Starting phenix.real_space_refine on Fri Feb 6 21:03:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kbx_62233/02_2026/9kbx_62233_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kbx_62233/02_2026/9kbx_62233.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 { model { file = "/net/cci-nas-00/data/ceres_data/9kbx_62233/02_2026/9kbx_62233_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kbx_62233/02_2026/9kbx_62233_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kbx_62233/02_2026/9kbx_62233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kbx_62233/02_2026/9kbx_62233.map" } 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= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 102 5.16 5 C 8702 2.51 5 N 2338 2.21 5 O 2648 1.98 5 H 13590 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27392 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2134 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "B" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2134 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 5753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5753 Classifications: {'peptide': 370} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "J" Number of atoms: 5753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5753 Classifications: {'peptide': 370} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "K" Number of atoms: 5753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5753 Classifications: {'peptide': 370} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "L" Number of atoms: 5753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5753 Classifications: {'peptide': 370} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.19, per 1000 atoms: 0.19 Number of scatterers: 27392 At special positions: 0 Unit cell: (106.24, 112.88, 164.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 102 16.00 P 8 15.00 Mg 4 11.99 O 2648 8.00 N 2338 7.00 C 8702 6.00 H 13590 1.00 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: 2.33 Conformation dependent library (CDL) restraints added in 814.5 milliseconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3248 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 24 sheets defined 53.6% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'A' and resid 33 through 50 removed outlier: 3.595A pdb=" N ASP A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 41 " --> pdb=" O MET A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 65 through 76 Processing helix chain 'A' and resid 107 through 123 Processing helix chain 'A' and resid 133 through 139 removed outlier: 3.670A pdb=" N LEU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 158 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.639A pdb=" N TYR B 22 " --> pdb=" O ASP B 18 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 23 " --> pdb=" O MET B 19 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 29 " --> pdb=" O TRP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 50 removed outlier: 3.738A pdb=" N MET B 37 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP B 40 " --> pdb=" O PRO B 36 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 41 " --> pdb=" O MET B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 65 through 78 Processing helix chain 'B' and resid 107 through 124 Processing helix chain 'B' and resid 133 through 139 removed outlier: 3.682A pdb=" N LEU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 158 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'H' and resid 55 through 61 Processing helix chain 'H' and resid 78 through 92 Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 4.152A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 181 through 194 removed outlier: 3.738A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 202 through 217 removed outlier: 3.730A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 233 Processing helix chain 'H' and resid 252 through 260 Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 261 through 262 No H-bonds generated for 'chain 'H' and resid 261 through 262' Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 273 through 284 Processing helix chain 'H' and resid 289 through 295 Processing helix chain 'H' and resid 301 through 306 removed outlier: 4.483A pdb=" N TYR H 306 " --> pdb=" O THR H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 321 removed outlier: 3.553A pdb=" N LEU H 320 " --> pdb=" O GLU H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 349 removed outlier: 3.595A pdb=" N SER H 348 " --> pdb=" O SER H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 355 removed outlier: 4.457A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 369 through 374 Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'J' and resid 78 through 92 Processing helix chain 'J' and resid 97 through 101 Processing helix chain 'J' and resid 112 through 126 removed outlier: 4.218A pdb=" N ARG J 116 " --> pdb=" O PRO J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 146 Processing helix chain 'J' and resid 172 through 175 Processing helix chain 'J' and resid 182 through 194 removed outlier: 3.766A pdb=" N THR J 194 " --> pdb=" O MET J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 202 through 217 removed outlier: 3.638A pdb=" N GLU J 207 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 233 Processing helix chain 'J' and resid 252 through 260 Proline residue: J 258 - end of helix Processing helix chain 'J' and resid 261 through 262 No H-bonds generated for 'chain 'J' and resid 261 through 262' Processing helix chain 'J' and resid 263 through 268 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 289 through 295 Processing helix chain 'J' and resid 301 through 306 removed outlier: 4.398A pdb=" N TYR J 306 " --> pdb=" O THR J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 321 Processing helix chain 'J' and resid 334 through 336 No H-bonds generated for 'chain 'J' and resid 334 through 336' Processing helix chain 'J' and resid 337 through 349 removed outlier: 3.631A pdb=" N SER J 348 " --> pdb=" O SER J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 