Starting phenix.real_space_refine on Tue Jun 10 13:18:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ru0_19501/06_2025/8ru0_19501.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ru0_19501/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ru0_19501/06_2025/8ru0_19501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ru0_19501/06_2025/8ru0_19501.map" model { file = "/net/cci-nas-00/data/ceres_data/8ru0_19501/06_2025/8ru0_19501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ru0_19501/06_2025/8ru0_19501.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.10, per 1000 atoms: 0.78 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: 3.29 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.20 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: 4.64 Time building geometry restraints manager: 3.43 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 371 or resid 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: 2.670 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 32.580 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.890 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP D 356 HIS 0.009 0.001 HIS D 87 PHE 0.010 0.001 PHE C 223 TYR 0.005 0.001 TYR C 218 ARG 0.002 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.26193 ( 560) hydrogen bonds : angle 7.79788 ( 1458) covalent geometry : bond 0.00174 (11911) covalent geometry : angle 0.49036 (16170) *********************** 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 : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 141 average time/residue: 0.2770 time to fit residues: 57.0557 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 : 1.256 ------------------------------------------------------------------------------- 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 123 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 85 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- 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 A 12 ASN A 101 HIS C 49 GLN C 297 ASN D 87 HIS D 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109566 restraints weight = 14972.588| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.04 r_work: 0.3162 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 11911 Z= 0.272 Angle : 0.667 7.337 16170 Z= 0.338 Chirality : 0.050 0.205 1793 Planarity : 0.005 0.044 2063 Dihedral : 9.362 140.146 1685 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 1.93 % Allowed : 17.60 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1456 helix: 0.48 (0.21), residues: 588 sheet: -0.55 (0.32), residues: 255 loop : -0.41 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 340 HIS 0.009 0.002 HIS D 87 PHE 0.014 0.002 PHE B 352 TYR 0.015 0.002 TYR C 294 ARG 0.004 0.000 ARG D 335 Details of bonding type rmsd hydrogen bonds : bond 0.05303 ( 560) hydrogen bonds : angle 5.42380 ( 1458) covalent geometry : bond 0.00663 (11911) covalent geometry : angle 0.66730 (16170) *********************** 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 172 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 GLN cc_start: 0.6465 (OUTLIER) cc_final: 0.4841 (mp-120) outliers start: 24 outliers final: 10 residues processed: 166 average time/residue: 0.2873 time to fit residues: 71.4142 Evaluate side-chains 150 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 2.079 ------------------------------------------------------------------------------- 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 288 ASP Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR 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 97 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 100 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 chunk 133 optimal weight: 0.0040 chunk 124 optimal weight: 5.9990 overall best weight: 0.4750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 115 ASN B 161 HIS A 12 ASN C 297 ASN D 87 HIS D 296 ASN D 314 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114342 restraints weight = 14863.177| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.09 r_work: 0.3224 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11911 Z= 0.095 Angle : 0.521 6.353 16170 Z= 0.257 Chirality : 0.044 0.167 1793 Planarity : 0.004 0.039 2063 Dihedral : 8.237 128.381 1680 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.92 % Favored : 98.01 % Rotamer: Outliers : 2.09 % Allowed : 17.44 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1456 helix: 0.98 (0.22), residues: 586 sheet: -0.31 (0.32), residues: 255 loop : -0.23 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.010 0.001 HIS D 87 PHE 0.006 0.001 PHE D 31 TYR 0.011 0.001 TYR C 294 ARG 0.004 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 560) hydrogen bonds : angle 4.96426 ( 1458) covalent geometry : bond 0.00200 (11911) covalent geometry : angle 0.52087 (16170) *********************** 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 168 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8265 (t0) REVERT: A 222 ASP cc_start: 0.6790 (m-30) cc_final: 0.5970 (p0) REVERT: C 222 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.6418 (p0) outliers start: 26 outliers final: 15 residues processed: 164 average time/residue: 0.2201 time to fit residues: 53.7172 Evaluate side-chains 153 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 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 99 GLU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 349 LEU 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 202 THR Chi-restraints excluded: chain D residue 299 MET 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 141 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 A 12 ASN C 49 GLN D 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.109108 restraints weight = 15010.370| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.07 r_work: 0.3164 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 11911 Z= 0.267 Angle : 0.638 6.917 16170 Z= 0.320 Chirality : 0.050 0.183 1793 Planarity : 0.005 0.047 2063 Dihedral : 7.771 120.378 1680 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.22 % Rotamer: Outliers : 3.46 % Allowed : 16.96 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1456 helix: 0.69 (0.22), residues: 582 sheet: -0.50 (0.31), residues: 260 loop : -0.69 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 340 HIS 0.011 0.002 HIS D 87 PHE 0.016 0.002 PHE B 352 TYR 0.016 0.002 TYR C 294 ARG 0.007 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 560) hydrogen bonds : angle 5.02484 ( 1458) covalent geometry : bond 0.00655 (11911) covalent geometry : angle 0.63758 (16170) *********************** 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 181 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 1.386 Fit side-chains revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: C 64 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8457 (pp) outliers start: 43 outliers final: 29 residues processed: 