Starting phenix.real_space_refine on Thu Mar 13 09:48:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdl_38280/03_2025/8xdl_38280.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdl_38280/03_2025/8xdl_38280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xdl_38280/03_2025/8xdl_38280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdl_38280/03_2025/8xdl_38280.map" model { file = "/net/cci-nas-00/data/ceres_data/8xdl_38280/03_2025/8xdl_38280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdl_38280/03_2025/8xdl_38280.cif" } resolution = 2.44 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= 0.000 sd= 0.024 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 6 5.49 5 Mg 3 5.21 5 S 62 5.16 5 C 5517 2.51 5 N 1474 2.21 5 O 1684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8746 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" 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: "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: "C" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 19, 'TRANS': 347} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.53, per 1000 atoms: 0.86 Number of scatterers: 8746 At special positions: 0 Unit cell: (98.28, 75.6, 136.92, 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 62 16.00 P 6 15.00 Mg 3 11.99 O 1684 8.00 N 1474 7.00 C 5517 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: 2.19 Conformation dependent library (CDL) restraints added in 976.7 milliseconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 18 sheets defined 51.8% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.661A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.905A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.506A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 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 285 removed outlier: 3.824A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 305 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 347 Processing helix chain 'A' and resid 348 through 353 removed outlier: 6.331A pdb=" N THR A 351 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.661A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.906A 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: 3.507A 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 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.824A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 305 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 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 6.331A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.662A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.906A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.506A 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 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.824A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 353 removed outlier: 6.331A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.719A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.362A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.719A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.363A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 removed outlier: 6.718A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.444A 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 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: 6.362A 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 241 464 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 2.59 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: 2844 1.34 - 1.46: 1933 1.46 - 1.58: 4038 1.58 - 1.69: 12 1.69 - 1.81: 110 Bond restraints: 8937 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.06e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" CB GLU C 99 " pdb=" CG GLU C 99 " ideal model delta sigma weight residual 1.520 1.598 -0.078 3.00e-02 1.11e+03 6.77e+00 bond pdb=" CB GLU A 99 " pdb=" CG GLU A 99 " ideal model delta sigma weight residual 1.520 1.598 -0.078 3.00e-02 1.11e+03 6.76e+00 ... (remaining 8932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 12041 3.43 - 6.86: 76 6.86 - 10.29: 12 10.29 - 13.72: 0 13.72 - 17.16: 3 Bond angle restraints: 12132 Sorted by residual: angle pdb=" CA GLU A 99 " pdb=" CB GLU A 99 " pdb=" CG GLU A 99 " ideal model delta sigma weight residual 114.10 131.26 -17.16 2.00e+00 2.50e-01 7.36e+01 angle pdb=" CA GLU C 99 " pdb=" CB GLU C 99 " pdb=" CG GLU C 99 " ideal model delta sigma weight residual 114.10 131.24 -17.14 2.00e+00 2.50e-01 7.34e+01 angle pdb=" CA GLU B 99 " pdb=" CB GLU B 99 " pdb=" CG GLU B 99 " ideal model delta sigma weight residual 114.10 131.18 -17.08 2.00e+00 2.50e-01 7.29e+01 angle pdb=" CB GLU B 99 " pdb=" CG GLU B 99 " pdb=" CD GLU B 99 " ideal model delta sigma weight residual 