353 removed outlier: 3.599A pdb=" N GLN J 353 " --> pdb=" O SER J 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 350 through 353' Processing helix chain 'J' and resid 359 through 366 Processing helix chain 'J' and resid 369 through 374 removed outlier: 3.696A pdb=" N CYS J 374 " --> pdb=" O VAL J 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 61 Processing helix chain 'K' and resid 78 through 93 Processing helix chain 'K' and resid 97 through 101 Processing helix chain 'K' and resid 112 through 126 removed outlier: 4.191A pdb=" N ARG K 116 " --> pdb=" O PRO K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 146 Processing helix chain 'K' and resid 172 through 175 removed outlier: 3.643A pdb=" N ILE K 175 " --> pdb=" O PRO K 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 172 through 175' Processing helix chain 'K' and resid 181 through 194 removed outlier: 3.700A pdb=" N THR K 194 " --> pdb=" O MET K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 197 No H-bonds generated for 'chain 'K' and resid 195 through 197' Processing helix chain 'K' and resid 202 through 217 removed outlier: 3.624A pdb=" N GLU K 207 " --> pdb=" O THR K 203 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 233 Processing helix chain 'K' and resid 234 through 237 Processing helix chain 'K' and resid 252 through 260 Proline residue: K 258 - end of helix Processing helix chain 'K' and resid 261 through 262 No H-bonds generated for 'chain 'K' and resid 261 through 262' Processing helix chain 'K' and resid 263 through 268 Processing helix chain 'K' and resid 273 through 285 removed outlier: 3.521A pdb=" N CYS K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 289 through 295 Processing helix chain 'K' and resid 301 through 306 removed outlier: 4.345A pdb=" N TYR K 306 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 337 through 349 removed outlier: 3.581A pdb=" N SER K 348 " --> pdb=" O SER K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 353 Processing helix chain 'K' and resid 359 through 366 Processing helix chain 'K' and resid 368 through 374 removed outlier: 4.087A pdb=" N ARG K 372 " --> pdb=" O SER K 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 61 removed outlier: 3.570A pdb=" N LYS L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 92 removed outlier: 3.623A pdb=" N LYS L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 101 Processing helix chain 'L' and resid 112 through 126 removed outlier: 4.153A pdb=" N ARG L 116 " --> pdb=" O PRO L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 145 Processing helix chain 'L' and resid 181 through 194 removed outlier: 3.740A pdb=" N THR L 194 " --> pdb=" O MET L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 197 No H-bonds generated for 'chain 'L' and resid 195 through 197' Processing helix chain 'L' and resid 202 through 217 removed outlier: 3.750A pdb=" N GLU L 207 " --> pdb=" O THR L 203 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE L 208 " --> pdb=" O ALA L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 233 Processing helix chain 'L' and resid 252 through 260 Proline residue: L 258 - end of helix Processing helix chain 'L' and resid 261 through 262 No H-bonds generated for 'chain 'L' and resid 261 through 262' Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'L' and resid 273 through 284 Processing helix chain 'L' and resid 289 through 295 Processing helix chain 'L' and resid 301 through 306 removed outlier: 4.440A pdb=" N TYR L 306 " --> pdb=" O THR L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 321 Processing helix chain 'L' and resid 337 through 349 removed outlier: 3.516A pdb=" N SER L 348 " --> pdb=" O SER L 344 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU L 349 " --> pdb=" O ILE L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 353 Processing helix chain 'L' and resid 359 through 366 removed outlier: 3.715A pdb=" N GLU L 364 " --> pdb=" O GLN L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.700A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'H' and resid 176 through 178 removed outlier: 6.529A pdb=" N ASN H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 169 through 170 removed outlier: 3.809A pdb=" N GLN J 41 " --> pdb=" O ALA H 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'J' and resid 29 through 32 removed outlier: 3.785A pdb=" N THR J 106 " --> pdb=" O CYS J 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'J' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'J' and resid 169 through 170 removed outlier: 6.514A pdb=" N ASN J 297 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.691A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N CYS K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'K' and resid 176 through 178 removed outlier: 6.465A pdb=" N ASN K 297 " --> pdb=" O ILE K 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 176 through 178 removed outlier: 4.028A pdb=" N GLN L 41 " --> pdb=" O ALA K 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.688A pdb=" N LEU L 8 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N THR L 106 " --> pdb=" O LEU L 8 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N CYS L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'L' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'L' and resid 169 through 170 removed outlier: 6.542A pdb=" N ASN L 297 " --> pdb=" O ILE L 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 238 through 241 692 hydrogen bonds defined for protein. 