180 ------------------------------------------------------------------------------- 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 16680 Z= 0.614 Angle : 0.792 16.224 22459 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 *********************** 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 : 2.152 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: 0.2927 time to fit residues: 208.2265 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 : 1.787 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117366 restraints weight = 23903.067| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.10 r_work: 0.3410 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 16680 Z= 0.180 Angle : 0.475 7.579 22459 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 *********************** 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 : 1.784 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: 0.8779 (m) cc_final: 0.8533 (p) REVERT: C 153 LEU cc_start: 0.9083 (mt) cc_final: 0.8798 (mp) REVERT: C 165 ASP cc_start: 0.8506 (m-30) cc_final: 0.8119 (p0) REVERT: C 252 THR cc_start: 0.8763 (t) cc_final: 0.8438 (p) REVERT: C 411 TRP cc_start: 0.5219 (t-100) cc_final: 0.3268 (p-90) REVERT: A 127 TYR cc_start: 0.8856 (m-10) cc_final: 0.8205 (m-80) REVERT: D 153 LEU cc_start: 0.8671 (mt) cc_final: 0.8362 (mt) REVERT: D 249 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8493 (mmmt) REVERT: D 371 ASP cc_start: 0.6652 (m-30) cc_final: 0.5880 (t0) REVERT: D 375 MET cc_start: 0.7896 (mtm) cc_final: 0.7243 (mtm) REVERT: E 184 TRP cc_start: 0.8071 (p-90) cc_final: 0.7806 (p-90) REVERT: E 195 GLU cc_start: 0.8573 (pt0) cc_final: 0.8287 (tp30) REVERT: E 196 HIS cc_start: 0.8122 (t-170) cc_final: 0.7517 (t70) REVERT: E 295 PHE cc_start: 0.7392 (t80) cc_final: 0.7013 (t80) REVERT: E 425 ASP cc_start: 0.8605 (t70) cc_final: 0.8157 (t0) REVERT: E 447 LEU cc_start: 0.8413 (tp) cc_final: 0.8134 (pp) REVERT: F 29 ASP cc_start: 0.7973 (t0) cc_final: 0.7511 (m-30) REVERT: F 46 GLN cc_start: 0.8687 (tp40) cc_final: 0.8326 (tp40) REVERT: F 51 GLN cc_start: 0.8480 (pt0) cc_final: 0.8024 (pm20) REVERT: F 359 MET cc_start: 0.8009 (ttt) cc_final: 0.7568 (ttt) REVERT: F 379 PHE cc_start: 0.8210 (m-10) cc_final: 0.7945 (t80) REVERT: F 382 LEU cc_start: 0.8517 (mt) cc_final: 0.8272 (tt) REVERT: F 400 LYS cc_start: 0.8732 (mttt) cc_final: 0.8437 (tttm) outliers start: 40 outliers final: 26 residues processed: 339 average time/residue: 0.2774 time to fit residues: 141.4269 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 : 1.785 ------------------------------------------------------------------------------- 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: 1.9990 chunk 75 optimal weight: 8.9990 chunk 113 optimal weight: 0.1980 chunk 170 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.151769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112417 restraints weight = 24190.225| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.38 r_work: 0.3321 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16680 Z= 0.157 Angle : 0.453 8.903 22459 Z= 0.242 Chirality : 0.038 0.171 2408 Planarity : 0.003 0.032 2676 Dihedral : 11.093 171.358 2486 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.35 % Allowed : 12.16 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.19), residues: 1837 helix: 2.25 (0.14), residues: 1326 sheet: 1.16 (0.48), residues: 105 loop : -0.51 (0.31), residues: 406 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 F 185 TYR 0.016 0.001 TYR E 377 ARG 0.004 0.000 ARG E 448 *********************** 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 336 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 295 time to evaluate : 1.712 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: 0.8919 (m) cc_final: 0.8472 (p) REVERT: C 165 ASP cc_start: 0.8544 (m-30) cc_final: 0.8126 (p0) REVERT: C 252 THR cc_start: 0.8753 (t) cc_final: 0.8363 (p) REVERT: C 411 TRP cc_start: 0.5072 (t-100) cc_final: 0.3205 (p-90) REVERT: A 36 LEU cc_start: 0.8823 (tp) cc_final: 0.8539 (mt) REVERT: A 127 TYR cc_start: 0.8802 (m-10) cc_final: 0.8132 (m-80) REVERT: B 245 GLU cc_start: 0.8097 (tp30) cc_final: 0.7831 (tp30) REVERT: D 239 GLN cc_start: 0.7272 (pp30) cc_final: 0.6991 (pp30) REVERT: D 371 ASP cc_start: 0.6521 (m-30) cc_final: 0.5793 (t0) REVERT: D 375 MET cc_start: 0.7673 (mtm) cc_final: 0.6978 (mtm) REVERT: E 40 ILE cc_start: 0.8470 (mt) cc_final: 0.8145 (mt) REVERT: E 184 TRP cc_start: 0.8215 (p-90) cc_final: 0.7883 (p-90) REVERT: E 196 HIS cc_start: 0.8216 (t-170) cc_final: 0.7607 (t70) REVERT: E 295 PHE cc_start: 0.7538 (t80) cc_final: 0.6751 (t80) REVERT: E 425 ASP cc_start: 0.8467 (t70) cc_final: 0.8254 (t0) REVERT: E 447 LEU cc_start: 0.8377 (tp) cc_final: 0.8116 (pp) REVERT: F 29 ASP cc_start: 0.7839 (t0) cc_final: 0.7286 (m-30) REVERT: F 37 MET cc_start: 0.8196 (mmt) cc_final: 0.7892 (mmm) REVERT: F 46 GLN cc_start: 0.8446 (tp40) cc_final: 0.7773 (tp-100) REVERT: F 51 GLN cc_start: 0.8216 (pt0) cc_final: 0.7626 (pm20) REVERT: F 359 MET cc_start: 0.7819 (ttt) cc_final: 0.7237 (ttt) REVERT: F 379 PHE cc_start: 0.8130 (m-10) cc_final: 0.7611 (t80) REVERT: F 382 LEU cc_start: 0.8441 (mt) cc_final: 0.8223 (tt) REVERT: F 400 LYS cc_start: 0.8808 (mttt) cc_final: 0.8509 (tmmt) outliers start: 41 outliers final: 31 residues processed: 321 average time/residue: 0.2635 time to fit residues: 128.6805 Evaluate side-chains 292 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 1.749 ------------------------------------------------------------------------------- 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 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 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 317 THR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 384 THR 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: 0.7980 chunk 157 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 104 HIS E 151 ASN E 298 HIS E 454 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.147813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108093 restraints weight = 24440.093| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.37 r_work: 0.3259 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16680 Z= 0.280 Angle : 0.508 9.627 22459 Z= 0.268 Chirality : 0.040 0.191 2408 Planarity : 0.003 0.028 2676 Dihedral : 10.934 174.669 2486 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.67 % Allowed : 12.39 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 1837 helix: 2.14 (0.14), residues: 1322 sheet: 1.19 (0.49), residues: 104 loop : -0.60 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 184 HIS 0.010 0.001 HIS A 253 PHE 0.026 0.001 PHE F 185 TYR 0.019 0.001 TYR E 377 ARG 0.006 0.000 ARG F 434 *********************** 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 333 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 269 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASP cc_start: 0.8611 (m-30) cc_final: 0.8181 (p0) REVERT: C 252 THR cc_start: 0.8935 (t) cc_final: 0.8581 (p) REVERT: C 411 TRP cc_start: 0.5120 (t-100) cc_final: 0.3568 (p90) REVERT: A 127 TYR cc_start: 0.8962 (m-80) cc_final: 0.8337 (m-80) REVERT: A 293 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8535 (p) REVERT: A 379 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7650 (tp) REVERT: B 51 LYS cc_start: 0.9050 (ptpt) cc_final: 0.8746 (ptpp) REVERT: B 243 LEU cc_start: 0.8788 (tp) cc_final: 0.8518 (tp) REVERT: B 245 GLU cc_start: 0.8243 (tp30) cc_final: 0.7988 (tp30) REVERT: D 153 LEU cc_start: 0.8580 (mt) cc_final: 0.8263 (tt) REVERT: D 245 GLU cc_start: 0.8554 (tp30) cc_final: 0.8168 (tp30) REVERT: D 371 ASP cc_start: 0.6788 (m-30) cc_final: 0.5882 (t0) REVERT: D 375 MET cc_start: 0.7767 (mtm) cc_final: 0.7106 (mtm) REVERT: E 184 TRP cc_start: 0.8218 (p-90) cc_final: 0.7986 (p-90) REVERT: E 196 HIS cc_start: 0.8221 (t-170) cc_final: 0.7752 (t70) REVERT: E 447 LEU