Starting phenix.real_space_refine on Thu Sep 18 11:06:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dx7_47282/09_2025/9dx7_47282.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dx7_47282/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dx7_47282/09_2025/9dx7_47282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dx7_47282/09_2025/9dx7_47282.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dx7_47282/09_2025/9dx7_47282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dx7_47282/09_2025/9dx7_47282.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.38, per 1000 atoms: 0.27 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: 1.38 Conformation dependent library (CDL) restraints added in 699.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.48 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: 2.64 Time building geometry restraints manager: 1.85 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 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 901 or (resid 902 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 O2 or name O4 )))) } ncs_group { reference = (chain 'E' and (resid 15 through 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 C17 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: 6.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.570 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.217 16695 Z= 0.480 Angle : 0.792 16.224 22489 Z= 0.327 Chirality : 0.037 0.173 2408 Planarity : 0.003 0.027 2676 Dihedral : 12.833 158.096 6256 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.54 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG D 403 TYR 0.011 0.001 TYR B 332 PHE 0.013 0.001 PHE F 417 TRP 0.012 0.001 TRP B 24 HIS 0.004 0.001 HIS F 196 Details of bonding type rmsd covalent geometry : bond 0.00954 (16680) covalent geometry : angle 0.79213 (22459) SS BOND : bond 0.00139 ( 15) SS BOND : angle 0.54685 ( 30) hydrogen bonds : bond 0.12053 ( 1087) hydrogen bonds : angle 4.63589 ( 3183) *********************** 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 : 0.730 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: 0.8025 (p0) REVERT: C 245 GLU cc_start: 0.8615 (tp30) cc_final: 0.8337 (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: 0.8482 (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: 0.8370 (mt) REVERT: E 196 HIS cc_start: 0.7981 (t-170) cc_final: 0.7648 (t70) 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: 0.8156 (pp) REVERT: F 29 ASP cc_start: 0.7993 (t0) cc_final: 0.7529 (m-30) REVERT: F 46 GLN cc_start: 0.8895 (tp40) cc_final: 0.8690 (tp40) REVERT: F 47 LEU cc_start: 0.8940 (mt) cc_final: 0.8703 (mp) REVERT: F 51 GLN cc_start: 0.8327 (pt0) cc_final: 0.7930 (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: 0.8411 (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: 0.6103 (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: 0.7877 (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: 0.1258 time to fit residues: 90.6968 Evaluate side-chains 294 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 149 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 ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS B 404 GLN D 46 GLN D 104 HIS D 409 ASN E 151 ASN E 298 HIS F 196 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.154146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116427 restraints weight = 23966.236| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.12 r_work: 0.3389 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16695 Z= 0.139 Angle : 0.484 6.915 22489 Z= 0.257 Chirality : 0.039 0.169 2408 Planarity : 0.003 0.050 2676 Dihedral : 12.148 166.894 2488 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.52 % Allowed : 10.84 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.19), residues: 1837 helix: 2.09 (0.14), residues: 1323 sheet: 1.06 (0.51), residues: 103 loop : -0.62 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 402 TYR 0.019 0.001 TYR F 187 PHE 0.025 0.001 PHE E 185 TRP 0.026 0.001 TRP F 184 HIS 0.009 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00315 (16680) covalent geometry : angle 0.48382 (22459) SS BOND : bond 0.00543 ( 15) SS BOND : angle 0.77931 ( 30) hydrogen bonds : bond 0.03523 ( 1087) hydrogen bonds : angle 3.63523 ( 3183) *********************** 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 357 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 313 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 THR cc_start: 0.8814 (m) cc_final: 0.8550 (p) REVERT: C 153 LEU cc_start: 