1833 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: 6.85 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 13558 1.12 - 1.30: 2445 1.30 - 1.48: 5343 1.48 - 1.65: 6168 1.65 - 1.83: 172 Bond restraints: 27686 Sorted by residual: bond pdb=" N ASP K 292 " pdb=" H ASP K 292 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ASP K 211 " pdb=" H ASP K 211 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N GLY J 150 " pdb=" H GLY J 150 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE2 PHE H 31 " pdb=" HE2 PHE H 31 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N VAL H 96 " pdb=" H VAL H 96 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 27681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.76: 47947 4.76 - 9.52: 2075 9.52 - 14.28: 49 14.28 - 19.04: 0 19.04 - 23.80: 3 Bond angle restraints: 50074 Sorted by residual: angle pdb=" O2B ADP J 401 " pdb=" PB ADP J 401 " pdb=" O3B ADP J 401 " ideal model delta sigma weight residual 119.90 96.10 23.80 3.00e+00 1.11e-01 6.30e+01 angle pdb=" O1B ADP L 401 " pdb=" PB ADP L 401 " pdb=" O3B ADP L 401 " ideal model delta sigma weight residual 119.90 96.70 23.20 3.00e+00 1.11e-01 5.98e+01 angle pdb=" O2B ADP K 401 " pdb=" PB ADP K 401 " pdb=" O3B ADP K 401 " ideal model delta sigma weight residual 119.90 98.14 21.76 3.00e+00 1.11e-01 5.26e+01 angle pdb=" CA HIS A 140 " pdb=" CB HIS A 140 " pdb=" CG HIS A 140 " ideal model delta sigma weight residual 113.80 120.34 -6.54 1.00e+00 1.00e+00 4.28e+01 angle pdb=" CA SER H 14 " pdb=" C SER H 14 " pdb=" N GLY H 15 " ideal model delta sigma weight residual 115.30 122.96 -7.66 1.33e+00 5.65e-01 3.31e+01 ... (remaining 50069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.81: 12520 33.81 - 67.62: 480 67.62 - 101.44: 39 101.44 - 135.25: 7 135.25 - 169.06: 2 Dihedral angle restraints: 13048 sinusoidal: 7184 harmonic: 5864 Sorted by residual: dihedral pdb=" O1B ADP H 401 " pdb=" O3A ADP H 401 " pdb=" PB ADP H 401 " pdb=" PA ADP H 401 " ideal model delta sinusoidal sigma weight residual 300.00 130.94 169.06 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' ADP J 401 " pdb=" O5' ADP J 401 " pdb=" PA ADP J 401 " pdb=" O2A ADP J 401 " ideal model delta sinusoidal sigma weight residual 300.00 158.51 141.50 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" O2A ADP K 401 " pdb=" O3A ADP K 401 " pdb=" PA ADP K 401 " pdb=" PB ADP K 401 " ideal model delta sinusoidal sigma weight residual -60.00 74.43 -134.43 1 2.00e+01 2.50e-03 4.08e+01 ... (remaining 13045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1419 0.093 - 0.187: 542 0.187 - 0.280: 136 0.280 - 0.373: 23 0.373 - 0.467: 8 Chirality restraints: 2128 Sorted by residual: chirality pdb=" CA THR L 324 " pdb=" N THR L 324 " pdb=" C THR L 324 " pdb=" CB THR L 324 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA LYS J 215 " pdb=" N LYS J 215 " pdb=" C LYS J 215 " pdb=" CB LYS J 215 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CA LYS L 61 " pdb=" N LYS L 61 " pdb=" C LYS L 61 " pdb=" CB LYS L 61 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.40e+00 ... (remaining 2125 not shown) Planarity restraints: 4106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 340 " 0.268 2.00e-02 2.50e+03 9.53e-02 3.63e+02 pdb=" CG TRP J 340 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP J 340 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TRP J 340 " -0.094 2.00e-02 2.50e+03 pdb=" NE1 TRP J 340 " -0.115 2.00e-02 2.50e+03 pdb=" CE2 TRP J 340 " -0.082 2.00e-02 2.50e+03 pdb=" CE3 TRP J 340 " -0.083 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 340 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 340 " -0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP J 340 " 0.033 2.00e-02 2.50e+03 pdb=" HD1 TRP J 340 " 0.041 2.00e-02 2.50e+03 pdb=" HE1 TRP J 340 " 0.007 2.00e-02 2.50e+03 pdb=" HE3 TRP J 340 " -0.087 2.00e-02 2.50e+03 pdb=" HZ2 TRP J 340 " 0.084 2.00e-02 2.50e+03 pdb=" HZ3 TRP J 340 " 0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP J 340 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 340 " 0.250 2.00e-02 2.50e+03 9.04e-02 3.27e+02 pdb=" CG TRP L 340 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP L 340 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP L 340 " -0.079 2.00e-02 2.50e+03 pdb=" NE1 TRP L 340 " -0.115 2.00e-02 2.50e+03 pdb=" CE2 TRP L 340 " -0.071 2.00e-02 2.50e+03 pdb=" CE3 TRP L 340 " -0.078 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 340 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 340 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP L 340 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP L 340 " 0.045 2.00e-02 2.50e+03 pdb=" HE1 TRP L 340 " -0.020 2.00e-02 2.50e+03 pdb=" HE3 TRP L 340 " -0.107 2.00e-02 2.50e+03 pdb=" HZ2 TRP L 340 " 0.087 2.00e-02 2.50e+03 pdb=" HZ3 TRP L 340 " 0.009 2.00e-02 2.50e+03 pdb=" HH2 TRP L 340 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 340 " 0.236 2.00e-02 2.50e+03 8.81e-02 3.11e+02 pdb=" CG TRP H 340 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP H 340 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP H 340 " -0.100 2.00e-02 2.50e+03 pdb=" NE1 TRP H 340 " -0.100 2.00e-02 2.50e+03 pdb=" CE2 TRP H 340 " -0.084 2.00e-02 2.50e+03 pdb=" CE3 TRP H 340 " -0.076 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 340 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 340 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP H 340 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 TRP H 340 " 0.066 2.00e-02 2.50e+03 pdb=" HE1 TRP H 340 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP H 340 " -0.078 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 340 " 0.068 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 340 " 0.015 2.00e-02 2.50e+03 pdb=" HH2 TRP H 340 " 0.125 2.00e-02 2.50e+03 ... (remaining 4103 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1750 2.19 - 2.79: 48230 2.79 - 3.40: 78368 3.40 - 4.00: 105974 4.00 - 4.60: 153858 Nonbonded interactions: 388180 Sorted by model distance: nonbonded pdb=" HG1 THR H 149 " pdb=" O TYR H 166 " model vdw 1.589 2.450 nonbonded pdb=" OD1 ASP A 127 " pdb=" HG1 THR A 129 " model vdw 1.613 2.450 nonbonded pdb=" HG1 THR H 66 " pdb=" OE2 GLU K 270 " model vdw 1.614 2.450 nonbonded pdb=" OE2 GLU L 125 " pdb=" HH TYR L 362 " model vdw 1.619 2.450 nonbonded pdb=" OD1 ASP K 154 " pdb=" HG SER K 300 " model vdw 1.623 2.450 ... (remaining 388175 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 3.860 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: 0.160 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.820 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 : 0.013 0.144 14096 Z= 0.808 Angle : 