112.60 122.39 -9.79 1.70e+00 3.46e-01 3.32e+01 angle pdb=" CB GLU A 99 " pdb=" CG GLU A 99 " pdb=" CD GLU A 99 " ideal model delta sigma weight residual 112.60 122.30 -9.70 1.70e+00 3.46e-01 3.26e+01 ... (remaining 12127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.14: 4805 20.14 - 40.28: 369 40.28 - 60.43: 161 60.43 - 80.57: 16 80.57 - 100.71: 21 Dihedral angle restraints: 5372 sinusoidal: 2168 harmonic: 3204 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -160.71 100.71 1 2.00e+01 2.50e-03 2.85e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 -160.70 100.69 1 2.00e+01 2.50e-03 2.85e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -160.67 100.67 1 2.00e+01 2.50e-03 2.84e+01 ... (remaining 5369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 929 0.038 - 0.076: 274 0.076 - 0.114: 122 0.114 - 0.152: 21 0.152 - 0.190: 3 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CA GLU A 99 " pdb=" N GLU A 99 " pdb=" C GLU A 99 " pdb=" CB GLU A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.02e-01 chirality pdb=" CA GLU C 99 " pdb=" N GLU C 99 " pdb=" C GLU C 99 " pdb=" CB GLU C 99 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA GLU B 99 " pdb=" N GLU B 99 " pdb=" C GLU B 99 " pdb=" CB GLU B 99 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.82e-01 ... (remaining 1346 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 332 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO C 333 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 332 " -0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO B 333 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 333 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 333 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 332 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO A 333 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " 0.031 5.00e-02 4.00e+02 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2245 2.81 - 3.33: 7859 3.33 - 3.85: 14292 3.85 - 4.38: 17662 4.38 - 4.90: 29218 Nonbonded interactions: 71276 Sorted by model distance: nonbonded pdb=" O GLY C 156 " pdb=" OG1 THR C 303 " model vdw 2.286 3.040 nonbonded pdb=" O GLY A 156 " pdb=" OG1 THR A 303 " model vdw 2.287 3.040 nonbonded pdb=" O GLY B 156 " pdb=" OG1 THR B 303 " model vdw 2.287 3.040 nonbonded pdb=" OD2 ASP C 211 " pdb=" OH TYR C 240 " model vdw 2.292 3.040 nonbonded pdb=" OD2 ASP B 211 " pdb=" OH TYR B 240 " model vdw 2.292 3.040 ... (remaining 71271 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 5 through 371 or resid 401 through 402)) selection = (chain 'B' and (resid 5 through 371 or resid 401 through 402)) selection = chain 'C' } 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: 9.030 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.180 Find NCS groups from input model: 0.360 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:11.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 0.004 0.078 8937 Z= 0.238 Angle : 0.775 17.156 12132 Z= 0.390 Chirality : 0.045 0.190 1349 Planarity : 0.006 0.056 1550 Dihedral : 18.263 100.710 3322 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 6.74 % Allowed : 12.30 % Favored : 80.96 % 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: 1.09 (0.24), residues: 1094 helix: 0.74 (0.24), residues: 435 sheet: 0.40 (0.33), residues: 207 loop : 1.16 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS A 161 PHE 0.009 0.001 PHE A 255 TYR 0.008 0.001 TYR C 294 ARG 0.003 0.000 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 173 time to evaluate : 1.057 Fit side-chains REVERT: A 44 MET cc_start: 0.3293 (mmm) cc_final: 0.3073 (mmm) REVERT: A 47 MET cc_start: 0.2932 (OUTLIER) cc_final: 0.2347 (mmt) REVERT: B 47 MET cc_start: 0.4723 (OUTLIER) cc_final: 0.3908 (mmm) REVERT: B 355 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6546 (mmt) REVERT: C 325 MET cc_start: 0.8223 (mmp) cc_final: 0.8016 (mmp) outliers start: 63 outliers final: 4 residues processed: 200 average time/residue: 1.4662 time to fit residues: 308.9854 Evaluate side-chains 128 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 355 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 225 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.128940 restraints weight = 8423.233| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.04 r_work: 0.3367 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8937 Z= 0.279 Angle : 0.723 8.817 12132 Z= 0.362 Chirality : 0.049 0.202 1349 Planarity : 0.006 0.052 1550 Dihedral : 8.356 97.811 1262 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.99 % Allowed : 15.19 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.38 (0.25), residues: 1094 helix: 1.25 (0.25), residues: 440 sheet: 0.47 (0.36), residues: 194 loop : 1.02 