cc_start: 0.8291 (tp) cc_final: 0.8008 (pp) REVERT: F 29 ASP cc_start: 0.8043 (t0) cc_final: 0.7502 (m-30) REVERT: F 46 GLN cc_start: 0.8611 (tp40) cc_final: 0.8329 (tp40) REVERT: F 51 GLN cc_start: 0.8408 (pt0) cc_final: 0.7787 (pm20) REVERT: F 379 PHE cc_start: 0.8316 (m-10) cc_final: 0.7657 (t80) REVERT: F 382 LEU cc_start: 0.8507 (mt) cc_final: 0.8250 (tt) REVERT: F 400 LYS cc_start: 0.8783 (mttt) cc_final: 0.8478 (tmmt) REVERT: F 438 PHE cc_start: 0.5871 (OUTLIER) cc_final: 0.5115 (t80) outliers start: 64 outliers final: 45 residues processed: 312 average time/residue: 0.2728 time to fit residues: 129.1206 Evaluate side-chains 300 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 252 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 293 VAL 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 280 CYS 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 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 Chi-restraints excluded: chain F residue 438 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 107 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 163 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 239 GLN A 253 HIS B 49 GLN D 104 HIS D 400 ASN E 151 ASN 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 = 0.3959 r_free = 0.3959 target = 0.149225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109633 restraints weight = 24795.025| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.41 r_work: 0.3279 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16680 Z= 0.188 Angle : 0.472 8.820 22459 Z= 0.251 Chirality : 0.039 0.192 2408 Planarity : 0.003 0.073 2676 Dihedral : 10.531 174.999 2486 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.21 % Allowed : 13.76 % Favored : 83.03 % 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: 2.34 (0.19), residues: 1837 helix: 2.21 (0.14), residues: 1322 sheet: 1.27 (0.49), residues: 104 loop : -0.61 (0.30), 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 0.019 0.001 TYR E 155 ARG 0.009 0.000 ARG A 403 *********************** 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: 56 poor density : 265 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASP cc_start: 0.8459 (m-30) cc_final: 0.8086 (p0) REVERT: C 252 THR cc_start: 0.8886 (t) cc_final: 0.8519 (p) REVERT: C 411 TRP cc_start: 0.5019 (t-100) cc_final: 0.3215 (p-90) REVERT: D 153 LEU cc_start: 0.8725 (mt) cc_final: 0.8525 (mt) REVERT: D 245 GLU cc_start: 0.8600 (tp30) cc_final: 0.8302 (tp30) REVERT: D 249 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8549 (pttt) REVERT: D 371 ASP cc_start: 0.6651 (m-30) cc_final: 0.5845 (t0) REVERT: D 375 MET cc_start: 0.7674 (mtm) cc_final: 0.6944 (mtm) REVERT: E 196 HIS cc_start: 0.8186 (t-170) cc_final: 0.7683 (t70) REVERT: E 447 LEU cc_start: 0.8297 (tp) cc_final: 0.8031 (pp) REVERT: F 29 ASP cc_start: 0.7960 (t0) cc_final: 0.7434 (m-30) REVERT: F 37 MET cc_start: 0.8173 (mmt) cc_final: 0.7868 (mmm) REVERT: F 46 GLN cc_start: 0.8503 (tp40) cc_final: 0.8242 (tp40) REVERT: F 51 GLN cc_start: 0.8146 (pt0) cc_final: 0.7585 (pm20) REVERT: F 359 MET cc_start: 0.7708 (ttt) cc_final: 0.7065 (ttt) REVERT: F 379 PHE cc_start: 0.8263 (m-10) cc_final: 0.7629 (t80) REVERT: F 400 LYS cc_start: 0.8800 (mttt) cc_final: 0.8472 (tttm) REVERT: F 438 PHE cc_start: 0.5663 (OUTLIER) cc_final: 0.4955 (t80) outliers start: 56 outliers final: 45 residues processed: 307 average time/residue: 0.2688 time to fit residues: 125.6120 Evaluate side-chains 291 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 245 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 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 D residue 95 THR 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 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 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: 3.9990 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: 0.6980 chunk 147 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 104 HIS E 151 