1.930 23.802 19118 Z= 1.266 Chirality : 0.105 0.467 2128 Planarity : 0.016 0.152 2448 Dihedral : 15.300 169.060 5252 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.61 % Allowed : 2.83 % Favored : 96.56 % Cbeta Deviations : 0.80 % 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 are not related in a simple way. whole: -0.76 (0.19), residues: 1740 helix: -1.38 (0.16), residues: 764 sheet: -0.38 (0.29), residues: 224 loop : 0.78 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG L 183 TYR 0.118 0.015 TYR J 306 PHE 0.064 0.013 PHE J 124 TRP 0.182 0.027 TRP J 340 HIS 0.017 0.003 HIS J 371 Details of bonding type rmsd covalent geometry : bond 0.01315 (14096) covalent geometry : angle 1.93025 (19118) hydrogen bonds : bond 0.20925 ( 684) hydrogen bonds : angle 7.60280 ( 1833) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 337 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.6679 (mmp) cc_final: 0.5881 (mmm) REVERT: A 64 ASN cc_start: 0.7071 (p0) cc_final: 0.6837 (p0) REVERT: B 31 GLU cc_start: 0.4944 (mp0) cc_final: 0.4727 (mp0) REVERT: B 59 MET cc_start: 0.6976 (mmp) cc_final: 0.6766 (mmm) REVERT: B 117 PHE cc_start: 0.7288 (t80) cc_final: 0.7080 (t80) REVERT: H 80 ASP cc_start: 0.7239 (m-30) cc_final: 0.6699 (m-30) REVERT: H 196 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8170 (ttt90) REVERT: J 227 MET cc_start: 0.8823 (mmm) cc_final: 0.8615 (mmm) REVERT: J 283 MET cc_start: 0.8679 (mmm) cc_final: 0.8384 (mmm) REVERT: K 123 MET cc_start: 0.9209 (mmm) cc_final: 0.8773 (mmp) REVERT: K 227 MET cc_start: 0.8804 (mmm) cc_final: 0.8505 (mmm) REVERT: K 250 ILE cc_start: 0.8491 (tt) cc_final: 0.8148 (mp) REVERT: L 106 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7999 (p) REVERT: L 116 ARG cc_start: 0.8327 (ptm160) cc_final: 0.8121 (ptp-170) REVERT: L 269 MET cc_start: 0.8169 (ptp) cc_final: 0.7859 (ptm) outliers start: 9 outliers final: 4 residues processed: 343 average time/residue: 1.3746 time to fit residues: 513.7658 Evaluate side-chains 226 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 220 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 196 ARG Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 327 ILE Chi-restraints excluded: chain L residue 341 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 HIS B 24 GLN H 41 GLN J 360 GLN K 59 GLN K 246 GLN L 59 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.102033 restraints weight = 43753.145| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.30 r_work: 0.2927 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14096 Z= 0.167 Angle : 0.719 8.158 19118 Z= 0.373 Chirality : 0.046 0.226 2128 Planarity : 0.005 0.056 2448 Dihedral : 10.867 138.155 1962 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.62 % Allowed : 9.99 % Favored : 88.39 % 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 are not related in a simple way. whole: 0.33 (0.20), residues: 1740 helix: -0.08 (0.18), residues: 776 sheet: -0.20 (0.30), residues: 268 loop : 1.10 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 116 TYR 0.013 0.001 TYR J 143 PHE 0.022 0.002 PHE A 58 TRP 0.018 0.003 TRP J 356 HIS 0.008 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00382 (14096) covalent geometry : angle 0.71901 (19118) hydrogen bonds : bond 0.05425 ( 684) hydrogen bonds : angle 5.42028 ( 1833) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7220 (mt-10) REVERT: B 24 GLN cc_start: 0.6786 (OUTLIER) cc_final: 0.6392 (tp40) REVERT: B 29 ARG cc_start: 0.3546 (OUTLIER) cc_final: 0.3298 (ptt180) REVERT: B 59 MET cc_start: 0.5942 (mmp) cc_final: 0.5682 (mmm) REVERT: B 117 PHE cc_start: 0.6472 (t80) cc_final: 0.6017 (t80) REVERT: B 124 LEU cc_start: 0.4766 (tp) cc_final: 0.4402 (mm) REVERT: H 227 MET cc_start: 0.8663 (mmm) cc_final: 0.8418 (mmm) REVERT: J 283 MET cc_start: 0.8897 (mmm) cc_final: 0.8560 (mmm) REVERT: J 313 MET cc_start: 0.8965 (tpt) cc_final: 0.8724 (tpt) REVERT: K 92 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7605 (t0) REVERT: K 123 MET cc_start: 0.9147 (mmm) cc_final: 0.8714 (mmp) REVERT: K 226 GLU cc_start: 0.8560 (tp30) cc_final: 0.8169 (mm-30) REVERT: K 227 MET cc_start: 0.8736 (mmm) cc_final: 0.8467 (mmm) REVERT: K 250 ILE cc_start: 0.8539 (tt) cc_final: 0.8101 (mp) REVERT: K 283 MET cc_start: 0.8896 (mmm) cc_final: 0.8643 (mmp) REVERT: K 326 LYS cc_start: 0.7888 (mttm) cc_final: 0.7589 (tttp) REVERT: K 328 LYS cc_start: 0.8426 (tttt) cc_final: 0.7736 (tptm) REVERT: L 82 MET cc_start: 0.8843 (tpt) cc_final: 0.8259 (tpt) REVERT: L 95 ARG cc_start: 0.7395 (mtp85) cc_final: 0.6891 (mtp85) REVERT: L 116 ARG cc_start: 0.8405 (ptm160) cc_final: 0.8173 (ptp-170) REVERT: L 292 ASP cc_start: 0.7921 (m-30) cc_final: 0.7690 (m-30) REVERT: L 326 LYS cc_start: 0.8317 (mtpp) cc_final: 0.7965 (tmtm) outliers start: 24 outliers final: 10 residues processed: 250 average time/residue: 1.3843 time to fit residues: 377.2842 Evaluate side-chains 217 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 92 ASN Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 132 MET Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 274 ILE Chi-restraints excluded: chain L residue 327 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 40 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 128 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 GLN H 246 GLN J 360 GLN K 78 ASN K 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.133213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.101606 restraints weight = 43546.089| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.30 r_work: 0.2921 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14096 Z= 0.134 Angle : 0.630 7.839 19118 Z= 0.318 Chirality : 0.044 0.167 2128 Planarity : 0.004 0.044 2448 Dihedral : 9.631 132.534 1950 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.89 % Allowed : 11.13 % Favored : 86.98 % 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 are not related in a simple way. whole: 0.70 (0.20), residues: 1740 helix: 0.34 (0.18), residues: 778 sheet: -0.14 (0.31), residues: 268 loop : 1.20 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 