Starting phenix.real_space_refine on Sat Aug 23 15:27:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tul_41624/08_2025/8tul_41624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tul_41624/08_2025/8tul_41624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tul_41624/08_2025/8tul_41624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tul_41624/08_2025/8tul_41624.map" model { file = "/net/cci-nas-00/data/ceres_data/8tul_41624/08_2025/8tul_41624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tul_41624/08_2025/8tul_41624.cif" } resolution = 2.8 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= 0.005 sd= 0.268 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 Mg 14 5.21 5 S 65 5.16 5 C 8195 2.51 5 N 2150 2.21 5 O 2646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13070 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2555 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 309} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.34, per 1000 atoms: 0.18 Number of scatterers: 13070 At special positions: 0 Unit cell: (106.24, 107.07, 140.27, 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 65 16.00 Mg 14 11.99 O 2646 8.00 N 2150 7.00 C 8195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.91 Conformation dependent library (CDL) restraints added in 576.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3020 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 68.1% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.675A pdb=" N GLN A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.754A pdb=" N GLY A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 219 Proline residue: A 209 - end of helix removed outlier: 3.607A pdb=" N ALA A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 removed outlier: 3.633A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.026A pdb=" N SER A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 359 removed outlier: 3.535A pdb=" N TYR A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 112 removed outlier: 3.676A pdb=" N GLN B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.754A pdb=" N GLY B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 219 Proline residue: B 209 - end of helix removed outlier: 3.607A pdb=" N ALA B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 268 removed outlier: 3.632A pdb=" N LEU B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 removed outlier: 4.026A pdb=" N SER B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 359 removed outlier: 3.535A pdb=" N TYR B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY B 356 " --> pdb=" O PHE B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.675A pdb=" N GLN C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 165 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.754A pdb=" N GLY C 173 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 219 Proline residue: C 209 - end of helix removed outlier: 3.607A pdb=" N ALA C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 268 removed outlier: 3.632A pdb=" N LEU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 4.027A pdb=" N SER C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 359 removed outlier: 3.535A pdb=" N TYR C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY C 356 " --> pdb=" O PHE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 112 removed outlier: 3.675A pdb=" N GLN D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 165 Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.755A pdb=" N GLY D 173 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 219 Proline residue: D 209 - end of helix removed outlier: 3.607A pdb=" N ALA D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 268 removed outlier: 3.632A pdb=" N LEU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP D 273 " --> pdb=" O CYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 282 removed outlier: 4.026A pdb=" N SER D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 359 removed outlier: 3.536A pdb=" N TYR D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN D 333 " --> pdb=" O ASP D 329 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY D 356 " --> pdb=" O PHE D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 removed outlier: 3.676A pdb=" N GLN E 109 " --> pdb=" O THR E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.754A