Starting phenix.real_space_refine on Wed Sep 17 22:05:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ru0_19501/09_2025/8ru0_19501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ru0_19501/09_2025/8ru0_19501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ru0_19501/09_2025/8ru0_19501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ru0_19501/09_2025/8ru0_19501.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ru0_19501/09_2025/8ru0_19501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ru0_19501/09_2025/8ru0_19501.map" } resolution = 3.08 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= 0.002 sd= 0.092 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 83 5.16 5 C 7343 2.51 5 N 1964 2.21 5 O 2254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11660 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2893 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2881 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2855 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.21, per 1000 atoms: 0.28 Number of scatterers: 11660 At special positions: 0 Unit cell: (77.4, 99, 165.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 83 16.00 P 12 15.00 Mg 4 11.99 O 2254 8.00 N 1964 7.00 C 7343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 437.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 23 sheets defined 49.9% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.516A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.539A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.120A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.767A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.761A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.022A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.233A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.317A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 296 removed outlier: 3.555A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.890A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.526A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.785A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.332A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.941A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.349A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.574A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.939A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.593A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 127 Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.520A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 296 removed outlier: 4.044A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.132A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 320 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.741A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 366 through 371 removed outlier: 3.977A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.907A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.261A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.090A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.811A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.572A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AB2, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.068A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.697A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.531A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.927A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.586A pdb=" N GLY D 20 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.834A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 176 through 178 removed outlier: 4.022A pdb=" N MET D 176 " --> pdb=" O ASN D 162 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN D 162 " --> pdb=" O MET D 176 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 165 through 166 Processing sheet with id=AC5, first strand: chain 'D' and resid 238 through 241 570 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3790 1.34 - 1.46: 2500 1.46 - 1.58: 5460 1.58 - 1.69: 14 1.69 - 1.81: 147 Bond restraints: 11911 Sorted by residual: bond pdb=" CA ASP D 222 " pdb=" CB ASP D 222 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.75e-02 3.27e+03 1.09e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" N GLY B 48 " pdb=" CA GLY B 48 " ideal model delta sigma weight residual 1.449 1.464 -0.014 1.45e-02 4.76e+03 9.95e-01 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 9.93e-01 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.33e-01 ... (remaining 11906 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 15811 1.27 - 2.53: 225 2.53 - 3.80: 96 3.80 - 5.06: 24 5.06 - 6.33: 14 Bond angle restraints: 16170 Sorted by residual: angle pdb=" N VAL D 45 " pdb=" CA VAL D 45 " pdb=" C VAL D 45 " ideal model delta sigma weight residual 113.39 109.25 4.14 1.47e+00 4.63e-01 7.94e+00 angle pdb=" C ASP D 222 " pdb=" CA ASP D 222 " pdb=" CB ASP D 222 " ideal model delta sigma weight residual 111.23 115.85 -4.62 1.68e+00 3.54e-01 7.58e+00 angle pdb=" CA GLN D 360 " pdb=" CB GLN D 360 " pdb=" CG GLN D 360 " ideal model delta sigma weight residual 114.10 119.09 -4.99 2.00e+00 2.50e-01 6.23e+00 angle pdb=" CA ASP D 222 " pdb=" CB ASP D 222 " pdb=" CG ASP D 222 " ideal model delta sigma weight residual 112.60 114.93 -2.33 1.00e+00 1.00e+00 5.41e+00 angle pdb=" C GLY D 150 " pdb=" N ILE D 151 " pdb=" CA ILE D 151 " ideal model delta sigma weight residual 121.97 126.14 -4.17 1.80e+00 3.09e-01 5.36e+00 ... (remaining 16165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 6948 35.20 - 70.40: 215 70.40 - 105.60: 8 105.60 - 140.80: 2 140.80 - 176.00: 3 Dihedral angle restraints: 7176 sinusoidal: 2912 harmonic: 4264 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 116.00 -176.00 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 115.04 -175.04 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.38 -168.38 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 