29 TYR 0.010 0.001 TYR J 294 PHE 0.012 0.001 PHE A 58 TRP 0.013 0.002 TRP H 356 HIS 0.007 0.001 HIS J 101 Details of bonding type rmsd covalent geometry : bond 0.00292 (14096) covalent geometry : angle 0.63036 (19118) hydrogen bonds : bond 0.04413 ( 684) hydrogen bonds : angle 4.99413 ( 1833) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 132 PHE cc_start: 0.7297 (p90) cc_final: 0.7090 (p90) REVERT: A 133 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7216 (mt-10) REVERT: B 29 ARG cc_start: 0.3570 (OUTLIER) cc_final: 0.3283 (ptt180) REVERT: B 59 MET cc_start: 0.5936 (mmp) cc_final: 0.5678 (mmm) REVERT: B 117 PHE cc_start: 0.6399 (t80) cc_final: 0.5983 (t80) REVERT: B 124 LEU cc_start: 0.4771 (tp) cc_final: 0.4423 (mm) REVERT: H 95 ARG cc_start: 0.7675 (mtt180) cc_final: 0.7378 (mpt-90) REVERT: H 227 MET cc_start: 0.8656 (mmm) cc_final: 0.8428 (mmm) REVERT: H 354 GLN cc_start: 0.7475 (pp30) cc_final: 0.7153 (mp-120) REVERT: J 283 MET cc_start: 0.8853 (mmm) cc_final: 0.8480 (mmm) REVERT: J 292 ASP cc_start: 0.8020 (m-30) cc_final: 0.7732 (m-30) REVERT: J 313 MET cc_start: 0.8956 (tpt) cc_final: 0.8706 (tpt) REVERT: K 123 MET cc_start: 0.9022 (mmm) cc_final: 0.8495 (mmp) REVERT: K 226 GLU cc_start: 0.8599 (tp30) cc_final: 0.8287 (mm-30) REVERT: K 227 MET cc_start: 0.8695 (mmm) cc_final: 0.8351 (mmm) REVERT: K 283 MET cc_start: 0.8859 (mmm) cc_final: 0.8573 (mmp) REVERT: K 313 MET cc_start: 0.8545 (mmm) cc_final: 0.8249 (mmm) REVERT: K 326 LYS cc_start: 0.7888 (mttm) cc_final: 0.7601 (tttp) REVERT: K 328 LYS cc_start: 0.8423 (tttt) cc_final: 0.7750 (tptm) REVERT: L 82 MET cc_start: 0.8867 (tpt) cc_final: 0.8307 (tpt) REVERT: L 292 ASP cc_start: 0.7911 (m-30) cc_final: 0.7677 (m-30) REVERT: L 326 LYS cc_start: 0.8324 (mtpp) cc_final: 0.8011 (tmtm) outliers start: 28 outliers final: 11 residues processed: 239 average time/residue: 1.3699 time to fit residues: 357.6954 Evaluate side-chains 213 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 196 ARG Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 274 ILE Chi-restraints excluded: chain L residue 327 ILE Chi-restraints excluded: chain L residue 341 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 130 optimal weight: 1.9990 chunk 169 optimal weight: 0.2980 chunk 107 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 65 optimal weight: 0.0070 chunk 113 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 GLN J 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.102901 restraints weight = 43319.009| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.30 r_work: 0.2938 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14096 Z= 0.102 Angle : 0.573 8.389 19118 Z= 0.280 Chirality : 0.042 0.160 2128 Planarity : 0.004 0.044 2448 Dihedral : 8.841 132.791 1950 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.21 % Allowed : 12.35 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1740 helix: 0.59 (0.19), residues: 802 sheet: -0.04 (0.31), residues: 268 loop : 1.24 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 29 TYR 0.009 0.001 TYR J 294 PHE 0.008 0.001 PHE A 58 TRP 0.013 0.001 TRP H 356 HIS 0.006 0.001 HIS J 101 Details of bonding type rmsd covalent geometry : bond 0.00225 (14096) covalent geometry : angle 0.57279 (19118) hydrogen bonds : bond 0.03590 ( 684) hydrogen bonds : angle 4.69437 ( 1833) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7249 (mt-10) REVERT: B 59 MET cc_start: 0.5923 (mmp) cc_final: 0.5639 (mmm) REVERT: B 117 PHE cc_start: 0.6467 (t80) cc_final: 0.6018 (t80) REVERT: B 124 LEU cc_start: 0.4761 (tp) cc_final: 0.4450 (mm) REVERT: H 18 LYS cc_start: 0.8268 (mtpp) cc_final: 0.8058 (mtpp) REVERT: H 91 TYR cc_start: 0.8592 (m-80) cc_final: 0.8132 (m-80) REVERT: J 96 VAL cc_start: 0.8326 (p) cc_final: 0.8090 (m) REVERT: J 107 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: J 283 MET cc_start: 0.8798 (mmm) cc_final: 0.8493 (mmm) REVERT: J 292 ASP cc_start: 0.8015 (m-30) cc_final: 0.7720 (m-30) REVERT: K 123 MET cc_start: 0.8984 (mmm) cc_final: 0.8218 (mmp) REVERT: K 226 GLU cc_start: 0.8619 (tp30) cc_final: 0.8255 (mm-30) REVERT: K 227 MET cc_start: 0.8679 (mmm) cc_final: 0.8392 (mmm) REVERT: K 283 MET cc_start: 0.8818 (mmm) cc_final: 0.8536 (mmp) REVERT: K 313 MET cc_start: 0.8510 (mmm) cc_final: 0.8218 (mmm) REVERT: K 326 LYS cc_start: 0.7877 (mttm) cc_final: 0.7615 (tttp) REVERT: K 328 LYS cc_start: 0.8433 (tttt) cc_final: 0.7793 (tptm) REVERT: L 82 MET cc_start: 0.8863 (tpt) cc_final: 0.8322 (tpt) REVERT: L 292 ASP cc_start: 0.7854 (m-30) cc_final: 0.7613 (m-30) REVERT: L 326 LYS cc_start: 0.8304 (mtpp) cc_final: 0.8048 (mttp) outliers start: 18 outliers final: 8 residues processed: 221 average time/residue: 1.3101 time to fit residues: 316.3426 Evaluate side-chains 213 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 204 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 241 GLU Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 274 ILE Chi-restraints excluded: chain L residue 327 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 GLN H 246 GLN H 354 GLN J 360 GLN K 297 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.130159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.098315 restraints weight = 43342.164| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.31 r_work: 0.2868 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14096 Z= 0.205 Angle : 0.677 9.617 19118 Z= 0.339 Chirality : 0.047 0.216 2128 Planarity : 0.005 0.048 2448 Dihedral : 8.537 114.302 1950 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.48 % Allowed : 12.69 % Favored : 85.83 % 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 are not related in a simple way. whole: 0.72 (0.21), residues: 1740 helix: 0.41 (0.18), residues: 802 sheet: -0.08 (0.31), residues: 276 loop : 1.17 (0.26), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 177 TYR 0.011 0.001 TYR H 166 PHE 0.012 0.002 PHE A 58 TRP 0.012 0.003 TRP H 340 HIS 0.005 0.001 HIS J 173 Details of bonding type rmsd covalent geometry : bond 0.00492 (14096) covalent geometry : angle 0.67705 (19118) hydrogen bonds : bond 0.04820 ( 684) hydrogen