ASN E 298 HIS F 284 GLN F 445 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.146006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106235 restraints weight = 24729.810| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.38 r_work: 0.3229 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16680 Z= 0.324 Angle : 0.540 9.637 22459 Z= 0.287 Chirality : 0.041 0.192 2408 Planarity : 0.003 0.028 2676 Dihedral : 10.922 175.344 2486 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.78 % Allowed : 13.82 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.19), residues: 1837 helix: 2.03 (0.14), residues: 1320 sheet: 1.25 (0.49), residues: 105 loop : -0.72 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 184 HIS 0.011 0.001 HIS A 253 PHE 0.025 0.002 PHE F 185 TYR 0.021 0.002 TYR E 377 ARG 0.004 0.000 ARG E 402 *********************** 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 307 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 241 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASP cc_start: 0.8493 (m-30) cc_final: 0.8111 (p0) REVERT: C 252 THR cc_start: 0.8871 (t) cc_final: 0.8525 (p) REVERT: C 411 TRP cc_start: 0.5118 (t-100) cc_final: 0.3682 (p90) REVERT: A 49 GLN cc_start: 0.8249 (mt0) cc_final: 0.8007 (mt0) REVERT: B 245 GLU cc_start: 0.8184 (tp30) cc_final: 0.7798 (tp30) REVERT: D 245 GLU cc_start: 0.8610 (tp30) cc_final: 0.8156 (tp30) REVERT: D 411 TRP cc_start: 0.2014 (OUTLIER) cc_final: 0.1279 (p-90) REVERT: E 196 HIS cc_start: 0.8274 (t-170) cc_final: 0.7749 (t70) REVERT: F 29 ASP cc_start: 0.8049 (t0) cc_final: 0.7611 (m-30) REVERT: F 45 MET cc_start: 0.8864 (tmm) cc_final: 0.8546 (tmm) REVERT: F 46 GLN cc_start: 0.8445 (tp40) cc_final: 0.7802 (tp40) REVERT: F 51 GLN cc_start: 0.8422 (pt0) cc_final: 0.7717 (pm20) REVERT: F 359 MET cc_start: 0.8268 (ttt) cc_final: 0.7350 (ttt) REVERT: F 379 PHE cc_start: 0.8293 (m-10) cc_final: 0.7657 (t80) REVERT: F 400 LYS cc_start: 0.8835 (mttt) cc_final: 0.8492 (tttm) REVERT: F 438 PHE cc_start: 0.5852 (OUTLIER) cc_final: 0.5016 (t80) outliers start: 66 outliers final: 51 residues processed: 289 average time/residue: 0.2782 time to fit residues: 122.2856 Evaluate side-chains 282 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 229 time to evaluate : 1.832 ------------------------------------------------------------------------------- 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 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 33 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 135 ILE 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 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 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 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: 0.8980 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN D 49 GLN E 151 ASN E 298 HIS E 332 ASN ** E 445 ASN ** 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 = 0.3943 r_free = 0.3943 target = 0.147773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108048 restraints weight = 24619.002| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.41 r_work: 0.3256 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16680 Z= 0.218 Angle : 0.505 10.735 22459 Z= 0.268 Chirality : 0.040 0.209 2408 Planarity : 0.003 0.029 2676 Dihedral : 10.652 174.917 2486 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.44 % Allowed : 15.02 % Favored : 81.54 % 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: 2.13 (0.19), residues: 1837 helix: 2.06 (0.14), residues: 1325 sheet: 1.20 (0.50), residues: 105 loop : -0.69 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 184 HIS 0.012 0.001 HIS A 253 PHE 0.027 0.001 PHE F 185 TYR 0.020 0.001 TYR E 155 ARG 0.008 0.000 ARG A 403 *********************** 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 308 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 248 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASP cc_start: 0.8385 (m-30) cc_final: 