0.9086 (mt) cc_final: 0.8809 (mp) REVERT: C 165 ASP cc_start: 0.8488 (m-30) cc_final: 0.8090 (p0) REVERT: C 252 THR cc_start: 0.8771 (t) cc_final: 0.8448 (p) REVERT: A 127 TYR cc_start: 0.8907 (m-10) cc_final: 0.8261 (m-80) REVERT: A 350 LYS cc_start: 0.7178 (mttt) cc_final: 0.6972 (mmtt) REVERT: B 245 GLU cc_start: 0.8183 (tp30) cc_final: 0.7858 (tp30) REVERT: D 153 LEU cc_start: 0.8670 (mt) cc_final: 0.8357 (mt) REVERT: D 371 ASP cc_start: 0.6655 (m-30) cc_final: 0.5897 (t0) REVERT: D 375 MET cc_start: 0.7924 (mtm) cc_final: 0.7203 (mtm) REVERT: D 402 LEU cc_start: 0.8251 (tp) cc_final: 0.7978 (tp) REVERT: E 184 TRP cc_start: 0.8036 (p-90) cc_final: 0.7771 (p-90) REVERT: E 195 GLU cc_start: 0.8535 (pt0) cc_final: 0.8286 (tp30) REVERT: E 196 HIS cc_start: 0.8116 (t-170) cc_final: 0.7610 (t70) REVERT: E 425 ASP cc_start: 0.8570 (t70) cc_final: 0.8301 (t0) REVERT: E 447 LEU cc_start: 0.8425 (tp) cc_final: 0.8145 (pp) REVERT: F 29 ASP cc_start: 0.7961 (t0) cc_final: 0.7505 (m-30) REVERT: F 46 GLN cc_start: 0.8696 (tp40) cc_final: 0.8023 (tp40) REVERT: F 51 GLN cc_start: 0.8449 (pt0) cc_final: 0.7996 (pm20) REVERT: F 359 MET cc_start: 0.8156 (ttt) cc_final: 0.7689 (ttt) REVERT: F 379 PHE cc_start: 0.8201 (m-10) cc_final: 0.7923 (t80) REVERT: F 382 LEU cc_start: 0.8525 (mt) cc_final: 0.8271 (tt) REVERT: F 400 LYS cc_start: 0.8725 (mttt) cc_final: 0.8448 (tttm) outliers start: 44 outliers final: 29 residues processed: 341 average time/residue: 0.1304 time to fit residues: 66.9590 Evaluate side-chains 293 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 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 355 SER Chi-restraints excluded: chain A residue 379 ILE 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 D residue 329 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 332 ASN 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 139 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 49 GLN B 404 GLN D 104 HIS E 46 GLN E 151 ASN E 284 GLN E 298 HIS F 445 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.150254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112771 restraints weight = 24260.755| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.00 r_work: 0.3359 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16695 Z= 0.197 Angle : 0.521 9.246 22489 Z= 0.276 Chirality : 0.040 0.175 2408 Planarity : 0.003 0.028 2676 Dihedral : 11.410 174.344 2486 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.56 % Allowed : 11.75 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.19), residues: 1837 helix: 2.05 (0.14), residues: 1320 sheet: 0.92 (0.49), residues: 105 loop : -0.67 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 434 TYR 0.019 0.002 TYR E 377 PHE 0.033 0.002 PHE D 393 TRP 0.027 0.001 TRP F 184 HIS 0.011 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00461 (16680) covalent geometry : angle 0.52014 (22459) SS BOND : bond 0.00592 ( 15) SS BOND : angle 1.06745 ( 30) hydrogen bonds : bond 0.03614 ( 1087) hydrogen bonds : angle 3.70529 ( 3183) *********************** 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 339 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 277 time to evaluate : 0.644 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 153 LEU cc_start: 0.9166 (mt) cc_final: 0.8942 (mp) REVERT: C 165 ASP cc_start: 0.8355 (m-30) cc_final: 0.8071 (p0) REVERT: C 252 THR cc_start: 0.8732 (t) cc_final: 0.8458 (p) REVERT: A 36 LEU cc_start: 0.9111 (tp) cc_final: 0.8851 (mt) REVERT: A 127 TYR cc_start: 0.8891 (m-80) cc_final: 0.8317 (m-80) REVERT: A 379 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7888 (tp) REVERT: A 404 GLN cc_start: 0.8718 (tp40) cc_final: 0.8183 (tp-100) REVERT: B 243 LEU cc_start: 0.8971 (tp) cc_final: 0.8707 (tp) REVERT: D 239 GLN cc_start: 0.7367 (pp30) cc_final: 0.7101 (pp30) REVERT: D 245 GLU cc_start: 0.8514 (tp30) cc_final: 0.8143 (tp30) REVERT: D 371 ASP cc_start: 0.6917 (m-30) cc_final: 0.6048 (t0) REVERT: D 375 MET cc_start: 0.7864 (mtm) cc_final: 0.7084 (mtm) REVERT: D 402 LEU cc_start: 0.8308 (tp) cc_final: 0.8091 (tp) REVERT: E 184 TRP cc_start: 0.7977 (p-90) cc_final: 0.7741 (p-90) REVERT: E 196 HIS cc_start: 0.8077 (t-170) cc_final: 0.7640 (t70) REVERT: E 296 ARG cc_start: 0.8697 (ttp-110) cc_final: 0.8494 (ttp-170) REVERT: E 447 LEU cc_start: 0.8377 (tp) cc_final: 0.8108 (pp) REVERT: F 29 ASP cc_start: 0.8060 (t0) cc_final: 0.7737 (m-30) REVERT: F 46 GLN cc_start: 0.8610 (tp40) cc_final: 0.7959 (tp40) REVERT: F 51 GLN cc_start: 0.8393 (pt0) cc_final: 0.8099 (pm20) REVERT: F 379 PHE cc_start: 0.8280 (m-10) cc_final: 0.7834 (t80) REVERT: F 382 LEU cc_start: 0.8582 (mt) cc_final: 0.8376 (tt) REVERT: F 438 PHE cc_start: 0.6222 (OUTLIER) cc_final: 0.5343 (t80) outliers start: 62 outliers final: 46 residues processed: 318 average time/residue: 0.1182 time to fit residues: 58.1900 Evaluate side-chains 296 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 95 THR Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 CYS 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 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 329 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 321 ILE 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 169 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 196 HIS Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 438 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 171 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 C 312 HIS A 253 HIS B 49 GLN E 151 ASN E 298 HIS E 454 HIS F 445 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.149269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109474 restraints weight = 24588.818| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.41 r_work: 0.3279 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16695 Z= 0.128 Angle : 0.467 8.536 22489 Z= 0.249 Chirality : 0.038 0.183 2408 Planarity : 0.003 0.030 2676 Dihedral : 10.760 174.572 2486 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.21 % Allowed : 13.25 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.19), residues: 1837 helix: 2.17 (0.14), residues: 1322 sheet: 1.14 (0.49), residues: 104 loop : -0.62 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 296 TYR 0.028 0.001 TYR E 168 PHE 0.026 0.001 PHE F 185 TRP 0.026 0.001 TRP F 184 HIS 0.011 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00289 (16680) covalent geometry : angle 0.46607 (22459) SS BOND : bond 0.00377 ( 15) SS BOND : angle 0.89833 ( 30) hydrogen bonds : bond 0.03308 ( 1087) hydrogen bonds : angle 3.56885 ( 3183) *********************** 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 336 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 280 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 THR cc_start: 0.8837 (m) cc_final: 0.8591 (p) REVERT: C 165 ASP cc_start: 0.8454 (m-30) cc_final: 0.8085 (p0) REVERT: C 252 THR cc_start: 0.8757 (t) cc_final: 0.8382 (p) REVERT: A 36 LEU cc_start: 0.8813 (tp) cc_final: 0.8502 (mt) REVERT: A 127 TYR cc_start: 0.8882 (m-80) cc_final: 0.8260 (m-80) REVERT: A 403 ARG cc_start: 0.8275 (ppt170) cc_final: 0.8054 (ppt170) REVERT: A 404 GLN cc_start: 0.8617 (tp40) cc_final: 0.8374 (tp40) REVERT: B 245 GLU cc_start: 0.8149 (tp30) cc_final: 0.7878 (tp30) REVERT: D 153 LEU cc_start: 0.8601 (mt) cc_final: 0.8313 (tt) REVERT: D 245 GLU cc_start: 0.8584 (tp30) cc_final: 0.8359 (tp30) REVERT: D 249 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8553 (pptt) REVERT: D 371 ASP cc_start: 0.6649 (m-30) cc_final: 0.5853 (t0) REVERT: D 375 MET cc_start: 0.7610 (mtm) cc_final: 0.6905 (mtm) REVERT: E 184 TRP cc_start: 0.8225 (p-90) cc_final: 0.7922 (p-90) REVERT: E 196 HIS cc_start: 0.8165 (t-170) cc_final: 0.7659 (t70) REVERT: E 296 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8280 (ttp-110) REVERT: E 447 LEU cc_start: 0.8298 (tp) cc_final: 0.8023 (pp) REVERT: F 29 ASP cc_start: 0.7974 (t0) cc_final: 0.7449 (m-30) REVERT: F 51 GLN cc_start: 0.8107 (pt0) cc_final: 0.7571 (pm20) REVERT: F 379 PHE cc_start: 0.8258 (m-10) cc_final: 0.7614 (t80) REVERT: F 382 LEU cc_start: 0.8470 (mt) cc_final: 0.8237 (tt) REVERT: F 400 LYS cc_start: 0.8804 (mttt) cc_final: 0.8466 (tmmt) outliers start: 56 outliers final: 44 residues processed: 317 average time/residue: 0.1218 time to fit residues: 59.5130 Evaluate side-chains 298 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 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 356 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 45 MET Chi-restraints excluded: chain E residue 175 ILE 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 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 210 THR Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 384 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 146 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 84 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 154 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 239 GLN A 253 HIS B 49 GLN D 267 GLN D 400 ASN E 46 GLN E 151 ASN E 298 HIS E 332 ASN E 445 