bonds : angle 4.82457 ( 1833) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7194 (mt-10) REVERT: B 59 MET cc_start: 0.5953 (mmp) cc_final: 0.5601 (mmm) REVERT: B 117 PHE cc_start: 0.6479 (t80) cc_final: 0.6051 (t80) REVERT: B 124 LEU cc_start: 0.4708 (tp) cc_final: 0.4445 (mm) REVERT: H 91 TYR cc_start: 0.8671 (m-80) cc_final: 0.8156 (m-80) REVERT: H 95 ARG cc_start: 0.7816 (mtt180) cc_final: 0.7513 (mpt-90) REVERT: H 121 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: H 196 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8482 (ttt-90) REVERT: J 107 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8516 (tt0) REVERT: J 283 MET cc_start: 0.8883 (mmm) cc_final: 0.8587 (mmm) REVERT: J 292 ASP cc_start: 0.8122 (m-30) cc_final: 0.7787 (m-30) REVERT: K 92 ASN cc_start: 0.7967 (t0) cc_final: 0.7762 (t0) REVERT: K 116 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.6854 (ptp90) REVERT: K 123 MET cc_start: 0.9012 (mmm) cc_final: 0.8439 (mmp) REVERT: K 226 GLU cc_start: 0.8652 (tp30) cc_final: 0.8320 (mm-30) REVERT: K 227 MET cc_start: 0.8639 (mmm) cc_final: 0.8372 (mmm) REVERT: K 326 LYS cc_start: 0.7943 (mttm) cc_final: 0.7571 (tttp) REVERT: L 95 ARG cc_start: 0.7363 (mtp85) cc_final: 0.6881 (mtt-85) REVERT: L 326 LYS cc_start: 0.8422 (mtpp) cc_final: 0.8157 (mttp) outliers start: 22 outliers final: 13 residues processed: 217 average time/residue: 1.2890 time to fit residues: 305.3366 Evaluate side-chains 213 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain H residue 121 GLN Chi-restraints excluded: chain H residue 196 ARG Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 116 ARG Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 241 GLU Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 274 ILE Chi-restraints excluded: chain L residue 327 ILE Chi-restraints excluded: chain L residue 341 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 246 GLN H 354 GLN J 360 GLN L 360 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.131668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.100123 restraints weight = 43260.025| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.30 r_work: 0.2895 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14096 Z= 0.134 Angle : 0.592 7.595 19118 Z= 0.294 Chirality : 0.043 0.177 2128 Planarity : 0.004 0.046 2448 Dihedral : 7.729 107.239 1950 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.28 % Allowed : 13.09 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.21), residues: 1740 helix: 0.55 (0.19), residues: 802 sheet: -0.03 (0.31), residues: 268 loop : 1.14 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 196 TYR 0.008 0.001 TYR J 143 PHE 0.009 0.001 PHE A 117 TRP 0.010 0.002 TRP H 356 HIS 0.004 0.001 HIS J 101 Details of bonding type rmsd covalent geometry : bond 0.00311 (14096) covalent geometry : angle 0.59247 (19118) hydrogen bonds : bond 0.03975 ( 684) hydrogen bonds : angle 4.67032 ( 1833) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.7176 (p90) cc_final: 0.6912 (p90) REVERT: A 133 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7184 (mt-10) REVERT: B 48 LEU cc_start: 0.5336 (OUTLIER) cc_final: 0.4632 (mm) REVERT: B 59 MET cc_start: 0.5891 (mmp) cc_final: 0.5549 (mmm) REVERT: B 117 PHE cc_start: 0.6461 (t80) cc_final: 0.6074 (t80) REVERT: B 124 LEU cc_start: 0.4679 (tp) cc_final: 0.4411 (mm) REVERT: H 44 MET cc_start: 0.8428 (ttp) cc_final: 0.7646 (ttp) REVERT: H 95 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7502 (mpt-90) REVERT: H 196 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8485 (ttt-90) REVERT: J 283 MET cc_start: 0.8850 (mmm) cc_final: 0.8588 (mmm) REVERT: J 292 ASP cc_start: 0.8097 (m-30) cc_final: 0.7778 (m-30) REVERT: J 355 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8138 (mtt) REVERT: K 92 ASN cc_start: 0.7886 (t0) cc_final: 0.7676 (t0) REVERT: K 116 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6839 (ptp90) REVERT: K 123 MET cc_start: 0.8994 (mmm) cc_final: 0.8451 (mmp) REVERT: K 226 GLU cc_start: 0.8655 (tp30) cc_final: 0.8334 (mm-30) REVERT: K 227 MET cc_start: 0.8626 (mmm) cc_final: 0.8381 (mmm) REVERT: K 313 MET cc_start: 0.8568 (mmm) cc_final: 0.8293 (mmm) REVERT: K 326 LYS cc_start: 0.7902 (mttm) cc_final: 0.7588 (tttp) REVERT: L 326 LYS cc_start: 0.8344 (mtpp) cc_final: 0.8102 (mttp) outliers start: 19 outliers final: 8 residues processed: 217 average time/residue: 1.3560 time to fit residues: 320.9433 Evaluate side-chains 214 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain H residue 196 ARG Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 355 MET Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 116 ARG Chi-restraints excluded: chain K residue 241 GLU Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 274 ILE Chi-restraints excluded: chain L residue 327 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 48 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 GLN H 246 GLN H 354 GLN J 225 ASN J 360 GLN L 360 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.131422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.099940 restraints weight = 43344.385| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.30 r_work: 0.2894 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14096 Z= 0.141 Angle : 0.596 7.629 19118 Z= 0.295 Chirality : 0.043 0.178 2128 Planarity : 0.004 0.046 2448 Dihedral : 7.591 104.705 1950 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.08 % Allowed : 13.29 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1740 helix: 0.60 (0.18), residues: 804 sheet: -0.05 (0.31), residues: 276 loop : 1.16 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 177 TYR 0.007 0.001 TYR J 143 PHE 0.008 0.001 PHE A 117 TRP 0.011 0.002 TRP H 79 HIS 0.004 0.001 HIS J 101 Details of bonding type rmsd covalent geometry : bond 0.00336 (14096) covalent geometry : angle 0.59641 (19118) hydrogen bonds : bond 0.04009 ( 684) hydrogen bonds : angle 4.63064 ( 1833) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 117 PHE cc_start: 0.6701 (t80) cc_final: 0.6420 (t80) REVERT: A 132 PHE cc_start: 0.7169 (p90) cc_final: 