pdb=" N GLY E 173 " --> pdb=" O SER E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 219 Proline residue: E 209 - end of helix removed outlier: 3.608A pdb=" N ALA E 217 " --> pdb=" O GLU E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 261 removed outlier: 3.533A pdb=" N LEU E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 268 removed outlier: 3.632A pdb=" N LEU E 268 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 removed outlier: 3.610A pdb=" N TRP E 273 " --> pdb=" O CYS E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.026A pdb=" N SER E 282 " --> pdb=" O VAL E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 359 removed outlier: 3.535A pdb=" N TYR E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN E 333 " --> pdb=" O ASP E 329 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY E 356 " --> pdb=" O PHE E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 399 removed outlier: 3.509A pdb=" N LEU E 396 " --> pdb=" O LEU E 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 102 removed outlier: 4.014A pdb=" N LYS A 141 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 102 removed outlier: 4.013A pdb=" N LYS B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 102 removed outlier: 4.014A pdb=" N LYS C 141 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 102 removed outlier: 4.014A pdb=" N LYS D 141 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 102 removed outlier: 4.014A pdb=" N LYS E 141 " --> pdb=" O LEU E 152 " (cutoff:3.500A) 900 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3259 1.33 - 1.45: 2212 1.45 - 1.57: 7409 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 13000 Sorted by residual: bond pdb=" C MET D 336 " pdb=" O MET D 336 " ideal model delta sigma weight residual 1.236 1.214 0.022 1.29e-02 6.01e+03 3.03e+00 bond pdb=" C MET E 336 " pdb=" O MET E 336 " ideal model delta sigma weight residual 1.236 1.215 0.022 1.29e-02 6.01e+03 2.80e+00 bond pdb=" C MET C 336 " pdb=" O MET C 336 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.29e-02 6.01e+03 2.75e+00 bond pdb=" C MET B 336 " pdb=" O MET B 336 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.29e-02 6.01e+03 2.75e+00 bond pdb=" C MET A 336 " pdb=" O MET A 336 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.29e-02 6.01e+03 2.72e+00 ... (remaining 12995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 17151 1.34 - 2.68: 344 2.68 - 4.02: 32 4.02 - 5.36: 18 5.36 - 6.70: 10 Bond angle restraints: 17555 Sorted by residual: angle pdb=" N GLY C 353 " pdb=" CA GLY C 353 " pdb=" C GLY C 353 " ideal model delta sigma weight residual 115.32 111.27 4.05 1.31e+00 5.83e-01 9.56e+00 angle pdb=" N GLY B 353 " pdb=" CA GLY B 353 " pdb=" C GLY B 353 " ideal model delta sigma weight residual 115.32 111.27 4.05 1.31e+00 5.83e-01 9.56e+00 angle pdb=" N GLY A 353 " pdb=" CA GLY A 353 " pdb=" C GLY A 353 " ideal model delta sigma weight residual 115.32 111.29 4.03 1.31e+00 5.83e-01 9.45e+00 angle pdb=" N GLY E 353 " pdb=" CA GLY E 353 " pdb=" C GLY E 353 " ideal model delta sigma weight residual 115.32 111.33 3.99 1.31e+00 5.83e-01 9.30e+00 angle pdb=" N GLY D 353 " pdb=" CA GLY D 353 " pdb=" C GLY D 353 " ideal model delta sigma weight residual 115.32 111.33 3.99 1.31e+00 5.83e-01 9.27e+00 ... (remaining 17550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6794 17.97 - 35.95: 823 35.95 - 53.92: 218 53.92 - 71.89: 50 71.89 - 89.87: 15 Dihedral angle restraints: 7900 sinusoidal: 3270 harmonic: 4630 Sorted by residual: dihedral pdb=" CB GLU E 110 " pdb=" CG GLU E 110 " pdb=" CD GLU E 110 " pdb=" OE1 GLU E 110 " ideal model delta sinusoidal sigma weight residual 0.00 89.87 -89.87 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 110 " pdb=" CG GLU A 110 " pdb=" CD GLU A 110 " pdb=" OE1 GLU A 110 " ideal model delta sinusoidal sigma weight residual 0.00 89.85 -89.85 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 110 " pdb=" CG GLU C 110 " pdb=" CD GLU C 110 " pdb=" OE1 GLU C 110 " ideal model delta sinusoidal sigma weight residual 0.00 89.84 -89.84 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1234 0.026 - 0.051: 495 0.051 - 0.077: 204 0.077 - 0.102: 51 0.102 - 0.128: 36 Chirality restraints: 2020 Sorted by residual: chirality pdb=" CA ILE B 126 " pdb=" N ILE B 126 " pdb=" C ILE