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.147839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.107899 restraints weight = 24701.766| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.41 r_work: 0.3253 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16695 Z= 0.163 Angle : 0.491 9.282 22489 Z= 0.260 Chirality : 0.039 0.188 2408 Planarity : 0.003 0.028 2676 Dihedral : 10.725 174.932 2486 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.73 % Allowed : 13.36 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.19), residues: 1837 helix: 2.15 (0.14), residues: 1322 sheet: 1.14 (0.49), residues: 105 loop : -0.67 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 434 TYR 0.020 0.001 TYR E 155 PHE 0.026 0.001 PHE F 185 TRP 0.026 0.001 TRP F 184 HIS 0.011 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00380 (16680) covalent geometry : angle 0.49005 (22459) SS BOND : bond 0.00373 ( 15) SS BOND : angle 0.90571 ( 30) hydrogen bonds : bond 0.03375 ( 1087) hydrogen bonds : angle 3.56954 ( 3183) *********************** 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 325 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 260 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 THR cc_start: 0.8953 (m) cc_final: 0.8585 (p) REVERT: C 165 ASP cc_start: 0.8411 (m-30) cc_final: 0.8057 (p0) REVERT: C 252 THR cc_start: 0.8755 (t) cc_final: 0.8385 (p) REVERT: A 36 LEU cc_start: 0.8842 (tp) cc_final: 0.8516 (mt) REVERT: B 245 GLU cc_start: 0.8097 (tp30) cc_final: 0.7616 (tp30) REVERT: D 153 LEU cc_start: 0.8722 (mt) cc_final: 0.8508 (mt) REVERT: D 245 GLU cc_start: 0.8556 (tp30) cc_final: 0.8350 (tp30) REVERT: D 249 LYS cc_start: 0.8929 (mmmt) cc_final: 0.8632 (pptt) REVERT: D 371 ASP cc_start: 0.6683 (m-30) cc_final: 0.5862 (t0) REVERT: D 375 MET cc_start: 0.7574 (mtm) cc_final: 0.6800 (mtm) REVERT: D 411 TRP cc_start: 0.1943 (OUTLIER) cc_final: 0.1238 (p-90) REVERT: E 184 TRP cc_start: 0.8214 (p-90) cc_final: 0.7941 (p-90) REVERT: E 196 HIS cc_start: 0.8169 (t-170) cc_final: 0.7606 (t70) REVERT: E 296 ARG cc_start: 0.8580 (ttp-110) cc_final: 0.8232 (ttp-110) REVERT: F 29 ASP cc_start: 0.7975 (t0) cc_final: 0.7549 (m-30) REVERT: F 51 GLN cc_start: 0.8136 (pt0) cc_final: 0.7551 (pm20) REVERT: F 359 MET cc_start: 0.8237 (ttt) cc_final: 0.7998 (ttt) REVERT: F 379 PHE cc_start: 0.8209 (m-10) cc_final: 0.7606 (t80) REVERT: F 382 LEU cc_start: 0.8485 (mt) cc_final: 0.8239 (tt) REVERT: F 400 LYS cc_start: 0.8827 (mttt) cc_final: 0.8494 (tttm) REVERT: F 441 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8448 (tm-30) outliers start: 65 outliers final: 53 residues processed: 305 average time/residue: 0.1232 time to fit residues: 57.3542 Evaluate side-chains 296 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 242 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 356 ILE 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 104 HIS 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 46 GLN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 91 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 157 optimal weight: 0.5980 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS A 253 HIS B 49 GLN D 267 GLN E 151 ASN E 298 HIS F 284 GLN F 445 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.148573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.108933 restraints weight = 24512.495| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.41 r_work: 0.3272 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16695 Z= 0.130 Angle : 0.474 10.397 22489 Z= 0.253 Chirality : 0.039 0.194 2408 Planarity : 0.003 0.077 2676 Dihedral : 10.533 175.097 2486 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.33 % Allowed : 14.79 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.19), residues: 1837 helix: 2.18 (0.14), residues: 1322 sheet: 1.22 (0.49), residues: 105 loop : -0.64 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 402 TYR 0.018 0.001 TYR E 377 PHE 0.026 0.001 PHE F 185 TRP 0.030 0.001 TRP F 184 HIS 0.012 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00299 (16680) covalent geometry : angle 0.47355 (22459) SS BOND : bond 0.00332 ( 15) SS BOND : angle 0.86353 ( 30) hydrogen bonds : bond 0.03279 ( 1087) hydrogen bonds : angle 3.55051 ( 3183) *********************** 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 317 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 259 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 THR cc_start: 0.8915 (m) cc_final: 0.8457 (p) REVERT: C 165 ASP cc_start: 0.8417 (m-30) cc_final: 0.8059 (p0) REVERT: C 252 THR