0.6897 (p90) REVERT: A 133 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7171 (mt-10) REVERT: B 48 LEU cc_start: 0.5535 (OUTLIER) cc_final: 0.4855 (mm) REVERT: B 59 MET cc_start: 0.5895 (mmp) cc_final: 0.5560 (mmm) REVERT: B 117 PHE cc_start: 0.6491 (t80) cc_final: 0.6107 (t80) REVERT: B 124 LEU cc_start: 0.4759 (tp) cc_final: 0.4454 (mm) REVERT: H 44 MET cc_start: 0.8425 (ttp) cc_final: 0.7700 (ttp) REVERT: H 91 TYR cc_start: 0.8637 (m-80) cc_final: 0.8208 (m-80) REVERT: H 95 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7431 (mpt-90) REVERT: J 283 MET cc_start: 0.8843 (mmm) cc_final: 0.8586 (mmm) REVERT: J 292 ASP cc_start: 0.8086 (m-30) cc_final: 0.7763 (m-30) REVERT: J 313 MET cc_start: 0.8905 (tpt) cc_final: 0.8695 (tpt) REVERT: J 355 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8160 (mtt) REVERT: K 92 ASN cc_start: 0.7922 (t0) cc_final: 0.7706 (t0) REVERT: K 116 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.6837 (ptp90) REVERT: K 123 MET cc_start: 0.8986 (mmm) cc_final: 0.8433 (mmp) REVERT: K 226 GLU cc_start: 0.8653 (tp30) cc_final: 0.8298 (mm-30) REVERT: K 227 MET cc_start: 0.8600 (mmm) cc_final: 0.8364 (mmm) REVERT: K 326 LYS cc_start: 0.7893 (mttm) cc_final: 0.7571 (tttp) REVERT: K 355 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8354 (mtt) REVERT: L 326 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8106 (mttp) outliers start: 16 outliers final: 9 residues processed: 213 average time/residue: 1.3396 time to fit residues: 311.5770 Evaluate side-chains 213 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 355 MET Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 116 ARG Chi-restraints excluded: chain K residue 241 GLU Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 355 MET Chi-restraints excluded: chain L residue 274 ILE Chi-restraints excluded: chain L residue 327 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 22 optimal weight: 0.3980 chunk 125 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 128 optimal weight: 0.2980 chunk 89 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 246 GLN H 354 GLN J 360 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.132760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.101493 restraints weight = 43401.362| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.30 r_work: 0.2917 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14096 Z= 0.106 Angle : 0.566 7.182 19118 Z= 0.276 Chirality : 0.042 0.168 2128 Planarity : 0.004 0.046 2448 Dihedral : 7.139 100.192 1950 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.94 % Allowed : 13.90 % Favored : 85.16 % 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 are not related in a simple way. whole: 1.05 (0.21), residues: 1740 helix: 0.81 (0.19), residues: 804 sheet: -0.00 (0.30), residues: 276 loop : 1.19 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 37 TYR 0.007 0.001 TYR J 143 PHE 0.008 0.001 PHE A 117 TRP 0.011 0.002 TRP H 356 HIS 0.004 0.001 HIS J 101 Details of bonding type rmsd covalent geometry : bond 0.00240 (14096) covalent geometry : angle 0.56575 (19118) hydrogen bonds : bond 0.03481 ( 684) hydrogen bonds : angle 4.50574 ( 1833) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 117 PHE cc_start: 0.6667 (t80) cc_final: 0.6397 (t80) REVERT: A 133 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7272 (mt-10) REVERT: B 59 MET cc_start: 0.5785 (mmp) cc_final: 0.5459 (mmm) REVERT: B 117 PHE cc_start: 0.6534 (t80) cc_final: 0.6166 (t80) REVERT: H 44 MET cc_start: 0.8378 (ttp) cc_final: 0.7586 (ttp) REVERT: H 45 VAL cc_start: 0.7456 (t) cc_final: 0.7007 (m) REVERT: H 91 TYR cc_start: 0.8635 (m-80) cc_final: 0.8201 (m-80) REVERT: H 95 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7410 (mpt-90) REVERT: J 83 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: J 283 MET cc_start: 0.8801 (mmm) cc_final: 0.8479 (mmm) REVERT: J 292 ASP cc_start: 0.8068 (m-30) cc_final: 0.7755 (m-30) REVERT: J 355 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8107 (mtt) REVERT: K 116 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.6853 (ptp90) REVERT: K 123 MET cc_start: 0.8961 (mmm) cc_final: 0.8255 (mmp) REVERT: K 226 GLU cc_start: 0.8627 (tp30) cc_final: 0.8246 (mm-30) REVERT: K 227 MET cc_start: 0.8572 (mmm) cc_final: 0.8326 (mmm) REVERT: K 313 MET cc_start: 0.8539 (mmm) cc_final: 0.8262 (mmm) REVERT: K 326 LYS cc_start: 0.7862 (mttm) cc_final: 0.7553 (tttp) REVERT: K 355 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8356 (mtt) REVERT: L 326 LYS cc_start: 0.8292 (mtpp) cc_final: 0.8060 (mttp) outliers start: 14 outliers final: 9 residues processed: 210 average time/residue: 1.3025 time to fit residues: 298.8993 Evaluate side-chains 207 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 355 MET Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 116 ARG Chi-restraints excluded: chain K residue 241 GLU Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 355 MET Chi-restraints excluded: chain L residue 274 ILE Chi-restraints excluded: chain L residue 327 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.0470 chunk 78 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 246 GLN H 354 GLN K 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.132671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.101473 restraints weight = 43321.384| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.29 r_work: 0.2917 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14096 Z= 0.109 Angle : 0.566 7.238 19118 Z= 0.275 Chirality : 0.042 0.168 2128 Planarity : 0.004 0.046 2448 Dihedral : 6.943 95.261 1950 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.08 % Allowed : 13.83 % Favored : 85.09 % 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 are not related in a simple way. whole: 1.16 (0.21), residues: 1740 helix: 0.92 (0.19), residues: 804 sheet: 0.03 (0.30), residues: 276 loop : 1.23 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 37 TYR 0.006 0.001 TYR J 143 PHE 0.007 0.001 PHE A 58 TRP 0.010 0.002 TRP H 79 HIS 0.004 0.001 HIS J 101 Details of bonding type rmsd covalent geometry : bond 