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 79 HIS 0.006 0.002 HIS A 161 PHE 0.013 0.002 PHE A 31 TYR 0.012 0.001 TYR C 166 ARG 0.005 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.945 Fit side-chains REVERT: A 215 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7596 (tppp) REVERT: A 227 MET cc_start: 0.8854 (mmm) cc_final: 0.8324 (mmm) REVERT: A 314 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: B 64 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8837 (pt) REVERT: B 72 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: B 314 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: B 336 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7790 (mttp) REVERT: B 355 MET cc_start: 0.8295 (mmt) cc_final: 0.7989 (mmm) REVERT: C 64 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8445 (pp) REVERT: C 100 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6696 (mt-10) REVERT: C 119 MET cc_start: 0.7985 (mtp) cc_final: 0.7774 (mtp) REVERT: C 211 ASP cc_start: 0.8255 (t70) cc_final: 0.8006 (t70) REVERT: C 313 MET cc_start: 0.8774 (tpt) cc_final: 0.8420 (tpt) REVERT: C 354 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7539 (pt0) outliers start: 28 outliers final: 11 residues processed: 153 average time/residue: 1.4173 time to fit residues: 228.7975 Evaluate side-chains 140 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 354 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.0270 chunk 41 optimal weight: 0.0570 chunk 21 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 225 ASN ** A 360 GLN ** 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 = 0.3612 r_free = 0.3612 target = 0.143101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126473 restraints weight = 8603.620| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.03 r_work: 0.3318 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8937 Z= 0.204 Angle : 0.640 7.747 12132 Z= 0.313 Chirality : 0.046 0.210 1349 Planarity : 0.005 0.034 1550 Dihedral : 7.551 93.452 1245 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.85 % Allowed : 14.87 % Favored : 81.28 % 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: 1.51 (0.25), residues: 1094 helix: 1.38 (0.25), residues: 440 sheet: 0.48 (0.34), residues: 205 loop : 1.11 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 340 HIS 0.005 0.001 HIS A 161 PHE 0.010 0.002 PHE A 31 TYR 0.008 0.001 TYR C 166 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.954 Fit side-chains REVERT: A 47 MET cc_start: 0.4098 (mpt) cc_final: 0.3670 (mmt) REVERT: A 237 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: A 354 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7378 (mp-120) REVERT: B 47 MET cc_start: 0.4251 (OUTLIER) cc_final: 0.3553 (mmm) REVERT: B 64 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8878 (pt) REVERT: B 314 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: B 355 MET cc_start: 0.8413 (mmt) cc_final: 0.8094 (mmm) REVERT: C 64 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8470 (pp) REVERT: C 100 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6852 (mt-10) REVERT: C 119 MET cc_start: 0.8015 (mtp) cc_final: 0.7811 (mtp) REVERT: C 211 ASP cc_start: 0.8300 (t70) cc_final: 0.8048 (t70) REVERT: C 354 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7677 (pt0) outliers start: 36 outliers final: 10 residues processed: 150 average time/residue: 1.4498 time to fit residues: 229.3427 Evaluate side-chains 144 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 354 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 225 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN C 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120541 restraints weight = 8452.987| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.02 r_work: 0.3225 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 8937 Z= 0.533 Angle : 0.889 11.420 12132 Z= 0.449 Chirality : 0.058 0.232 1349 Planarity : 0.007 0.093 1550 Dihedral : 8.543 111.352 1245 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.39 % Allowed : 14.97 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.86 (0.25), residues: 1094 helix: 0.81 (0.24), residues: 452 sheet: 0.24 (0.35), residues: 194 loop : 0.72 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP A 340 HIS 0.007 0.002 HIS B 161 PHE 0.018 0.003 PHE C 31 TYR 0.015 0.002 TYR B 133 ARG 0.009 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.966 Fit side-chains REVERT: A 47 MET cc_start: 0.4665 (mpt) cc_final: 0.4441 (mmt) REVERT: A 215 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7699 (tppp) REVERT: A 314 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: A 326 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7485 (mmpt) REVERT: B 39 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7316 (mtm180) REVERT: B 72 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: B 314 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: B 355 MET cc_start: 0.8560 (mmt) cc_final: 0.8329 (mmm) REVERT: C 100 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7119 (tp30) REVERT: C 211 ASP cc_start: 0.8388 (t70) cc_final: 0.8187 (t70) REVERT: C 314 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: C 354 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.8002 (pt0) outliers start: 41 outliers final: 17 residues processed: 153 average time/residue: 1.4686 time to fit residues: 236.7213 Evaluate side-chains 141 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 0.0010 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 0.0670 overall best weight: 0.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.125908 restraints weight = 8533.941| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.04 r_work: 0.3312 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8937 Z= 0.179 Angle : 0.624 7.247 12132 Z= 0.305 Chirality : 0.046 0.202 1349 Planarity : 0.004 0.036 1550 Dihedral : 7.784 98.502 1245 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.57 % Allowed : 16.36 % Favored : 81.07 % 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: 1.34 (0.25), residues: 1094 helix: 1.14 (0.25), residues: 453 sheet: 0.43 (0.34), residues: 207 loop : 1.13 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 340 HIS 0.004 0.001 HIS A 161 PHE 0.011 0.001 PHE C 255 TYR 0.009 0.001 TYR C 166 ARG 0.004 0.000 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.944 Fit side-chains REVERT: A 47 MET cc_start: 0.4751 (mpt) cc_final: 0.4428 (mmt) REVERT: A 237 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: A 314 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: A 326 LYS cc_start: 0.7741 (mmmt) cc_final: 0.7369 (mmpt) REVERT: B 39 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7315 (mtm180) REVERT: B 72 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: B 314 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: B 355 MET cc_start: 0.8380 (mmt) cc_final: 0.8144 (mmm) REVERT: C 100 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: C 125 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: C 211 ASP cc_start: 0.8382 (t70) cc_final: 0.8154 (t70) REVERT: C 326 LYS cc_start: 0.8029 (tptt) cc_final: 0.7824 (tptp) REVERT: C 354 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7914 (pt0) outliers start: 24 outliers final: 10 residues processed: 144 average time/residue: 1.5005 time to fit residues: 227.9546 Evaluate side-chains 145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 354 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 0.0770 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 225 ASN B 12 ASN C 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123772 restraints weight = 8513.095| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.04 r_work: 0.3283 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8937 Z= 0.266 Angle : 0.689 8.526 12132 Z= 0.339 Chirality : 0.049 0.218 1349 Planarity : 0.005 0.048 1550 Dihedral : 7.874 99.138 1245 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.10 % Allowed : 16.58 % Favored : 80.32 % 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: 1.25 (0.25), residues: 1094 helix: 1.11 (0.25), residues: 452 sheet: 0.36 (0.36), residues: 194 loop : 1.00 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 340 HIS 0.005 0.001 HIS B 161 PHE 0.013 0.002 PHE C 255 TYR 0.010 0.001 TYR C 166 ARG 0.006 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.040 Fit side-chains REVERT: A 47 MET cc_start: 0.5031 (mpt) cc_final: 0.4562 (mmt) REVERT: A 236 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7704 (mm) REVERT: A 237 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: A 314 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: A 326 LYS cc_start: 0.7757 (mmmt) cc_final: 0.7369 (mmpt) REVERT: B 39 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7309 (mtm180) REVERT: B 72 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: B 314 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: B 355 MET cc_start: 0.8428 (mmt) cc_final: 0.8209 (mmm) REVERT: C 100 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7098 (tt0) REVERT: C 125 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: C 211 ASP cc_start: 0.8350 (t70) cc_final: 0.8105 (t70) REVERT: C 284 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7019 (tmtt) REVERT: C 314 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8174 (tt0) outliers start: 29 outliers final: 12 residues processed: 144 average time/residue: 1.4610 time to fit residues: 222.1439 Evaluate side-chains 144 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 