7173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1226 0.035 - 0.070: 386 0.070 - 0.105: 133 0.105 - 0.140: 45 0.140 - 0.175: 3 Chirality restraints: 1793 Sorted by residual: chirality pdb=" CA ASP D 222 " pdb=" N ASP D 222 " pdb=" C ASP D 222 " pdb=" CB ASP D 222 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CB THR B 202 " pdb=" CA THR B 202 " pdb=" OG1 THR B 202 " pdb=" CG2 THR B 202 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 1790 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 366 " 0.026 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO C 367 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 367 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 367 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 222 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C ASP C 222 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP C 222 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE C 223 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO B 243 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.017 5.00e-02 4.00e+02 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 109 2.63 - 3.20: 10032 3.20 - 3.77: 17143 3.77 - 4.33: 25091 4.33 - 4.90: 41933 Nonbonded interactions: 94308 Sorted by model distance: nonbonded pdb="MG MG C 402 " pdb=" O2 PO4 C 403 " model vdw 2.068 2.170 nonbonded pdb="MG MG D 401 " pdb=" O1G ATP D 402 " model vdw 2.148 2.170 nonbonded pdb=" OD1 ASP A 157 " pdb=" O3' ADP A 401 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASP B 157 " pdb=" O3' ADP B 401 " model vdw 2.249 3.040 nonbonded pdb=" O GLY B 156 " pdb=" OG1 THR B 303 " model vdw 2.253 3.040 ... (remaining 94303 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 371 or resid 402)) selection = (chain 'B' and (resid 6 through 371 or resid 402)) selection = (chain 'C' and (resid 6 through 371 or resid 402)) selection = (chain 'D' and resid 6 through 401) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.360 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.002 0.023 11911 Z= 0.087 Angle : 0.490 6.327 16170 Z= 0.244 Chirality : 0.041 0.175 1793 Planarity : 0.003 0.040 2063 Dihedral : 16.571 176.002 4448 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.13 % Favored : 97.80 % Rotamer: Outliers : 0.24 % Allowed : 17.20 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.22), residues: 1456 helix: 0.31 (0.21), residues: 598 sheet: -0.48 (0.32), residues: 266 loop : -0.21 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 95 TYR 0.005 0.001 TYR C 218 PHE 0.010 0.001 PHE C 223 TRP 0.010 0.001 TRP D 356 HIS 0.009 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00174 (11911) covalent geometry : angle 0.49036 (16170) hydrogen bonds : bond 0.26193 ( 560) hydrogen bonds : angle 7.79788 ( 1458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 141 average time/residue: 0.1071 time to fit residues: 22.0493 Evaluate side-chains 139 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 355 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN B 115 ASN B 161 HIS A 12 ASN C 49 GLN D 87 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112047 restraints weight = 14880.322| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.08 r_work: 0.3196 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11911 Z= 0.172 Angle : 0.585 7.248 16170 Z= 0.293 Chirality : 0.046 0.176 1793 Planarity : 0.004 0.039 2063 Dihedral : 9.415 144.837 1685 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 1.93 % Allowed : 16.80 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.22), residues: 1456 helix: 0.76 (0.22), residues: 590 sheet: -0.42 (0.32), residues: 255 loop : -0.11 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 335 TYR 0.012 0.001 TYR C 294 PHE 0.009 0.001 PHE B 200 TRP 0.013 0.002 TRP C 340 HIS 0.009 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00407 (11911) covalent geometry : angle 0.58456 (16170) hydrogen bonds : bond 0.04670 ( 560) hydrogen bonds : angle 5.34485 ( 1458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.4723 (mp-120) outliers start: 24 outliers final: 11 residues processed: 166 average time/residue: 0.1039 time to fit residues: 25.6092 Evaluate side-chains 150 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 135 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN A 12 ASN C 49 GLN C 297 ASN D 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.112430 restraints weight = 14949.509| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.08 r_work: 0.3196 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11911 Z= 0.152 Angle : 0.551 6.328 16170 Z= 0.273 Chirality : 0.045 0.168 1793 Planarity : 0.004 0.041 2063 Dihedral : 8.470 131.251 1683 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.34 % Favored : 97.60 % Rotamer: Outliers : 2.57 % Allowed : 16.48 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.22), residues: 1456 helix: 0.93 (0.22), residues: 584 sheet: -0.35 (0.32), residues: 253 loop : -0.27 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.008 0.001 TYR D 279 PHE 0.009 0.001 PHE B 352 TRP 0.012 0.002 TRP C 340 HIS 0.011 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00361 (11911) covalent geometry : angle 0.55121 (16170) hydrogen bonds : bond 0.04031 ( 560) hydrogen bonds : angle 5.01092 ( 1458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.6809 (m-30) cc_final: 0.5981 (p0) REVERT: C 49 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.5305 (mp-120) REVERT: C 222 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6447 (p0) outliers start: 32 outliers final: 18 residues processed: 166 average time/residue: 0.0973 time to fit residues: 24.1876 Evaluate side-chains 156 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 42 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN D 87 HIS D 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111158 restraints weight = 15030.324| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.10 r_work: 0.3179 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11911 