0.8039 (p0) REVERT: C 252 THR cc_start: 0.8799 (t) cc_final: 0.8431 (p) REVERT: C 411 TRP cc_start: 0.4964 (t-100) cc_final: 0.3478 (p-90) REVERT: B 245 GLU cc_start: 0.8074 (tp30) cc_final: 0.7812 (tp30) REVERT: D 153 LEU cc_start: 0.8767 (mt) cc_final: 0.8437 (tt) REVERT: D 245 GLU cc_start: 0.8625 (tp30) cc_final: 0.8393 (tp30) REVERT: D 249 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8514 (pptt) REVERT: D 375 MET cc_start: 0.7601 (mtm) cc_final: 0.7141 (mtm) REVERT: D 411 TRP cc_start: 0.1938 (OUTLIER) cc_final: 0.1182 (p-90) REVERT: E 196 HIS cc_start: 0.8230 (t-170) cc_final: 0.7684 (t70) REVERT: F 29 ASP cc_start: 0.7972 (t0) cc_final: 0.7527 (m-30) REVERT: F 45 MET cc_start: 0.8922 (tmm) cc_final: 0.8656 (tmm) REVERT: F 46 GLN cc_start: 0.8365 (tp40) cc_final: 0.7866 (tp40) REVERT: F 51 GLN cc_start: 0.8196 (pt0) cc_final: 0.7590 (pm20) REVERT: F 379 PHE cc_start: 0.8222 (m-10) cc_final: 0.7601 (t80) REVERT: F 382 LEU cc_start: 0.8472 (mt) cc_final: 0.8224 (tt) REVERT: F 400 LYS cc_start: 0.8836 (mttt) cc_final: 0.8499 (tttm) outliers start: 60 outliers final: 49 residues processed: 295 average time/residue: 0.2672 time to fit residues: 120.1967 Evaluate side-chains 282 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 232 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 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 33 VAL 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 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 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 205 PHE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 25 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 175 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 HIS A 253 HIS D 49 GLN E 151 ASN E 298 HIS E 445 ASN ** F 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.148340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108771 restraints weight = 24584.726| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.41 r_work: 0.3266 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16680 Z= 0.199 Angle : 0.497 11.313 22459 Z= 0.266 Chirality : 0.040 0.195 2408 Planarity : 0.003 0.031 2676 Dihedral : 10.473 174.737 2486 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.33 % Allowed : 15.19 % 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: 2.19 (0.19), residues: 1837 helix: 2.09 (0.14), residues: 1321 sheet: 1.23 (0.49), residues: 107 loop : -0.61 (0.30), residues: 409 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 0.026 0.001 PHE F 185 TYR 0.019 0.001 TYR E 377 ARG 0.008 0.000 ARG E 402 *********************** 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 305 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 247 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASP cc_start: 0.8434 (m-30) cc_final: 0.8067 (p0) REVERT: C 252 THR cc_start: 0.8816 (t) cc_final: 0.8452 (p) REVERT: C 411 TRP cc_start: 0.4968 (t-100) cc_final: 0.3475 (p-90) REVERT: B 245 GLU cc_start: 0.8045 (tp30) cc_final: 0.7780 (tp30) REVERT: D 153 LEU cc_start: 0.8895 (mt) cc_final: 0.8532 (tt) REVERT: D 245 GLU cc_start: 0.8594 (tp30) cc_final: 0.8366 (tp30) REVERT: D 249 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8564 (pptt) REVERT: D 375 MET cc_start: 0.7586 (mtm) cc_final: 0.7041 (mtm) REVERT: D 411 TRP cc_start: 0.1901 (OUTLIER) cc_final: 0.1153 (p-90) REVERT: E 196 HIS cc_start: 0.8260 (t-170) cc_final: 0.7703 (t70) REVERT: E 294 LYS cc_start: 0.8934 (mttt) cc_final: 0.8663 (mmtm) REVERT: E 324 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7149 (mm) REVERT: F 29 ASP cc_start: 0.7970 (t0) cc_final: 0.7502 (m-30) REVERT: F 37 MET cc_start: 0.8074 (mmt) cc_final: 0.7788 (mmm) REVERT: F 45 MET cc_start: 0.8868 (tmm) cc_final: 0.8604 (tmm) REVERT: F 51 GLN cc_start: 0.8116 (pt0) cc_final: 0.7549 (pm20) REVERT: F 379 PHE cc_start: 0.8225 (m-10) cc_final: 0.7600 (t80) REVERT: F 382 LEU cc_start: 0.8480 (mt) cc_final: 0.8228 (tt) REVERT: F 400 LYS cc_start: 