B 126 " pdb=" CB ILE B 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE E 126 " pdb=" N ILE E 126 " pdb=" C ILE E 126 " pdb=" CB ILE E 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE D 126 " pdb=" N ILE D 126 " pdb=" C ILE D 126 " pdb=" CB ILE D 126 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 2017 not shown) Planarity restraints: 2230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 145 " -0.064 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO C 146 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 145 " 0.064 5.00e-02 4.00e+02 9.60e-02 1.47e+01 pdb=" N PRO E 146 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO E 146 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO E 146 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 145 " 0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 146 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.052 5.00e-02 4.00e+02 ... (remaining 2227 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 241 2.68 - 3.23: 11958 3.23 - 3.79: 20225 3.79 - 4.34: 29920 4.34 - 4.90: 48448 Nonbonded interactions: 110792 Sorted by model distance: nonbonded pdb="MG MG E 500 " pdb=" O HOH D 646 " model vdw 2.121 2.170 nonbonded pdb="MG MG A 502 " pdb=" O HOH E 645 " model vdw 2.121 2.170 nonbonded pdb="MG MG D 500 " pdb=" O HOH C 646 " model vdw 2.122 2.170 nonbonded pdb="MG MG C 501 " pdb=" O HOH B 646 " model vdw 2.122 2.170 nonbonded pdb="MG MG B 500 " pdb=" O HOH A 646 " model vdw 2.122 2.170 ... (remaining 110787 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 84 through 502) selection = chain 'B' selection = (chain 'C' and resid 84 through 502) selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.690 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.003 0.039 13000 Z= 0.141 Angle : 0.482 6.696 17555 Z= 0.262 Chirality : 0.035 0.128 2020 Planarity : 0.005 0.096 2230 Dihedral : 16.924 89.866 4880 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.14 % Allowed : 23.56 % Favored : 74.31 % 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: 0.50 (0.21), residues: 1575 helix: 0.68 (0.15), residues: 1000 sheet: 1.99 (0.42), residues: 145 loop : -0.91 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 228 TYR 0.008 0.001 TYR D 299 PHE 0.006 0.001 PHE B 352 TRP 0.004 0.001 TRP D 196 HIS 0.003 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00313 (13000) covalent geometry : angle 0.48215 (17555) hydrogen bonds : bond 0.18889 ( 900) hydrogen bonds : angle 6.33769 ( 2640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.527 Fit side-chains REVERT: C 203 LYS cc_start: 0.8819 (mttt) cc_final: 0.8614 (mttt) REVERT: C 270 VAL cc_start: 0.7502 (t) cc_final: 0.6930 (m) REVERT: E 170 GLN cc_start: 0.8549 (mt0) cc_final: 0.8324 (mt0) REVERT: E 368 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.5699 (mp0) REVERT: E 390 ARG cc_start: 0.7275 (mmt180) cc_final: 0.7022 (mmt180) outliers start: 30 outliers final: 19 residues processed: 199 average time/residue: 0.5209 time to fit residues: 113.0228 Evaluate side-chains 181 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 368 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 HIS ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 HIS ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN D 122 HIS ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN E 122 HIS ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.192433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131606 restraints weight = 11892.056| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.59 r_work: 0.3046 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13000 Z= 0.157 Angle : 0.508 8.776 17555 Z= 0.267 Chirality : 0.038 0.129 2020 Planarity : 0.005 0.065 2230 Dihedral : 5.131 33.917 1740 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.49 % Allowed : 21.21 % Favored : 75.30 % 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: 2.16 (0.22), residues: 1575 helix: 2.07 (0.16), residues: 1035 sheet: 2.11 (0.41), residues: 145 loop : -0.59 (0.34), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 332 TYR 0.012 0.002 TYR C 299 PHE 0.019 0.002 PHE E 186 TRP 0.007 0.001 TRP D 196 HIS 0.005 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00362 (13000) covalent geometry : angle 0.50790 (17555) hydrogen bonds : bond 0.05975 ( 900) hydrogen bonds : angle 3.85666 ( 2640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 0.340 Fit side-chains REVERT: A 270 VAL cc_start: 0.7275 (OUTLIER) cc_final: 0.6586 (m) REVERT: A 337 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8330 (ttp-110) REVERT: B 270 VAL cc_start: 0.7358 (OUTLIER) cc_final: 0.6737 (m) REVERT: B 337 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8166 (ttp-110) REVERT: C 124 MET cc_start: 0.9185 (tpt) cc_final: 0.8911 (tpt) REVERT: C 203 LYS cc_start: 0.8734 (mttt) cc_final: 0.8528 (mttt) REVERT: C 270 VAL cc_start: 0.7312 (OUTLIER) cc_final: 0.6634 (m) REVERT: C 329 ASP cc_start: 0.8499 (m-30) cc_final: 0.8282 (m-30) REVERT: C 337 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8169 (ttp-110) REVERT: E 124 MET cc_start: 0.9182 (tpt) cc_final: 0.8849 (tpt) REVERT: E 270 VAL cc_start: 0.7216 (OUTLIER) cc_final: 0.6582 (m) REVERT: E 337 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8179 (ttp-110) outliers start: 49 outliers final: 13 residues processed: 216 average time/residue: 0.5022 time to fit residues: 118.1147 Evaluate side-chains 192 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 337 ARG Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 363 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 12 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 327 ASN B 298 ASN B 327 ASN E 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.191540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.124731 restraints weight = 11957.372| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.80 r_work: 0.2968 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13000 Z= 0.198 Angle : 0.550 9.364 17555 Z= 0.283 Chirality : 0.040 0.132 2020 Planarity : 0.004 0.052 2230 Dihedral : 4.192 32.909 1710 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.06 % Allowed : 21.78 % Favored : 74.16 % 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: 2.33 (0.22), residues: 1575 helix: 2.21 (0.16), residues: 1035 sheet: 1.92 (0.40), residues: 145 loop : -0.42 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 332 TYR 0.017 0.002 TYR D 299 PHE 0.019 0.002 PHE E 359 TRP 0.008 0.001 TRP E 196 HIS 0.006 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00480 (13000) covalent geometry : angle 0.54963 (17555) hydrogen bonds : bond 0.05958 ( 900) hydrogen bonds : angle 3.68897 ( 2640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 174 time to evaluate : 0.339 Fit side-chains REVERT: A 210 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7838 (mt) REVERT: A 337 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8134 (ttp-110) REVERT: B 270 VAL cc_start: 0.7214 (OUTLIER) cc_final: 0.6655 (m) REVERT: B 337 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8037 (ttp-110) REVERT: C 265 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7469 (tt) REVERT: C 270 VAL cc_start: 0.7151 (OUTLIER) cc_final: 0.6858 (t) REVERT: C 314 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.8231 (ttm170) REVERT: C 329 ASP cc_start: 0.8427 (m-30) cc_final: 0.8211 (m-30) REVERT: C 387 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7276 (mt) REVERT: D 329 ASP cc_start: 0.8576 (m-30) cc_final: 0.8290 (m-30) REVERT: E 124 MET cc_start: 0.9209 (tpt) cc_final: 0.8850 (tpt) REVERT: E 337 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.8008 (ttp-110) outliers start: 57 outliers final: 28 residues processed: 215 average time/residue: 0.4933 time to fit residues: 115.9656 Evaluate side-chains 199 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 390 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 27 optimal weight: 4.9990 chunk 148 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 127 optimal weight: 0.0870 chunk 102 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 19 optimal weight: 0.0970 chunk 31 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 ASN E 194 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.195738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135234 restraints weight = 11969.175| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.67 r_work: 0.3046 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13000 Z= 0.111 Angle : 0.451 8.371 17555 Z= 0.235 Chirality : 0.037 0.131 2020 Planarity : 0.004 0.053 2230 Dihedral : 3.799 26.238 1710 