171 average time/residue: 0.2140 time to fit residues: 54.9618 Evaluate side-chains 166 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 111 ASN 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 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 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 87 HIS 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 165 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 124 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 HIS 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 = 0.3600 r_free = 0.3600 target = 0.135560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111270 restraints weight = 14777.534| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.06 r_work: 0.3193 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11911 Z= 0.163 Angle : 0.568 6.301 16170 Z= 0.283 Chirality : 0.046 0.166 1793 Planarity : 0.004 0.045 2063 Dihedral : 7.235 108.685 1680 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 2.89 % Allowed : 18.41 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1456 helix: 0.81 (0.22), residues: 582 sheet: -0.38 (0.32), residues: 254 loop : -0.64 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.012 0.001 HIS D 87 PHE 0.010 0.001 PHE B 352 TYR 0.015 0.001 TYR C 294 ARG 0.005 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 560) hydrogen bonds : angle 4.87124 ( 1458) covalent geometry : bond 0.00392 (11911) covalent geometry : angle 0.56754 (16170) *********************** 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 173 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: C 64 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8451 (pp) REVERT: C 314 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6388 (tp40) REVERT: D 253 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7361 (mp0) outliers start: 36 outliers final: 23 residues processed: 164 average time/residue: 0.2109 time to fit residues: 51.5110 Evaluate side-chains 163 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 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 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 D residue 47 MET Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 148 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 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 16 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN A 12 ASN ** 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 = 0.3592 r_free = 0.3592 target = 0.134915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110499 restraints weight = 14986.026| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.08 r_work: 0.3174 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11911 Z= 0.189 Angle : 0.580 6.385 16170 Z= 0.289 Chirality : 0.047 0.167 1793 Planarity : 0.004 0.044 2063 Dihedral : 7.062 104.201 1680 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.29 % Rotamer: Outliers : 3.54 % Allowed : 17.85 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.22), residues: 1456 helix: 0.80 (0.22), residues: 583 sheet: -0.36 (0.32), residues: 254 loop : -0.71 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.004 0.001 HIS B 88 PHE 0.011 0.001 PHE B 352 TYR 0.017 0.001 TYR C 294 ARG 0.005 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 560) hydrogen bonds : angle 4.81771 ( 1458) covalent geometry : bond 0.00461 (11911) covalent geometry : angle 0.58040 (16170) *********************** 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 187 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: B 104 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8220 (tp) REVERT: C 64 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8480 (pp) REVERT: C 314 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6405 (tp40) REVERT: D 253 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7401 (mp0) outliers start: 44 outliers final: 33 residues processed: 179 average time/residue: 0.2155 time to fit residues: 57.9060 Evaluate side-chains 179 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 111 ASN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 351 THR 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 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 143 TYR Chi-restraints excluded: chain D residue 148 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 338 SER 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 56 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 112 optimal weight: 0.0050 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114240 restraints weight = 14934.306| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.09 r_work: 0.3232 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11911 Z= 0.093 Angle : 0.515 6.022 16170 Z= 0.252 Chirality : 0.043 0.167 1793 Planarity : 0.004 0.047 2063 Dihedral : 6.609 91.020 1680 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.20 % Favored : 97.73 % Rotamer: Outliers : 2.57 % Allowed : 18.89 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.22), residues: 1456 helix: 1.17 (0.22), residues: 581 sheet: -0.14 (0.32), residues: 250 loop : -0.46 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.010 0.001 HIS D 87 PHE 0.008 0.001 PHE A 255 TYR 0.010 0.001 TYR C 294 ARG 0.004 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.02899 ( 560) hydrogen bonds : angle 4.60069 ( 1458) covalent geometry : bond 0.00199 (11911) covalent geometry : angle 0.51458 (16170) *********************** 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 182 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: B 104 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8199 (tp) REVERT: C 11 ASP cc_start: 0.8108 (t0) cc_final: 0.7896 (t70) REVERT: C 64 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8396 (pp) REVERT: D 47 MET cc_start: 0.5657 (OUTLIER) cc_final: 0.4204 (tmm) REVERT: D 253 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7546 (mp0) outliers start: 32 outliers final: 19 residues processed: 172 average time/residue: 0.2155 time to fit residues: 55.6884 Evaluate side-chains 159 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 202 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain A residue 47 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 288 ASP Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 47 MET 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 253 GLU Chi-restraints excluded: chain D residue 299 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 33 optimal weight: 0.0470 chunk 96 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 5 optimal weight: 0.0270 chunk 135 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN C 297 ASN D 87 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 = 0.3599 r_free = 0.3599 target = 0.135680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110994 restraints weight = 14872.748| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.10 r_work: 0.3193 