Starting phenix.real_space_refine on Wed Jan 15 21:38:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdl_38280/01_2025/8xdl_38280.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdl_38280/01_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_38280/01_2025/8xdl_38280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdl_38280/01_2025/8xdl_38280.map" model { file = "/net/cci-nas-00/data/ceres_data/8xdl_38280/01_2025/8xdl_38280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdl_38280/01_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-5571/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: 8.46, per 1000 atoms: 0.97 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 988.1 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: 1.23 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: 2.86 Time building geometry restraints manager: 2.54 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: 8.480 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: 0.060 Set scattering table: 0.070 Process input model: 25.980 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.700 ------------------------------------------------------------------------------- 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 : 0.986 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: 1.5555 time to fit residues: 327.6553 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 : 1.123 ------------------------------------------------------------------------------- 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 = 8423.238| |-----------------------------------------------------------------------------| 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: 0.3262 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.966 Fit side-chains REVERT: A 215 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7600 (tppp) REVERT: A 227 MET cc_start: 0.8851 (mmm) cc_final: 0.8321 (mmm) REVERT: A 314 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: B 64 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8838 (pt) REVERT: B 72 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: B 314 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: B 336 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7794 (mttp) REVERT: B 355 MET cc_start: 0.8295 (mmt) cc_final: 0.7988 (mmm) REVERT: C 64 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8447 (pp) REVERT: C 100 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6693 (mt-10) REVERT: C 119 MET cc_start: 0.7987 (mtp) cc_final: 0.7777 (mtp) REVERT: C 211 ASP cc_start: 0.8257 (t70) cc_final: 0.8008 (t70) REVERT: C 313 MET cc_start: 0.8775 (tpt) cc_final: 0.8420 (tpt) REVERT: C 354 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7546 (pt0) outliers start: 28 outliers final: 11 residues processed: 153 average time/residue: 1.5130 time to fit residues: 244.0630 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 : 1.037 ------------------------------------------------------------------------------- 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: 0.5980 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 41 optimal weight: 0.0030 chunk 21 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127024 restraints weight = 8614.721| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.04 r_work: 0.3324 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2392 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= 0.192 Angle : 0.629 7.672 12132 Z= 0.307 Chirality : 0.046 0.210 1349 Planarity : 0.005 0.034 1550 Dihedral : 7.484 91.961 1245 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.74 % Allowed : 14.65 % Favored : 81.60 % 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: 1.53 (0.25), residues: 1094 helix: 1.40 (0.25), residues: 441 sheet: 0.49 (0.34), residues: 205 loop : 1.14 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 340 HIS 0.005 0.001 HIS A 161 PHE 0.010 0.001 PHE A 31 TYR 0.008 0.001 TYR C 166 ARG 0.003 0.000 ARG A 312 *********************** 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 162 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.028 Fit side-chains REVERT: A 47 MET cc_start: 0.4107 (mpt) cc_final: 0.3700 (mmt) REVERT: A 237 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: A 354 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7364 (mp-120) REVERT: B 47 MET cc_start: 0.4220 (OUTLIER) cc_final: 0.3526 (mmm) REVERT: B 64 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8867 (pt) REVERT: B 314 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: B 355 MET cc_start: 0.8397 (mmt) cc_final: 0.8075 (mmm) REVERT: C 64 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8453 (pp) REVERT: C 100 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6849 (mt-10) REVERT: C 211 ASP cc_start: 0.8296 (t70) cc_final: 0.8085 (t70) REVERT: C 354 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7667 (pt0) outliers start: 35 outliers final: 10 residues processed: 151 average time/residue: 1.4772 time to fit residues: 235.4856 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 : 0.974 ------------------------------------------------------------------------------- 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: 1.9990 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 121 GLN C 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.137146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120194 restraints weight = 8470.992| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.02 r_work: 0.3224 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 8937 Z= 0.548 Angle : 0.902 11.466 12132 Z= 0.456 Chirality : 0.059 0.236 1349 Planarity : 0.007 0.095 1550 Dihedral : 8.558 110.765 1245 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: 0.84 (0.25), residues: 1094 helix: 0.79 (0.24), residues: 452 sheet: 0.22 (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 0.016 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 165 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 1.073 Fit side-chains REVERT: A 47 MET cc_start: 0.4632 (mpt) cc_final: 0.4417 (mmt) REVERT: A 215 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7701 (tppp) REVERT: A 314 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: A 326 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7484 (mmpt) REVERT: B 39 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7329 (mtm180) REVERT: B 72 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: B 314 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: B 355 MET cc_start: 0.8557 (mmt) cc_final: 0.8325 (mmm) REVERT: C 100 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7063 (tp30) REVERT: C 211 ASP cc_start: 0.8390 (t70) cc_final: 0.8144 (t70) REVERT: C 314 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: C 354 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.8016 (pt0) outliers start: 41 outliers final: 17 residues processed: 153 average time/residue: 1.5036 time to fit residues: 242.5208 Evaluate side-chains 144 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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: 