0.8872 (mttt) cc_final: 0.8534 (tttm) outliers start: 58 outliers final: 46 residues processed: 290 average time/residue: 0.2646 time to fit residues: 117.0293 Evaluate side-chains 282 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 160 LEU 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 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 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 185 PHE 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 166 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 0.0980 chunk 116 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 D 49 GLN D 104 HIS D 267 GLN D 400 ASN E 151 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS ** F 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.149038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.109649 restraints weight = 24794.264| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.41 r_work: 0.3278 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16680 Z= 0.183 Angle : 0.493 11.955 22459 Z= 0.264 Chirality : 0.040 0.208 2408 Planarity : 0.003 0.030 2676 Dihedral : 10.295 174.662 2486 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.33 % Allowed : 15.31 % 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: 2.24 (0.19), residues: 1837 helix: 2.12 (0.14), residues: 1322 sheet: 1.29 (0.50), residues: 107 loop : -0.58 (0.30), residues: 408 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 0.028 0.001 PHE A 250 TYR 0.020 0.001 TYR E 155 ARG 0.008 0.000 ARG A 403 *********************** 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 307 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 249 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASP cc_start: 0.8430 (m-30) cc_final: 0.8074 (p0) REVERT: C 252 THR cc_start: 0.8810 (t) cc_final: 0.8440 (p) REVERT: C 411 TRP cc_start: 0.4957 (t-100) cc_final: 0.3452 (p-90) REVERT: A 394 LEU cc_start: 0.8572 (tp) cc_final: 0.8220 (tt) REVERT: B 245 GLU cc_start: 0.8084 (tp30) cc_final: 0.7805 (tp30) REVERT: D 153 LEU cc_start: 0.8882 (mt) cc_final: 0.8522 (tt) REVERT: D 245 GLU cc_start: 0.8596 (tp30) cc_final: 0.8309 (tp30) REVERT: D 249 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8629 (pttt) REVERT: D 375 MET cc_start: 0.7579 (mtm) cc_final: 0.7059 (mtm) REVERT: D 411 TRP cc_start: 0.1918 (OUTLIER) cc_final: 0.1152 (p-90) REVERT: E 184 TRP cc_start: 0.8205 (p-90) cc_final: 0.7953 (p-90) REVERT: E 196 HIS cc_start: 0.8253 (t-170) cc_final: 0.7673 (t70) REVERT: E 324 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7055 (mm) REVERT: F 29 ASP cc_start: 0.7920 (t0) cc_final: 0.7458 (m-30) REVERT: F 37 MET cc_start: 0.8046 (mmt) cc_final: 0.7756 (mmm) REVERT: F 45 MET cc_start: 0.8921 (tmm) cc_final: 0.8677 (tmm) REVERT: F 51 GLN cc_start: 0.8036 (pt0) cc_final: 0.7477 (pm20) REVERT: F 291 LYS cc_start: 0.8262 (mmmt) cc_final: 0.8034 (ptpp) REVERT: F 379 PHE cc_start: 0.8213 (m-10) cc_final: 0.7591 (t80) REVERT: F 382 LEU cc_start: 0.8499 (mt) cc_final: 0.8229 (tt) REVERT: F 400 LYS cc_start: 0.8874 (mttt) cc_final: 0.8538 (tttm) outliers start: 58 outliers final: 48 residues processed: 294 average time/residue: 0.2572 time to fit residues: 116.3534 Evaluate side-chains 290 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 240 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 160 LEU 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 307 THR 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 135 ILE Chi-restraints excluded: chain D residue 267 GLN 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 39 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 127 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 D 104 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3960 r_free = 0.3960 target = 0.149126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109616 restraints weight = 24785.268| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.44 r_work: 0.3275 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16680 