Z= 0.182 Angle : 0.570 6.488 16170 Z= 0.282 Chirality : 0.046 0.164 1793 Planarity : 0.004 0.043 2063 Dihedral : 7.638 119.248 1680 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.05 % Rotamer: Outliers : 2.97 % Allowed : 16.72 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.22), residues: 1456 helix: 0.91 (0.22), residues: 582 sheet: -0.38 (0.31), residues: 260 loop : -0.43 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 210 TYR 0.011 0.001 TYR A 143 PHE 0.011 0.001 PHE B 352 TRP 0.013 0.002 TRP C 340 HIS 0.011 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00445 (11911) covalent geometry : angle 0.56969 (16170) hydrogen bonds : bond 0.04063 ( 560) hydrogen bonds : angle 4.88996 ( 1458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8757 (tp) REVERT: C 64 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8353 (pp) outliers start: 37 outliers final: 24 residues processed: 169 average time/residue: 0.0949 time to fit residues: 24.2990 Evaluate side-chains 162 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 99 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN A 12 ASN D 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114084 restraints weight = 14995.955| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.84 r_work: 0.3211 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11911 Z= 0.169 Angle : 0.562 6.208 16170 Z= 0.279 Chirality : 0.046 0.163 1793 Planarity : 0.004 0.043 2063 Dihedral : 7.249 109.744 1680 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 3.30 % Allowed : 16.88 % Favored : 79.82 % 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 aren not related in a simple way. whole: 0.09 (0.22), residues: 1456 helix: 0.93 (0.22), residues: 582 sheet: -0.35 (0.31), residues: 260 loop : -0.48 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 210 TYR 0.008 0.001 TYR C 362 PHE 0.011 0.001 PHE B 352 TRP 0.013 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00409 (11911) covalent geometry : angle 0.56151 (16170) hydrogen bonds : bond 0.03901 ( 560) hydrogen bonds : angle 4.83710 ( 1458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: B 180 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8851 (tp) REVERT: C 64 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8526 (pp) REVERT: C 314 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.6490 (tp40) outliers start: 41 outliers final: 28 residues processed: 173 average time/residue: 0.0945 time to fit residues: 24.6833 Evaluate side-chains 172 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 24 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 67 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 101 HIS C 161 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.114969 restraints weight = 14922.417| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.84 r_work: 0.3208 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11911 Z= 0.141 Angle : 0.539 6.243 16170 Z= 0.266 Chirality : 0.045 0.161 1793 Planarity : 0.004 0.041 2063 Dihedral : 6.862 100.570 1680 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 3.05 % Allowed : 16.96 % Favored : 79.98 % 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 aren not related in a simple way. whole: 0.21 (0.22), residues: 1456 helix: 1.04 (0.22), residues: 583 sheet: -0.25 (0.32), residues: 254 loop : -0.46 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 210 TYR 0.011 0.001 TYR A 143 PHE 0.009 0.001 PHE B 352 TRP 0.013 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00336 (11911) covalent geometry : angle 0.53947 (16170) hydrogen bonds : bond 0.03534 ( 560) hydrogen bonds : angle 4.70679 ( 1458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: B 104 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8219 (tp) REVERT: B 180 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8817 (tp) REVERT: C 11 ASP cc_start: 0.8148 (t0) cc_final: 0.7898 (t70) REVERT: D 253 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7601 (mp0) outliers start: 38 outliers final: 26 residues processed: 175 average time/residue: 0.0952 time to fit residues: 25.2209 Evaluate side-chains 170 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 55 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 131 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN D 87 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.117132 restraints weight = 14755.516| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.83 r_work: 0.3237 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11911 Z= 0.097 Angle : 0.513 6.069 16170 Z= 0.252 Chirality : 0.044 0.158 1793 Planarity : 0.004 0.038 2063 Dihedral : 6.543 92.536 1680 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.27 % Favored : 97.66 % Rotamer: Outliers : 1.85 % Allowed : 18.49 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.22), residues: 1456 helix: 1.25 (0.22), residues: 585 sheet: -0.11 (0.33), residues: 250 loop : -0.30 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 210 TYR 0.008 0.001 TYR B 218 PHE 0.007 0.001 PHE A 255 TRP 0.011 0.001 TRP C 340 HIS 0.009 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00212 (11911) covalent geometry : angle 0.51346 (16170) hydrogen bonds : bond 0.02981 ( 560) hydrogen bonds : angle 4.57057 ( 1458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: C 11 ASP cc_start: 0.8073 (t0) cc_final: 0.7857 (t70) REVERT: C 64 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8469 (pp) REVERT: D 253 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7707 (mp0) outliers start: 23 outliers final: 16 residues processed: 166 average time/residue: 0.0950 time to fit residues: 23.7526 Evaluate side-chains 160 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 95 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 57 optimal weight: 0.7980 chunk 38 optimal weight: 0.0980 chunk 96 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN D 87 HIS D 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.141143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118960 