cc_start: 0.8752 (t) cc_final: 0.8376 (p) REVERT: A 36 LEU cc_start: 0.8832 (tp) cc_final: 0.8500 (mt) REVERT: A 127 TYR cc_start: 0.8871 (m-80) cc_final: 0.8230 (m-80) REVERT: D 153 LEU cc_start: 0.8749 (mt) cc_final: 0.8509 (mt) REVERT: D 245 GLU cc_start: 0.8559 (tp30) cc_final: 0.8349 (tp30) REVERT: D 249 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8677 (pptt) REVERT: D 371 ASP cc_start: 0.6662 (m-30) cc_final: 0.5870 (t0) REVERT: D 375 MET cc_start: 0.7540 (mtm) cc_final: 0.6773 (mtm) REVERT: D 411 TRP cc_start: 0.1960 (OUTLIER) cc_final: 0.1241 (p-90) REVERT: E 184 TRP cc_start: 0.8166 (p-90) cc_final: 0.7889 (p-90) REVERT: E 196 HIS cc_start: 0.8189 (t-170) cc_final: 0.7624 (t70) REVERT: E 296 ARG cc_start: 0.8604 (ttp-110) cc_final: 0.8239 (ttp-110) REVERT: F 29 ASP cc_start: 0.7950 (t0) cc_final: 0.7426 (m-30) REVERT: F 37 MET cc_start: 0.8129 (mmt) cc_final: 0.7829 (mmm) REVERT: F 51 GLN cc_start: 0.8106 (pt0) cc_final: 0.7527 (pm20) REVERT: F 291 LYS cc_start: 0.8288 (mmmt) cc_final: 0.7996 (ptpp) REVERT: F 359 MET cc_start: 0.8139 (ttt) cc_final: 0.7900 (ttt) REVERT: F 379 PHE cc_start: 0.8218 (m-10) cc_final: 0.7596 (t80) REVERT: F 382 LEU cc_start: 0.8457 (mt) cc_final: 0.8211 (tt) REVERT: F 400 LYS cc_start: 0.8828 (mttt) cc_final: 0.8491 (tttm) REVERT: F 438 PHE cc_start: 0.5744 (OUTLIER) cc_final: 0.5295 (t80) outliers start: 58 outliers final: 49 residues processed: 304 average time/residue: 0.1169 time to fit residues: 55.3451 Evaluate side-chains 294 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 243 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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 356 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 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 135 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 411 TRP Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 78 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 267 GLN D 400 ASN E 151 ASN E 284 GLN E 298 HIS F 196 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 = 0.3939 r_free = 0.3939 target = 0.147471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107879 restraints weight = 24616.789| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.39 r_work: 0.3254 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16695 Z= 0.160 Angle : 0.508 10.905 22489 Z= 0.268 Chirality : 0.040 0.223 2408 Planarity : 0.003 0.065 2676 Dihedral : 10.595 175.041 2486 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.73 % Allowed : 14.97 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.19), residues: 1837 helix: 2.08 (0.14), residues: 1326 sheet: 1.22 (0.49), residues: 105 loop : -0.64 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 434 TYR 0.022 0.001 TYR E 155 PHE 0.026 0.001 PHE F 185 TRP 0.033 0.001 TRP F 184 HIS 0.012 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00373 (16680) covalent geometry : angle 0.50703 (22459) SS BOND : bond 0.00371 ( 15) SS BOND : angle 0.90504 ( 30) hydrogen bonds : bond 0.03373 ( 1087) hydrogen bonds : angle 3.59408 ( 3183) *********************** 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 315 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 250 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 THR cc_start: 0.8953 (m) cc_final: 0.8477 (p) REVERT: C 165 ASP cc_start: 0.8513 (m-30) cc_final: 0.8193 (t0) REVERT: C 252 THR cc_start: 0.8876 (t) cc_final: 0.8526 (p) REVERT: A 46 GLN cc_start: 0.7625 (tp40) cc_final: 0.7366 (tp40) REVERT: B 245 GLU cc_start: 0.8172 (tp30) cc_final: 0.7790 (tp30) REVERT: D 245 GLU cc_start: 0.8556 (tp30) cc_final: 0.8108 (tp30) REVERT: D 249 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8792 (mmmt) REVERT: D 253 HIS cc_start: 0.7894 (t70) cc_final: 0.7595 (t70) REVERT: D 371 ASP cc_start: 0.6834 (m-30) cc_final: 0.5981 (t0) REVERT: D 375 MET cc_start: 0.7708 (mtm) cc_final: 0.6909 (mtm) REVERT: D 411 TRP cc_start: 0.1984 (OUTLIER) cc_final: 0.1204 (p-90) REVERT: E 196 HIS cc_start: 0.8243 (t-170) cc_final: 0.7666 (t70) REVERT: E 293 ARG cc_start: 0.8288 (ttm110) cc_final: 0.8072 (ttm110) REVERT: E 296 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8251 (ttp-110) REVERT: F 29 ASP cc_start: 0.8018 (t0) cc_final: 0.7577 (m-30) REVERT: F 51 GLN cc_start: 0.8327 (pt0) cc_final: 0.7672 (pm20) REVERT: F 359 MET cc_start: 0.8341 (ttt) cc_final: 0.8070 (ttt) REVERT: F 379 PHE cc_start: 0.8289 (m-10) cc_final: 0.7634 (t80) REVERT: F 382 LEU cc_start: 0.8465 (mt) cc_final: 0.8199 (tt) REVERT: F 400 LYS cc_start: 0.8870 (mttt) cc_final: 0.8519 (tttm) REVERT: F 438 PHE cc_start: 0.5868 (OUTLIER) cc_final: 0.5265 (t80) outliers start: 65 outliers final: 54 residues processed: 300 average time/residue: 0.1190 time to fit residues: 55.5846 Evaluate side-chains 295 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 239 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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 307 THR 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 356 ILE 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 38 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 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 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 438 PHE Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 438 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 139 optimal weight: 3.9990 chunk 155 optimal weight: 0.2980 chunk 13 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS A 253 HIS B 49 GLN D 267 GLN E 151 ASN E 284 GLN E 298 HIS ** F 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.148278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108797 restraints weight = 24777.984| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.41 r_work: 0.3268 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16695 Z= 0.136 Angle : 0.500 11.681 22489 Z= 0.264 Chirality : 0.040 0.209 2408 Planarity : 0.003 0.059 2676 Dihedral : 10.447 174.820 2486 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.61 % Allowed : 15.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.19), residues: 1837 helix: 2.12 (0.14), residues: 1326 sheet: 1.25 (0.50), residues: 105 loop : -0.62 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 434 TYR 0.017 0.001 TYR E 377 PHE 0.026 0.001 PHE F 185 TRP 0.034 0.001 TRP F 184 HIS 0.013 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00313 (16680) covalent geometry : angle 0.49987 (22459) SS BOND : bond 0.00322 ( 15) SS BOND : angle 0.81405 ( 30) hydrogen bonds : bond 0.03281 ( 1087) hydrogen bonds : angle 3.58360 ( 3183) *********************** 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 315 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 252 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 THR cc_start: 0.8930 (m) cc_final: 0.8438 (p) REVERT: C 165 ASP cc_start: 0.8431 (m-30) cc_final: 0.8070 (p0) REVERT: C 252 THR cc_start: 0.8777 (t) cc_final: 0.8404 (p) REVERT: A 46 GLN cc_start: 0.7537 (tp40) cc_final: 0.7270 (tp40) REVERT: B 245 GLU cc_start: 0.8054 (tp30) cc_final: 0.7783 (tp30) REVERT: D 46 GLN cc_start: 0.7873 (tp-100) cc_final: 0.7397 (tp40) REVERT: D 153 LEU cc_start: 0.8730 (mt) cc_final: 0.8485 (tt) REVERT: D 245 GLU cc_start: 0.8555 (tp30) cc_final: 0.8098 (tp30) REVERT: D 249 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8783 (mmmt) REVERT: D 371 ASP cc_start: 0.6654 (m-30) cc_final: 0.5844 (t0) REVERT: D 375 MET cc_start: 0.7569 (mtm) cc_final: 0.6782 (mtm) REVERT: D 411 TRP cc_start: 0.1902 (OUTLIER) cc_final: 0.1157 (p-90) REVERT: E 196 HIS cc_start: 0.8235 (t-170) cc_final: 0.7642 (t70) REVERT: E 293 ARG cc_start: 0.8244 (ttm110) cc_final: 0.8024 (ttm110) REVERT: E 296 ARG cc_start: 0.8655 (ttp-110) cc_final: 0.8235 (ttp-110) REVERT: F 29 ASP cc_start: 0.7972 (t0) cc_final: 0.7506 (m-30) REVERT: F 51 GLN cc_start: 0.8114 (pt0) cc_final: 0.7538 (pm20) REVERT: F 359 MET cc_start: 0.8099 (ttt) cc_final: 0.7774 (ttt) REVERT: F 379 PHE cc_start: 0.8224 (m-10) cc_final: 0.7589 (t80) REVERT: F 382 LEU cc_start: 0.8468 (mt) cc_final: 0.8216 (tt) REVERT: F 400 LYS cc_start: 0.8840 (mttt) cc_final: 0.8550 (ttpp) REVERT: F 438 PHE cc_start: 0.5878 (OUTLIER) cc_final: 0.5311 (t80) outliers start: 63 outliers final: 56 residues processed: 302 average time/residue: 0.1182 time to fit residues: 56.1877 Evaluate side-chains 302 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 307 THR 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 356 ILE 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 339 THR Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 411 TRP Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 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 179 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 332 ASN Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 438 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 161 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 112 optimal weight: 0.0670 chunk 12 optimal weight: 0.0000 chunk 42 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 66 optimal weight: 0.0770 