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.56 % Allowed : 22.35 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.70 (0.22), residues: 1575 helix: 2.57 (0.16), residues: 1035 sheet: 1.83 (0.40), residues: 145 loop : -0.41 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 136 TYR 0.008 0.001 TYR B 195 PHE 0.025 0.001 PHE E 186 TRP 0.008 0.001 TRP B 196 HIS 0.003 0.001 HIS D 331 Details of bonding type rmsd covalent geometry : bond 0.00235 (13000) covalent geometry : angle 0.45126 (17555) hydrogen bonds : bond 0.04673 ( 900) hydrogen bonds : angle 3.45265 ( 2640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 0.331 Fit side-chains REVERT: A 270 VAL cc_start: 0.7182 (OUTLIER) cc_final: 0.6867 (t) REVERT: A 338 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8436 (tt) REVERT: B 270 VAL cc_start: 0.7252 (OUTLIER) cc_final: 0.6685 (m) REVERT: B 314 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.8170 (mmt-90) REVERT: B 337 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8060 (ttp-110) REVERT: C 124 MET cc_start: 0.9256 (tpt) cc_final: 0.9017 (tpt) REVERT: C 270 VAL cc_start: 0.7242 (OUTLIER) cc_final: 0.6708 (m) REVERT: C 314 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.8094 (mmt-90) REVERT: C 387 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7347 (mt) REVERT: D 210 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7891 (mt) REVERT: D 314 ARG cc_start: 0.8363 (ttm-80) cc_final: 0.8113 (mmt-90) REVERT: E 124 MET cc_start: 0.9245 (tpt) cc_final: 0.8712 (tpt) REVERT: E 270 VAL cc_start: 0.7134 (OUTLIER) cc_final: 0.6537 (m) REVERT: E 314 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7966 (mmt-90) REVERT: E 337 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8054 (ttp-110) outliers start: 50 outliers final: 11 residues processed: 217 average time/residue: 0.5442 time to fit residues: 128.3812 Evaluate side-chains 193 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 337 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 148 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN B 327 ASN C 327 ASN D 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.190686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124925 restraints weight = 12026.822| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.83 r_work: 0.2952 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13000 Z= 0.254 Angle : 0.601 9.886 17555 Z= 0.306 Chirality : 0.043 0.136 2020 Planarity : 0.005 0.052 2230 Dihedral : 4.063 33.393 1707 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.99 % Allowed : 21.64 % Favored : 74.38 % 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 (0.21), residues: 1575 helix: 2.19 (0.16), residues: 1035 sheet: 1.83 (0.40), residues: 145 loop : -0.47 (0.34), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 332 TYR 0.020 0.003 TYR D 299 PHE 0.018 0.002 PHE B 359 TRP 0.006 0.001 TRP B 196 HIS 0.008 0.002 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00625 (13000) covalent geometry : angle 0.60051 (17555) hydrogen bonds : bond 0.06161 ( 900) hydrogen bonds : angle 3.63869 ( 2640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 0.456 Fit side-chains REVERT: B 194 GLN cc_start: 0.8406 (tp40) cc_final: 0.8151 (tp40) REVERT: B 270 VAL cc_start: 0.7341 (OUTLIER) cc_final: 0.6776 (m) REVERT: B 337 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8021 (ttp-110) REVERT: C 160 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6283 (mt-10) REVERT: C 265 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7425 (tt) REVERT: C 268 LEU cc_start: 0.8330 (mt) cc_final: 0.8118 (mp) REVERT: C 270 VAL cc_start: 0.7163 (OUTLIER) cc_final: 0.6605 (m) REVERT: C 314 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8218 (ttm170) REVERT: C 387 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7268 (mt) REVERT: D 210 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7832 (mt) REVERT: D 314 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.8179 (ttm170) REVERT: E 270 VAL cc_start: 0.7121 (t) cc_final: 0.6560 (m) REVERT: E 337 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8017 (ttp-110) outliers start: 56 outliers final: 32 residues processed: 223 average time/residue: 0.5593 time to fit residues: 135.6766 Evaluate side-chains 218 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 