restraints weight = 14826.952| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.80 r_work: 0.3264 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11911 Z= 0.089 Angle : 0.504 6.196 16170 Z= 0.246 Chirality : 0.043 0.158 1793 Planarity : 0.004 0.035 2063 Dihedral : 6.119 80.001 1680 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.47 % Favored : 97.46 % Rotamer: Outliers : 1.77 % Allowed : 18.97 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.22), residues: 1456 helix: 1.43 (0.22), residues: 585 sheet: 0.00 (0.32), residues: 252 loop : -0.18 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 210 TYR 0.010 0.001 TYR A 143 PHE 0.007 0.001 PHE A 255 TRP 0.009 0.001 TRP C 340 HIS 0.009 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00193 (11911) covalent geometry : angle 0.50412 (16170) hydrogen bonds : bond 0.02698 ( 560) hydrogen bonds : angle 4.42223 ( 1458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: C 11 ASP cc_start: 0.8025 (t0) cc_final: 0.7820 (t70) REVERT: C 64 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8420 (pp) REVERT: C 169 TYR cc_start: 0.7070 (m-80) cc_final: 0.6773 (m-10) REVERT: C 222 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6542 (p0) REVERT: D 253 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7844 (mp0) outliers start: 22 outliers final: 15 residues processed: 167 average time/residue: 0.1031 time to fit residues: 25.7074 Evaluate side-chains 160 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 278 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 29 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 118 optimal weight: 0.0370 chunk 53 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN D 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116768 restraints weight = 14789.659| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.80 r_work: 0.3231 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11911 Z= 0.126 Angle : 0.533 6.403 16170 Z= 0.262 Chirality : 0.045 0.196 1793 Planarity : 0.004 0.037 2063 Dihedral : 6.233 82.562 1680 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.47 % Favored : 97.46 % Rotamer: Outliers : 2.25 % Allowed : 18.33 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.22), residues: 1456 helix: 1.35 (0.22), residues: 586 sheet: -0.01 (0.32), residues: 252 loop : -0.25 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 210 TYR 0.007 0.001 TYR C 306 PHE 0.009 0.001 PHE B 352 TRP 0.010 0.001 TRP C 340 HIS 0.010 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00297 (11911) covalent geometry : angle 0.53250 (16170) hydrogen bonds : bond 0.03153 ( 560) hydrogen bonds : angle 4.46170 ( 1458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: C 64 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8460 (pp) REVERT: C 169 TYR cc_start: 0.7120 (m-80) cc_final: 0.6845 (m-10) REVERT: D 253 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7812 (mp0) outliers start: 28 outliers final: 23 residues processed: 166 average time/residue: 0.0965 time to fit residues: 24.2863 Evaluate side-chains 168 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 18 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 96 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN D 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117403 restraints weight = 14888.628| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.82 r_work: 0.3238 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11911 Z= 0.107 Angle : 0.522 6.245 16170 Z= 0.256 Chirality : 0.044 0.163 1793 Planarity : 0.004 0.036 2063 Dihedral : 6.193 81.598 1680 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.40 % Favored : 97.53 % Rotamer: Outliers : 2.41 % Allowed : 18.17 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.22), residues: 1456 helix: 1.40 (0.22), residues: 586 sheet: 0.05 (0.32), residues: 253 loop : -0.23 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 210 TYR 0.010 0.001 TYR A 143 PHE 0.008 0.001 PHE A 255 TRP 0.010 0.001 TRP C 340 HIS 0.011 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00244 (11911) covalent geometry : angle 0.52184 (16170) hydrogen bonds : bond 0.02967 ( 560) hydrogen bonds : angle 4.44432 ( 1458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: B 104 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8202 (tp) REVERT: C 64 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8460 (pp) REVERT: C 169 TYR cc_start: 0.7089 (m-80) cc_final: 0.6811 (m-10) REVERT: D 253 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7812 (mp0) outliers start: 30 outliers final: 24 residues processed: 166 average time/residue: 0.0948 time to fit residues: 23.7494 Evaluate side-chains 169 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 105 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 108 optimal weight: 0.0870 chunk 85 optimal weight: 1.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN D 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116265 restraints weight = 14835.549| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.81 r_work: 0.3224 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11911 Z= 0.137 Angle : 0.539 6.346 16170 Z= 0.265 Chirality : 0.045 0.167 1793 Planarity : 0.004 0.038 2063 Dihedral : 6.265 84.230 1680 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.25 % Rotamer: Outliers : 2.65 % Allowed : 18.01 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.22), residues: 1456 helix: 1.31 (0.22), residues: 586 sheet: 0.02 (0.32), residues: 253 loop : -0.29 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 210 TYR 0.007 0.001 TYR D 279 PHE 0.010 0.001 PHE B 352 TRP 0.011 0.001 TRP C 340 HIS 0.011 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00327 (11911) covalent geometry : angle 0.53883 (16170) hydrogen bonds : bond 0.03233 ( 560) hydrogen bonds : angle 4.48458 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2960.76 seconds wall clock time: 51 minutes 31.89 seconds (3091.89 seconds total)