Z= 0.197 Angle : 0.509 11.378 22459 Z= 0.272 Chirality : 0.040 0.209 2408 Planarity : 0.003 0.030 2676 Dihedral : 10.230 174.571 2486 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.04 % Allowed : 15.83 % Favored : 81.14 % 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: 2.19 (0.19), residues: 1837 helix: 2.08 (0.14), residues: 1322 sheet: 1.29 (0.50), residues: 107 loop : -0.57 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 184 HIS 0.013 0.001 HIS A 253 PHE 0.029 0.001 PHE F 185 TYR 0.021 0.001 TYR E 377 ARG 0.009 0.000 ARG A 403 ********************** 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 298 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 245 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 ASP cc_start: 0.8433 (m-30) cc_final: 0.8070 (p0) REVERT: C 252 THR cc_start: 0.8815 (t) cc_final: 0.8441 (p) REVERT: C 411 TRP cc_start: 0.4861 (t-100) cc_final: 0.3399 (p-90) REVERT: B 245 GLU cc_start: 0.8091 (tp30) cc_final: 0.7810 (tp30) REVERT: D 153 LEU cc_start: 0.8866 (mt) cc_final: 0.8521 (tt) REVERT: D 245 GLU cc_start: 0.8592 (tp30) cc_final: 0.8303 (tp30) REVERT: D 249 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8645 (pttt) REVERT: D 375 MET cc_start: 0.7586 (mtm) cc_final: 0.7086 (mtm) REVERT: D 411 TRP cc_start: 0.1818 (OUTLIER) cc_final: 0.1039 (p-90) REVERT: E 184 TRP cc_start: 0.8126 (p-90) cc_final: 0.7898 (p-90) REVERT: E 196 HIS cc_start: 0.8296 (t-170) cc_final: 0.7725 (t70) REVERT: E 294 LYS cc_start: 0.8990 (mptt) cc_final: 0.8746 (mmtm) REVERT: E 324 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7020 (mm) REVERT: F 29 ASP cc_start: 0.7915 (t0) cc_final: 0.7331 (m-30) REVERT: F 37 MET cc_start: 0.7995 (mmt) cc_final: 0.7702 (mmm) REVERT: F 45 MET cc_start: 0.8917 (tmm) cc_final: 0.8674 (tmm) REVERT: F 46 GLN cc_start: 0.8195 (tp40) cc_final: 0.7816 (tp40) REVERT: F 51 GLN cc_start: 0.8020 (pt0) cc_final: 0.7461 (pm20) REVERT: F 291 LYS cc_start: 0.8319 (mmmt) cc_final: 0.8093 (ptpp) REVERT: F 379 PHE cc_start: 0.8225 (m-10) cc_final: 0.7589 (t80) REVERT: F 382 LEU cc_start: 0.8493 (mt) cc_final: 0.8220 (tt) REVERT: F 400 LYS cc_start: 0.8876 (mttt) cc_final: 0.8528 (tttm) outliers start: 53 outliers final: 46 residues processed: 286 average time/residue: 0.2659 time to fit residues: 116.4984 Evaluate side-chains 286 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 160 LEU 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 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 307 THR 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 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 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 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 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: 5.9990 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 112 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 49 GLN D 104 HIS D 267 GLN E 46 GLN E 151 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 HIS E 454 HIS ** F 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.148644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.110133 restraints weight = 24739.590| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.39 r_work: 0.3296 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16680 Z= 0.170 Angle : 0.499 9.564 22459 Z= 0.267 Chirality : 0.039 0.207 2408 Planarity : 0.003 0.030 2676 Dihedral : 10.079 174.499 2486 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.15 % Allowed : 15.65 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.19), residues: 1837 helix: 2.14 (0.14), residues: 1322 sheet: 1.37 (0.50), residues: 107 loop : -0.55 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 411 HIS 0.013 0.001 HIS A 253 PHE 0.030 0.001 PHE F 185 TYR 0.022 0.001 TYR E 377 ARG 0.007 0.000 ARG D 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7902.92 seconds wall clock time: 141 minutes 34.25 seconds (8494.25 seconds total)