225 ASN C 162 ASN C 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.139703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.122960 restraints weight = 8453.311| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.03 r_work: 0.3272 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8937 Z= 0.300 Angle : 0.716 8.576 12132 Z= 0.353 Chirality : 0.050 0.217 1349 Planarity : 0.005 0.054 1550 Dihedral : 7.895 98.829 1245 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.32 % Allowed : 16.26 % Favored : 80.43 % 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: 1.17 (0.25), residues: 1094 helix: 1.04 (0.24), residues: 452 sheet: 0.34 (0.36), residues: 198 loop : 0.97 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 340 HIS 0.006 0.001 HIS B 161 PHE 0.014 0.002 PHE C 255 TYR 0.010 0.001 TYR C 166 ARG 0.007 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.010 Fit side-chains REVERT: A 47 MET cc_start: 0.5164 (mpt) cc_final: 0.4717 (mmt) REVERT: A 99 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6924 (tp30) REVERT: A 215 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7552 (tppp) REVERT: A 236 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7683 (mm) REVERT: A 237 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: A 314 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: A 326 LYS cc_start: 0.7782 (mmmt) cc_final: 0.7371 (mmpt) REVERT: A 354 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7406 (pm20) REVERT: A 355 MET cc_start: 0.7114 (mpt) cc_final: 0.6847 (mmt) REVERT: B 39 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7329 (mtm180) REVERT: B 44 MET cc_start: 0.5769 (mmm) cc_final: 0.5478 (mtp) REVERT: B 72 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: B 314 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: B 355 MET cc_start: 0.8458 (mmt) cc_final: 0.8241 (mmm) REVERT: C 100 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: C 125 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: C 211 ASP cc_start: 0.8355 (t70) cc_final: 0.8115 (t70) REVERT: C 314 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8196 (tt0) outliers start: 31 outliers final: 13 residues processed: 148 average time/residue: 1.5310 time to fit residues: 238.4187 Evaluate side-chains 143 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 105 optimal weight: 0.0870 chunk 98 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 97 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 225 ASN B 12 ASN C 162 ASN C 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.149220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.129263 restraints weight = 8641.219| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.34 r_work: 0.3409 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8937 Z= 0.229 Angle : 0.661 7.516 12132 Z= 0.324 Chirality : 0.047 0.207 1349 Planarity : 0.005 0.038 1550 Dihedral : 7.680 97.073 1245 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.42 % Allowed : 16.68 % Favored : 79.89 % 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: 1.26 (0.25), residues: 1094 helix: 1.15 (0.24), residues: 452 sheet: 0.37 (0.36), residues: 198 loop : 0.98 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 340 HIS 0.005 0.001 HIS A 161 PHE 0.013 0.002 PHE C 255 TYR 0.009 0.001 TYR C 166 ARG 0.007 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5191 (mpt) cc_final: 0.4511 (mmt) REVERT: A 237 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: A 314 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: A 326 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7112 (mmpt) REVERT: A 354 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7251 (pm20) REVERT: A 355 MET cc_start: 0.7102 (mpt) cc_final: 0.6805 (mmt) REVERT: B 39 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7284 (mtm180) REVERT: B 44 MET cc_start: 0.5423 (mmm) cc_final: 0.5174 (mtp) REVERT: B 72 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: B 314 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: B 326 LYS cc_start: 0.7995 (mptt) cc_final: 0.7676 (mmpt) REVERT: B 355 MET cc_start: 0.8355 (mmt) cc_final: 0.8104 (mmm) REVERT: C 100 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: C 125 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: C 211 ASP cc_start: 0.8405 (t70) cc_final: 0.8015 (t70) outliers start: 32 outliers final: 15 residues processed: 146 average time/residue: 1.4973 time to fit residues: 230.2649 Evaluate side-chains 146 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 0.0370 chunk 27 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 225 ASN C 162 ASN C 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128553 restraints weight = 8586.193| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.33 r_work: 