0.00253 (14096) covalent geometry : angle 0.56586 (19118) hydrogen bonds : bond 0.03484 ( 684) hydrogen bonds : angle 4.45961 ( 1833) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 117 PHE cc_start: 0.6675 (t80) cc_final: 0.6406 (t80) REVERT: A 133 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 48 LEU cc_start: 0.5629 (OUTLIER) cc_final: 0.4819 (mm) REVERT: B 59 MET cc_start: 0.5865 (mmp) cc_final: 0.5532 (mmm) REVERT: B 117 PHE cc_start: 0.6530 (t80) cc_final: 0.6163 (t80) REVERT: H 44 MET cc_start: 0.8359 (ttp) cc_final: 0.7666 (ttp) REVERT: H 45 VAL cc_start: 0.7453 (t) cc_final: 0.7048 (m) REVERT: H 91 TYR cc_start: 0.8652 (m-80) cc_final: 0.8248 (m-80) REVERT: H 95 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7412 (mpt-90) REVERT: J 83 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: J 283 MET cc_start: 0.8799 (mmm) cc_final: 0.8481 (mmm) REVERT: J 292 ASP cc_start: 0.8047 (m-30) cc_final: 0.7740 (m-30) REVERT: J 355 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8109 (mtt) REVERT: K 116 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.6841 (ptp90) REVERT: K 123 MET cc_start: 0.8953 (mmm) cc_final: 0.8260 (mmp) REVERT: K 226 GLU cc_start: 0.8622 (tp30) cc_final: 0.8250 (mm-30) REVERT: K 227 MET cc_start: 0.8560 (mmm) cc_final: 0.8308 (mmm) REVERT: K 313 MET cc_start: 0.8543 (mmm) cc_final: 0.8263 (mmm) REVERT: K 326 LYS cc_start: 0.7849 (mttm) cc_final: 0.7549 (tttp) REVERT: K 355 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8379 (mtt) REVERT: L 326 LYS cc_start: 0.8339 (mtpp) cc_final: 0.8067 (mttp) outliers start: 16 outliers final: 9 residues processed: 208 average time/residue: 1.2669 time to fit residues: 288.0839 Evaluate side-chains 210 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 355 MET Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 116 ARG Chi-restraints excluded: chain K residue 241 GLU Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 355 MET Chi-restraints excluded: chain L residue 274 ILE Chi-restraints excluded: chain L residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 105 optimal weight: 2.9990 chunk 137 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 26 optimal weight: 0.0770 chunk 109 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 246 GLN H 354 GLN K 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.102479 restraints weight = 43237.836| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.29 r_work: 0.2934 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14096 Z= 0.096 Angle : 0.550 7.406 19118 Z= 0.266 Chirality : 0.041 0.156 2128 Planarity : 0.004 0.046 2448 Dihedral : 6.674 89.278 1950 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.01 % Allowed : 14.17 % Favored : 84.82 % 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 are not related in a simple way. whole: 1.20 (0.21), residues: 1740 helix: 1.03 (0.19), residues: 804 sheet: 0.08 (0.31), residues: 268 loop : 1.10 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 95 TYR 0.006 0.001 TYR J 143 PHE 0.006 0.001 PHE H 262 TRP 0.011 0.001 TRP H 356 HIS 0.004 0.001 HIS J 101 Details of bonding type rmsd covalent geometry : bond 0.00218 (14096) covalent geometry : angle 0.54959 (19118) hydrogen bonds : bond 0.03273 ( 684) hydrogen bonds : angle 4.39748 ( 1833) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 117 PHE cc_start: 0.6640 (t80) cc_final: 0.6360 (t80) REVERT: A 133 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7292 (mt-10) REVERT: B 59 MET cc_start: 0.5857 (mmp) cc_final: 0.5533 (mmm) REVERT: B 64 ASN cc_start: 0.5337 (p0) cc_final: 0.5043 (p0) REVERT: B 117 PHE cc_start: 0.6493 (t80) cc_final: 0.6122 (t80) REVERT: H 44 MET cc_start: 0.8291 (ttp) cc_final: 0.7538 (ttp) REVERT: H 45 VAL cc_start: 0.7419 (t) cc_final: 0.7015 (m) REVERT: H 91 TYR cc_start: 0.8644 (m-80) cc_final: 0.8265 (m-80) REVERT: H 95 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7390 (mpt-90) REVERT: J 83 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: J 283 MET cc_start: 0.8769 (mmm) cc_final: 0.8463 (mmm) REVERT: J 292 ASP cc_start: 0.8039 (m-30) cc_final: 0.7734 (m-30) REVERT: J 355 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8081 (mtt) REVERT: K 226 GLU cc_start: 0.8591 (tp30) cc_final: 0.8277 (mm-30) REVERT: K 227 MET cc_start: 0.8524 (mmm) cc_final: 0.8280 (mmm) REVERT: K 313 MET cc_start: 0.8519 (mmm) cc_final: 0.8231 (mmm) REVERT: K 326 LYS cc_start: 0.7850 (mttm) cc_final: 0.7547 (tttp) REVERT: K 355 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8365 (mtt) REVERT: L 326 LYS cc_start: 0.8340 (mtpp) cc_final: 0.8074 (mttp) outliers start: 15 outliers final: 8 residues processed: 212 average time/residue: 1.3336 time to fit residues: 308.7042 Evaluate side-chains 207 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 355 MET Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 241 GLU Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 355 MET Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 53 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN H 246 GLN H 354 GLN K 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.100487 restraints weight = 42946.363| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.29 r_work: 0.2906 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14096 Z= 0.140 Angle : 0.588 7.647 19118 Z= 0.289 Chirality : 0.043 0.171 2128 Planarity : 0.004 0.047 2448 Dihedral : 6.996 84.862 1950 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.15 % Allowed : 14.24 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.21), residues: 1740 helix: 0.93 (0.19), residues: 804 sheet: 0.04 (0.31), residues: 276 loop : 1.28 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 147 TYR 0.007 0.001 TYR J 143 PHE 0.008 0.001 PHE H 262 TRP 0.010 0.002 TRP H 79 HIS 0.003 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00335 (14096) covalent geometry : angle 0.58846 (19118) hydrogen bonds : bond 0.03844 ( 684) hydrogen bonds : angle 4.48006 ( 1833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10039.71 seconds wall clock time: 170 minutes 6.51 seconds (10206.51 seconds total)