390 ARG Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 110 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 GLN B 298 ASN E 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.195558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132691 restraints weight = 11982.889| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.70 r_work: 0.3062 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13000 Z= 0.117 Angle : 0.467 8.671 17555 Z= 0.242 Chirality : 0.037 0.134 2020 Planarity : 0.004 0.046 2230 Dihedral : 3.683 25.818 1707 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.27 % Allowed : 22.70 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.65 (0.22), residues: 1575 helix: 2.54 (0.16), residues: 1040 sheet: 1.79 (0.40), residues: 145 loop : -0.50 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 136 TYR 0.008 0.001 TYR D 299 PHE 0.025 0.001 PHE E 186 TRP 0.008 0.001 TRP B 196 HIS 0.003 0.001 HIS D 331 Details of bonding type rmsd covalent geometry : bond 0.00255 (13000) covalent geometry : angle 0.46702 (17555) hydrogen bonds : bond 0.04649 ( 900) hydrogen bonds : angle 3.41007 ( 2640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.430 Fit side-chains REVERT: A 268 LEU cc_start: 0.8383 (mt) cc_final: 0.8108 (mp) REVERT: A 270 VAL cc_start: 0.7153 (t) cc_final: 0.6751 (t) REVERT: B 270 VAL cc_start: 0.7302 (OUTLIER) cc_final: 0.6822 (m) REVERT: B 314 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.8128 (mmt-90) REVERT: B 337 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8045 (ttp-110) REVERT: C 270 VAL cc_start: 0.7220 (OUTLIER) cc_final: 0.6693 (m) REVERT: C 314 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.8057 (mmt-90) REVERT: C 387 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7337 (mt) REVERT: D 270 VAL cc_start: 0.7371 (t) cc_final: 0.6990 (m) REVERT: D 314 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.8086 (mmt-90) REVERT: E 124 MET cc_start: 0.9251 (tpt) cc_final: 0.8759 (tpt) REVERT: E 270 VAL cc_start: 0.7211 (OUTLIER) cc_final: 0.6682 (m) REVERT: E 314 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.7927 (mmt-90) REVERT: E 337 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7986 (ttp-110) outliers start: 46 outliers final: 15 residues processed: 211 average time/residue: 0.5313 time to fit residues: 121.7359 Evaluate side-chains 188 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 112 optimal weight: 0.1980 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 327 ASN B 298 ASN B 327 ASN C 298 ASN C 327 ASN D 298 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.193155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.128455 restraints weight = 11931.809| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.73 r_work: 0.3017 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13000 Z= 0.164 Angle : 0.527 9.531 17555 Z= 0.269 Chirality : 0.039 0.136 2020 Planarity : 0.004 0.045 2230 Dihedral : 3.685 13.400 1705 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.63 % Allowed : 22.49 % Favored : 73.88 % 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: 2.52 (0.21), residues: 1575 helix: 2.60 (0.16), residues: 1005 sheet: 1.85 (0.41), residues: 145 loop : -0.79 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 332 TYR 0.015 0.002 TYR D 299 PHE 0.016 0.002 PHE A 186 TRP 0.006 0.001 TRP B 196 HIS 0.005 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00390 (13000) covalent geometry : angle 0.52691 (17555) hydrogen bonds : bond 0.05250 ( 900) hydrogen bonds : angle 3.47898 ( 2640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 0.412 Fit side-chains REVERT: A 228 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6571 (mtt-85) REVERT: A 268 LEU cc_start: 0.8350 (mt) cc_final: 0.8068 (mp) REVERT: A 270 VAL cc_start: 0.6986 (t) cc_final: 0.6697 (t) REVERT: B 270 VAL cc_start: 0.7359 (OUTLIER) cc_final: 0.6802 (m) REVERT: B 314 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8179 (ttm170) REVERT: B 337 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7947 (ttp-110) REVERT: B 383 MET cc_start: 0.6728 (mmt) cc_final: 0.6299 (mmm) REVERT: C 270 VAL cc_start: 0.7277 (OUTLIER) cc_final: 0.6739 (m) REVERT: C 314 ARG cc_start: 0.8413 (ttm-80) cc_final: 0.8068 (mmt-90) REVERT: C 387 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7321 (mt) REVERT: D 210 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7850 (mt) REVERT: D 270 VAL cc_start: 0.7376 (t) cc_final: 0.6926 (m) REVERT: D 314 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.8127 (ttm170) REVERT: E 124 MET cc_start: 0.9245 (tpt) cc_final: 0.8745 (tpt) REVERT: E 337 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8100 (ttp-110) outliers start: 51 outliers final: 28 residues processed: 203 average time/residue: 0.5391 time to fit residues: 119.1606 Evaluate side-chains 204 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.191975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.122434 restraints weight = 11825.329| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.83 r_work: 0.3001 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13000 Z= 0.192 Angle : 0.555 9.260 17555 Z= 0.283 Chirality : 0.040 0.135 2020 Planarity : 0.004 0.044 2230 Dihedral : 3.805 13.564 1705 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.27 % Allowed : 22.92 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.37 (0.21), residues: 1575 helix: 2.45 (0.16), residues: 1005 sheet: 1.86 (0.41), residues: 145 loop : -0.79 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 332 TYR 0.017 0.002 TYR C 299 PHE 0.024 0.002 PHE E 186 TRP 0.006 0.001 TRP E 196 HIS 0.006 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00464 (13000) covalent geometry : angle 0.55476 (17555) hydrogen bonds : bond 0.05605 ( 900) hydrogen bonds : angle 3.54564 ( 2640) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 0.585 Fit side-chains REVERT: A 210 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7785 (mt) REVERT: A 268 LEU cc_start: 0.8410 (mt) cc_final: 0.8183 (mp) REVERT: B 270 VAL cc_start: 0.7503 (OUTLIER) cc_final: 0.6863 (m) REVERT: B 314 ARG cc_start: 0.8644 (ttm-80) cc_final: 0.8429 (ttm170) REVERT: B 337 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8161 (ttp-110) REVERT: C 265 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7346 (tt) REVERT: C 270 VAL cc_start: 0.7336 (OUTLIER) cc_final: 0.6720 (m) REVERT: C 387 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7160 (mt) REVERT: D 210 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7800 (mt) REVERT: D 270 VAL cc_start: 0.7451 (t) cc_final: 0.6953 (m) REVERT: D 314 ARG cc_start: 0.8605 (ttm-80) cc_final: 0.8345 (ttm170) REVERT: E 124 MET cc_start: 0.9236 (tpt) cc_final: 0.8715 (tpt) REVERT: E 268 LEU cc_start: 0.8438 (mt) cc_final: 0.8215 (mp) REVERT: E 270 VAL cc_start: 0.7279 (t) cc_final: 0.6705 (m) REVERT: E 337 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8131 (ttp-110) outliers start: 46 outliers final: 27 residues processed: 202 average time/residue: 0.5244 time to fit residues: 115.5746 Evaluate side-chains 203 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 88 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 236 GLN C 236 GLN C 298 ASN D 236 GLN E 236 GLN E 298 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.194247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132393 restraints weight = 11975.737| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.70 r_work: 0.3021 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13000 Z= 0.131 Angle : 0.498 8.796 17555 Z= 0.256 Chirality : 0.038 0.133 2020 Planarity : 0.004 0.044 2230 Dihedral : 3.655 13.451 1705 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.42 % Allowed : 24.13 % Favored : 73.45 % 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: 2.55 (0.21), residues: 1575 helix: 2.64 (0.16), residues: 1005 sheet: 1.86 (0.41), residues: 145 loop : -0.81 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 314 TYR 0.012 0.002 TYR D 299 PHE 0.019 0.001 PHE A 186 TRP 0.008 0.001 TRP D 196 HIS 0.004 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00297 (13000) covalent geometry : angle 0.49759 (17555) hydrogen bonds : bond 0.04911 ( 900) hydrogen bonds : angle 3.45768 ( 2640) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.345 Fit side-chains REVERT: A 268 LEU cc_start: 0.8373 (mt) cc_final: 0.8132 (mp) REVERT: A 270 VAL cc_start: 0.7154 (t) cc_final: 0.6595 (m) REVERT: B 270 VAL cc_start: 0.7456 (t) cc_final: 0.6857 (m) REVERT: B 314 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.8205 (ttm170) REVERT: B 337 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8081 (ttp-110) REVERT: B 383 MET cc_start: 0.6795 (mmt) cc_final: 0.6394 (mmm) REVERT: C 270 VAL cc_start: 0.7373 (OUTLIER) cc_final: 0.6784 (m) REVERT: C 387 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7344 (mt) REVERT: D 210 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7880 (mt) REVERT: D 270 VAL cc_start: 0.7457 (t) cc_final: 0.6971 (m) REVERT: D 314 ARG cc_start: 0.8363 (ttm-80) cc_final: 0.8142 (ttm170) REVERT: E 124 MET cc_start: 0.9264 (tpt) cc_final: 0.8749 (tpt) REVERT: E 337 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7979 (ttp-110) outliers start: 34 outliers final: 23 residues processed: 188 average time/residue: 0.5154 time to fit residues: 105.7145 Evaluate side-chains 194 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 40 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN B 298 ASN C 298 ASN D 298 ASN E 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.194026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134434 restraints weight = 11934.073| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.61 r_work: 0.3032 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13000 Z= 0.139 Angle : 0.500 8.793 17555 Z= 0.258 Chirality : 0.038 0.134 2020 Planarity : 0.004 0.044 2230 Dihedral : 3.639 13.497 1705 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.28 % Allowed : 24.27 % Favored : 73.45 % 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: 2.58 (0.21), residues: 1575 helix: 2.66 (0.16), residues: 1005 sheet: 1.88 (0.41), residues: 145 loop : -0.82 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 332 TYR 0.014 0.002 TYR D 299 PHE 0.024 0.001 PHE E 186 TRP 0.008 0.001 TRP E 196 HIS 0.004 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00322 (13000) covalent geometry : angle 0.50044 (17555) hydrogen bonds : bond 0.04962 ( 900) hydrogen bonds : angle 3.43332 ( 2640) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.444 Fit side-chains REVERT: A 268 LEU cc_start: 0.8401 (mt) cc_final: 0.8163 (mp) REVERT: A 270 VAL cc_start: 0.7200 (t) cc_final: 0.6648 (m) REVERT: B 270 VAL cc_start: 0.7488 (t) cc_final: 0.6878 (m) REVERT: B 314 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.8176 (ttm170) REVERT: B 337 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8086 (ttp-110) REVERT: B 383 MET cc_start: 0.6806 (mmt) cc_final: 0.6398 (mmm) REVERT: C 270 VAL cc_start: 0.7427 (OUTLIER) cc_final: 0.6833 (m) REVERT: C 387 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7370 (mt) REVERT: D 210 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7887 (mt) REVERT: D 270 VAL cc_start: 0.7481 (t) cc_final: 0.7011 (m) REVERT: D 314 ARG cc_start: 0.8376 (ttm-80) cc_final: 0.8129 (ttm170) REVERT: E 124 MET cc_start: 0.9265 (tpt) cc_final: 0.8735 (tpt) REVERT: E 337 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.8095 (ttp-110) outliers start: 32 outliers final: 23 residues processed: 193 average time/residue: 0.5153 time to fit residues: 108.6024 Evaluate side-chains 192 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 232 HIS Chi-restraints excluded: chain E residue 337 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN B 298 ASN C 298 ASN E 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.194680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128643 restraints weight = 11847.155| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.88 r_work: 0.3023 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13000 Z= 0.157 Angle : 0.523 9.000 17555 Z= 0.268 Chirality : 0.039 0.135 2020 Planarity : 0.004 0.043 2230 Dihedral : 3.690 13.492 1705 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.42 % Allowed : 24.13 % Favored : 73.45 % 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: 2.50 (0.21), residues: 1575 helix: 2.59 (0.16), residues: 1005 sheet: 1.88 (0.41), residues: 145 loop : -0.81 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 332 TYR 0.015 0.002 TYR D 299 PHE 0.026 0.002 PHE E 186 TRP 0.007 0.001 TRP C 196 HIS 0.005 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00372 (13000) covalent geometry : angle 0.52256 (17555) hydrogen bonds : bond 0.05179 ( 900) hydrogen bonds : angle 3.46271 ( 2640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4322.25 seconds wall clock time: 74 minutes 11.09 seconds (4451.09 seconds total)