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11911 Z= 0.139 Angle : 0.543 6.293 16170 Z= 0.268 Chirality : 0.045 0.185 1793 Planarity : 0.004 0.040 2063 Dihedral : 6.620 92.642 1680 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.05 % Rotamer: Outliers : 2.65 % Allowed : 19.05 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1456 helix: 1.11 (0.22), residues: 583 sheet: -0.15 (0.32), residues: 254 loop : -0.49 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.009 0.001 HIS D 87 PHE 0.008 0.001 PHE B 352 TYR 0.011 0.001 TYR A 143 ARG 0.004 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 560) hydrogen bonds : angle 4.59372 ( 1458) covalent geometry : bond 0.00332 (11911) covalent geometry : angle 0.54334 (16170) *********************** 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 167 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: B 104 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8180 (tp) REVERT: C 11 ASP cc_start: 0.8107 (t0) cc_final: 0.7895 (t70) REVERT: C 64 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8346 (pp) REVERT: D 253 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7563 (mp0) outliers start: 33 outliers final: 23 residues processed: 162 average time/residue: 0.2056 time to fit residues: 50.0218 Evaluate side-chains 161 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 202 THR Chi-restraints excluded: chain A residue 47 MET 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 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 349 LEU Chi-restraints excluded: chain C residue 351 THR 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 299 MET Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 1 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 73 optimal weight: 0.0050 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111687 restraints weight = 14925.587| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.05 r_work: 0.3193 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11911 Z= 0.154 Angle : 0.558 6.286 16170 Z= 0.276 Chirality : 0.046 0.177 1793 Planarity : 0.004 0.041 2063 Dihedral : 6.689 92.889 1680 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 2.89 % Allowed : 18.89 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1456 helix: 1.06 (0.22), residues: 584 sheet: -0.18 (0.32), residues: 254 loop : -0.54 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.010 0.001 HIS D 87 PHE 0.009 0.001 PHE B 352 TYR 0.008 0.001 TYR D 279 ARG 0.004 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 560) hydrogen bonds : angle 4.62537 ( 1458) covalent geometry : bond 0.00372 (11911) covalent geometry : angle 0.55804 (16170) *********************** 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 173 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: B 104 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8128 (tp) REVERT: C 11 ASP cc_start: 0.8081 (t0) cc_final: 0.7869 (t70) REVERT: C 64 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8375 (pp) REVERT: C 325 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6137 (mmt) REVERT: D 47 MET cc_start: 0.5656 (OUTLIER) cc_final: 0.4211 (tmm) REVERT: D 253 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7497 (mp0) outliers start: 36 outliers final: 28 residues processed: 164 average time/residue: 0.2192 time to fit residues: 54.4096 Evaluate side-chains 170 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 202 THR Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 351 THR 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 300 SER Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 47 MET 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 299 MET 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 115 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 142 optimal weight: 0.0010 chunk 144 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.137502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113172 restraints weight = 14733.170| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.07 r_work: 0.3205 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11911 Z= 0.117 Angle : 0.531 6.168 16170 Z= 0.261 Chirality : 0.044 0.166 1793 Planarity : 0.004 0.040 2063 Dihedral : 6.522 87.317 1680 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 2.65 % Allowed : 19.37 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1456 helix: 1.20 (0.22), residues: 583 sheet: -0.10 (0.32), residues: 252 loop : -0.48 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 340 HIS 0.010 0.001 HIS D 87 PHE 0.008 0.001 PHE A 255 TYR 0.010 0.001 TYR A 143 ARG 0.003 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 560) hydrogen bonds : angle 4.53469 ( 1458) covalent geometry : bond 0.00273 (11911) covalent geometry : angle 0.53092 (16170) ********************** 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 170 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: B 104 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8131 (tp) REVERT: C 11 ASP cc_start: 0.8050 (t0) cc_final: 0.7847 (t70) REVERT: C 64 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8326 (pp) REVERT: D 253 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7560 (mp0) outliers start: 33 outliers final: 27 residues processed: 164 average time/residue: 0.2172 time to fit residues: 53.6722 Evaluate side-chains 167 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 202 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 351 THR 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 288 ASP Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 303 THR 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 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 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 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 61 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN C 101 HIS D 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.108259 restraints weight = 14991.265| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.07 r_work: 0.3145 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 11911 Z= 0.292 Angle : 0.665 6.721 16170 Z= 0.336 Chirality : 0.051 0.195 1793 Planarity : 0.005 0.046 2063 Dihedral : 7.201 104.482 1680 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.60 % Favored : 95.33 % Rotamer: Outliers : 3.22 % Allowed : 18.89 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1456 helix: 0.71 (0.22), residues: 584 sheet: -0.42 (0.32), residues: 255 loop : -0.82 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 340 HIS 0.010 0.002 HIS D 87 PHE 0.016 0.002 PHE B 352 TYR 0.012 0.002 TYR C 169 ARG 0.005 0.001 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 560) hydrogen bonds : angle 4.88780 ( 1458) covalent geometry : bond 0.00718 (11911) covalent geometry : angle 0.66488 (16170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6221.82 seconds wall clock time: 109 minutes 37.32 seconds (6577.32 seconds total)