overall best weight: 0.3080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS A 253 HIS D 267 GLN D 400 ASN E 151 ASN E 284 GLN 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 = 0.3983 r_free = 0.3983 target = 0.151041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.112133 restraints weight = 24618.105| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.40 r_work: 0.3315 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16695 Z= 0.102 Angle : 0.482 9.861 22489 Z= 0.254 Chirality : 0.039 0.211 2408 Planarity : 0.003 0.048 2676 Dihedral : 10.017 174.998 2486 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.52 % Allowed : 16.63 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.20), residues: 1837 helix: 2.26 (0.14), residues: 1325 sheet: 1.32 (0.49), residues: 107 loop : -0.61 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 434 TYR 0.018 0.001 TYR E 155 PHE 0.030 0.001 PHE A 250 TRP 0.034 0.001 TRP F 184 HIS 0.013 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00221 (16680) covalent geometry : angle 0.48213 (22459) SS BOND : bond 0.00239 ( 15) SS BOND : angle 0.66998 ( 30) hydrogen bonds : bond 0.03065 ( 1087) hydrogen bonds : angle 3.46029 ( 3183) *********************** 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 315 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 271 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 THR cc_start: 0.8884 (m) cc_final: 0.8433 (p) REVERT: C 165 ASP cc_start: 0.8407 (m-30) cc_final: 0.8083 (p0) REVERT: C 252 THR cc_start: 0.8701 (t) cc_final: 0.8323 (p) REVERT: A 46 GLN cc_start: 0.7489 (tp40) cc_final: 0.7230 (tp40) REVERT: A 127 TYR cc_start: 0.8858 (m-80) cc_final: 0.8203 (m-80) REVERT: A 342 TRP cc_start: 0.8735 (t60) cc_final: 0.8533 (t60) REVERT: B 243 LEU cc_start: 0.8754 (tp) cc_final: 0.8456 (tp) REVERT: B 245 GLU cc_start: 0.8104 (tp30) cc_final: 0.7828 (tp30) REVERT: B 293 VAL cc_start: 0.8946 (t) cc_final: 0.8532 (t) REVERT: D 46 GLN cc_start: 0.7804 (tp-100) cc_final: 0.7299 (tp40) REVERT: D 153 LEU cc_start: 0.8818 (mt) cc_final: 0.8578 (tt) REVERT: D 245 GLU cc_start: 0.8557 (tp30) cc_final: 0.8305 (tp30) REVERT: D 249 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8723 (pttt) REVERT: D 371 ASP cc_start: 0.6672 (m-30) cc_final: 0.6044 (t0) REVERT: D 375 MET cc_start: 0.7476 (mtm) cc_final: 0.6804 (mtm) REVERT: D 411 TRP cc_start: 0.1768 (OUTLIER) cc_final: 0.1003 (p-90) REVERT: E 184 TRP cc_start: 0.8193 (p-90) cc_final: 0.7898 (p-90) REVERT: E 196 HIS cc_start: 0.8211 (t-170) cc_final: 0.7617 (t70) REVERT: E 296 ARG cc_start: 0.8655 (ttp-110) cc_final: 0.8287 (ttp-110) REVERT: F 29 ASP cc_start: 0.7913 (t0) cc_final: 0.7337 (m-30) REVERT: F 37 MET cc_start: 0.8006 (mmt) cc_final: 0.7699 (mmm) REVERT: F 51 GLN cc_start: 0.8102 (pt0) cc_final: 0.7492 (pm20) REVERT: F 166 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.7005 (t80) REVERT: F 291 LYS cc_start: 0.8287 (mmmt) cc_final: 0.8065 (ptpp) REVERT: F 359 MET cc_start: 0.8031 (ttt) cc_final: 0.7675 (ttp) REVERT: F 379 PHE cc_start: 0.8222 (m-10) cc_final: 0.7599 (t80) REVERT: F 382 LEU cc_start: 0.8454 (mt) cc_final: 0.8180 (tt) REVERT: F 400 LYS cc_start: 0.8825 (mttt) cc_final: 0.8512 (tttm) REVERT: F 438 PHE cc_start: 0.5457 (OUTLIER) cc_final: 0.4920 (t80) outliers start: 44 outliers final: 34 residues processed: 309 average time/residue: 0.1199 time to fit residues: 57.8016 Evaluate side-chains 295 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 258 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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 356 ILE Chi-restraints excluded: chain A residue 379 ILE 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 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 326 TYR Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 438 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 48 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS A 253 HIS D 253 HIS E 151 ASN E 284 GLN E 298 HIS E 454 HIS ** F 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.148615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109052 restraints weight = 24706.171| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.40 r_work: 0.3283 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16695 Z= 0.141 Angle : 0.513 9.190 22489 Z= 0.271 Chirality : 0.040 0.200 2408 Planarity : 0.003 0.045 2676 Dihedral : 10.098 174.812 2486 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.58 % Allowed : 16.69 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.19), residues: 