0.3400 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8937 Z= 0.263 Angle : 0.694 8.553 12132 Z= 0.341 Chirality : 0.049 0.229 1349 Planarity : 0.005 0.047 1550 Dihedral : 7.792 98.053 1245 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.89 % Allowed : 17.54 % Favored : 79.57 % 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: 1.19 (0.25), residues: 1094 helix: 1.10 (0.24), residues: 452 sheet: 0.33 (0.36), residues: 198 loop : 0.93 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 86 HIS 0.005 0.001 HIS B 161 PHE 0.013 0.002 PHE C 255 TYR 0.009 0.001 TYR C 166 ARG 0.007 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5264 (mpt) cc_final: 0.4580 (mmt) REVERT: A 237 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: A 314 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: A 326 LYS cc_start: 0.7795 (mmmt) cc_final: 0.7153 (mmpt) REVERT: A 354 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7288 (pm20) REVERT: A 355 MET cc_start: 0.6973 (mpt) cc_final: 0.6686 (mmt) REVERT: B 39 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7245 (mtm180) REVERT: B 44 MET cc_start: 0.5414 (mmm) cc_final: 0.5158 (mtp) REVERT: B 72 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7702 (mt-10) REVERT: B 314 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: B 355 MET cc_start: 0.8373 (mmt) cc_final: 0.8126 (mmm) REVERT: C 100 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: C 125 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: C 211 ASP cc_start: 0.8401 (t70) cc_final: 0.7999 (t70) outliers start: 27 outliers final: 15 residues processed: 142 average time/residue: 1.5365 time to fit residues: 229.6102 Evaluate side-chains 144 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 53 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.0170 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 225 ASN C 162 ASN C 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.150564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130768 restraints weight = 8563.377| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.32 r_work: 0.3428 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8937 Z= 0.188 Angle : 0.632 7.844 12132 Z= 0.308 Chirality : 0.046 0.225 1349 Planarity : 0.004 0.035 1550 Dihedral : 7.528 95.964 1245 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.57 % Allowed : 17.97 % Favored : 79.47 % 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: 1.42 (0.25), residues: 1094 helix: 1.27 (0.25), residues: 452 sheet: 0.41 (0.35), residues: 208 loop : 1.11 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 86 HIS 0.004 0.001 HIS A 161 PHE 0.012 0.001 PHE C 255 TYR 0.007 0.001 TYR B 306 ARG 0.007 0.000 ARG A 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5319 (mpt) cc_final: 0.4680 (mmt) REVERT: A 237 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8152 (mt-10) REVERT: A 314 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: A 354 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: A 355 MET cc_start: 0.6915 (mpt) cc_final: 0.6658 (mmt) REVERT: B 39 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7252 (mtm180) REVERT: B 72 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: B 314 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: B 326 LYS cc_start: 0.7980 (mptt) cc_final: 0.7661 (mmpt) REVERT: B 355 MET cc_start: 0.8287 (mmt) cc_final: 0.8038 (mmm) REVERT: C 100 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6898 (tt0) REVERT: C 125 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: C 211 ASP cc_start: 0.8390 (t70) cc_final: 0.8002 (t70) outliers start: 24 outliers final: 12 residues processed: 147 average time/residue: 1.5640 time to fit residues: 241.9540 Evaluate side-chains 145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 0.4980 chunk 108 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 225 ASN B 12 ASN C 162 ASN C 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127457 restraints weight = 8512.290| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.05 r_work: 0.3381 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8937 Z= 0.298 Angle : 0.719 8.468 12132 Z= 0.354 Chirality : 0.050 0.231 1349 Planarity : 0.005 0.053 1550 Dihedral : 7.811 98.775 1245 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.67 % Allowed : 18.18 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.19 (0.25), residues: 1094 helix: 1.10 (0.24), residues: 452 sheet: 0.32 (0.36), residues: 198 loop : 0.94 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 86 HIS 0.005 0.002 HIS B 161 PHE 0.013 0.002 PHE C 31 TYR 0.010 0.001 TYR C 166 ARG 0.008 0.001 ARG A 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7962.44 seconds wall clock time: 136 minutes 33.44 seconds (8193.44 seconds total)