1837 helix: 2.19 (0.14), residues: 1323 sheet: 1.26 (0.48), residues: 109 loop : -0.58 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 293 TYR 0.024 0.001 TYR B 284 PHE 0.028 0.001 PHE F 185 TRP 0.075 0.002 TRP A 168 HIS 0.013 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00327 (16680) covalent geometry : angle 0.51275 (22459) SS BOND : bond 0.00312 ( 15) SS BOND : angle 0.85869 ( 30) hydrogen bonds : bond 0.03264 ( 1087) hydrogen bonds : angle 3.53872 ( 3183) ********************** 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 300 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 THR cc_start: 0.8884 (m) cc_final: 0.8412 (p) REVERT: C 165 ASP cc_start: 0.8443 (m-30) cc_final: 0.8099 (p0) REVERT: C 252 THR cc_start: 0.8753 (t) cc_final: 0.8381 (p) REVERT: A 46 GLN cc_start: 0.7553 (tp40) cc_final: 0.7248 (tp40) REVERT: A 127 TYR cc_start: 0.8867 (m-80) cc_final: 0.8168 (m-80) REVERT: B 245 GLU cc_start: 0.8097 (tp30) cc_final: 0.7815 (tp30) REVERT: D 46 GLN cc_start: 0.7812 (tp-100) cc_final: 0.7293 (tp40) REVERT: D 153 LEU cc_start: 0.8864 (mt) cc_final: 0.8587 (tt) REVERT: D 245 GLU cc_start: 0.8575 (tp30) cc_final: 0.8321 (tp30) REVERT: D 249 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8740 (pttt) REVERT: D 371 ASP cc_start: 0.6665 (m-30) cc_final: 0.6017 (t0) REVERT: D 375 MET cc_start: 0.7533 (mtm) cc_final: 0.6781 (mtm) REVERT: D 411 TRP cc_start: 0.1929 (OUTLIER) cc_final: 0.1183 (p-90) REVERT: E 184 TRP cc_start: 0.8128 (p-90) cc_final: 0.7881 (p-90) REVERT: E 196 HIS cc_start: 0.8266 (t-170) cc_final: 0.7681 (t70) REVERT: E 293 ARG cc_start: 0.8301 (ttm110) cc_final: 0.8071 (ttm110) REVERT: E 296 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.8306 (ttp-110) REVERT: F 29 ASP cc_start: 0.7959 (t0) cc_final: 0.7384 (m-30) REVERT: F 51 GLN cc_start: 0.8097 (pt0) cc_final: 0.7480 (pm20) REVERT: F 166 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7066 (t80) REVERT: F 359 MET cc_start: 0.8087 (ttt) cc_final: 0.7725 (ttp) REVERT: F 379 PHE cc_start: 0.8185 (m-10) cc_final: 0.7607 (t80) REVERT: F 382 LEU cc_start: 0.8479 (mt) cc_final: 0.8195 (tt) REVERT: F 400 LYS cc_start: 0.8824 (mttt) cc_final: 0.8517 (tttm) REVERT: F 438 PHE cc_start: 0.5732 (OUTLIER) cc_final: 0.5153 (t80) outliers start: 45 outliers final: 39 residues processed: 293 average time/residue: 0.1215 time to fit residues: 55.2575 Evaluate side-chains 287 residues out of total 1744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 245 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 153 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 163 CYS Chi-restraints excluded: chain A residue 275 PHE 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 356 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 253 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 326 TYR 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 166 PHE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 384 THR Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 438 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 20 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 162 optimal weight: 0.0050 chunk 48 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- 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 239 GLN A 253 HIS D 253 HIS D 267 GLN D 400 ASN E 151 ASN E 284 GLN E 298 HIS E 454 HIS ** F 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.148819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109410 restraints weight = 24653.220| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.39 r_work: 0.3279 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16695 Z= 0.144 Angle : 0.513 9.200 22489 Z= 0.273 Chirality : 0.040 0.216 2408 Planarity : 0.003 0.042 2676 Dihedral : 10.113 174.328 2486 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.87 % Allowed : 16.51 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.19), residues: 1837 helix: 2.16 (0.14), residues: 1320 sheet: 1.16 (0.49), residues: 110 loop : -0.53 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 402 TYR 0.021 0.001 TYR E 155 PHE 0.030 0.001 PHE A 250 TRP 0.074 0.002 TRP A 168 HIS 0.013 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00332 (16680) covalent geometry : angle 0.51224 (22459) SS BOND : bond 0.00332 ( 15) SS BOND : angle 0.88702 ( 30) hydrogen bonds : bond 0.03305 ( 1087) hydrogen bonds : angle 3.57236 ( 3183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4074.34 seconds wall clock time: 70 minutes 49.64 seconds (4249.64 seconds total)