0.0870 chunk 10 optimal weight: 0.7980 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: 0.9980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 = 0.142428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.125877 restraints weight = 8532.125| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.04 r_work: 0.3308 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2751 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= 0.186 Angle : 0.629 7.280 12132 Z= 0.308 Chirality : 0.046 0.205 1349 Planarity : 0.004 0.036 1550 Dihedral : 7.818 98.469 1245 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.46 % Allowed : 16.58 % 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: 1.33 (0.25), residues: 1094 helix: 1.13 (0.25), residues: 453 sheet: 0.42 (0.34), residues: 207 loop : 1.12 (0.29), residues: 434 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 0.011 0.001 PHE C 255 TYR 0.009 0.001 TYR C 166 ARG 0.003 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 150 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.801 Fit side-chains REVERT: A 47 MET cc_start: 0.4800 (mpt) cc_final: 0.4479 (mmt) REVERT: A 237 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: A 314 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: A 326 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7369 (mmpt) REVERT: B 39 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7308 (mtm180) REVERT: B 72 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: B 314 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: B 355 MET cc_start: 0.8378 (mmt) cc_final: 0.8141 (mmm) REVERT: C 100 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: C 125 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: C 211 ASP cc_start: 0.8379 (t70) cc_final: 0.8147 (t70) REVERT: C 326 LYS cc_start: 0.8037 (tptt) cc_final: 0.7833 (tptp) outliers start: 23 outliers final: 9 residues processed: 143 average time/residue: 1.5612 time to fit residues: 235.3956 Evaluate side-chains 141 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 0.0020 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 chunk 74 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 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: 0.5980 overall best weight: 0.4546 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.141923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125370 restraints weight = 8543.134| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.03 r_work: 0.3304 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8937 Z= 0.201 Angle : 0.634 7.980 12132 Z= 0.309 Chirality : 0.046 0.215 1349 Planarity : 0.005 0.034 1550 Dihedral : 7.625 95.990 1245 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.21 % Allowed : 16.36 % 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: 1.46 (0.25), residues: 1094 helix: 1.20 (0.25), residues: 453 sheet: 0.49 (0.35), residues: 208 loop : 1.24 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 340 HIS 0.005 0.001 HIS B 161 PHE 0.012 0.002 PHE C 255 TYR 0.009 0.001 TYR C 166 ARG 0.006 0.000 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 159 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 1.017 Fit side-chains REVERT: A 47 MET cc_start: 0.4913 (mpt) cc_final: 0.4439 (mmt) REVERT: A 99 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6964 (tp30) REVERT: A 237 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8127 (mt-10) REVERT: A 314 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: A 326 LYS cc_start: 0.7741 (mmmt) cc_final: 0.7326 (mmpt) REVERT: A 354 GLN cc_start: 0.7732 (mt0) cc_final: 0.7384 (mp10) REVERT: B 39 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7317 (mtm180) REVERT: B 72 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: B 314 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: B 355 MET cc_start: 0.8463 (mmt) cc_final: 0.8227 (mmm) REVERT: C 100 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: C 125 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: C 211 ASP cc_start: 0.8366 (t70) cc_final: 0.8120 (t70) REVERT: C 284 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7020 (tmtt) REVERT: C 314 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8207 (tt0) outliers start: 30 outliers final: 11 residues processed: 149 average time/residue: 1.5281 time to fit residues: 240.1988 Evaluate side-chains 144 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 9 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.149195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129436 restraints weight = 8535.345| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.30 r_work: 0.3408 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8937 Z= 0.236 Angle : 0.665 8.203 12132 Z= 0.325 Chirality : 0.048 0.227 1349 Planarity : 0.005 0.041 1550 Dihedral : 7.725 97.997 1245 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.99 % Allowed : 17.11 % 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: 1.39 (0.25), residues: 1094 helix: 1.16 (0.24), residues: 452 sheet: 0.45 (0.35), residues: 208 loop : 1.19 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 340 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 0.006 0.000 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 153 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.4926 (mpt) cc_final: 0.4475 (mmt) REVERT: A 237 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: A 314 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: A 326 LYS cc_start: 0.7779 (mmmt) cc_final: 0.7130 (mmpt) REVERT: A 354 GLN cc_start: 0.7748 (mt0) cc_final: 0.7432 (mp10) REVERT: B 39 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7297 (mtm180) REVERT: B 44 MET cc_start: 0.5657 (mmm) cc_final: 0.5263 (mtp) REVERT: B 47 MET cc_start: 0.4512 (mmt) cc_final: 0.3835 (mmm) REVERT: B 72 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: B 314 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: B 334 GLU cc_start: 0.7694 (pm20) cc_final: 0.7423 (pm20) REVERT: B 355 MET cc_start: 0.8395 (mmt) cc_final: 0.8135 (mmm) REVERT: C 95 ARG cc_start: 0.8056 (mmt180) cc_final: 0.7819 (mtt90) REVERT: C 100 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6917 (tt0) REVERT: C 125 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: C 211 ASP cc_start: 0.8404 (t70) cc_final: 0.8062 (t70) REVERT: C 314 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8175 (tt0) outliers start: 28 outliers final: 14 residues processed: 144 average time/residue: 1.5750 time to fit residues: 238.4791 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 : 1.060 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 78 optimal weight: 0.0010 chunk 105 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 chunk 89 optimal weight: 0.8980 overall best weight: 0.4544 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.150253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130314 restraints weight = 8660.803| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.33 r_work: 0.3421 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2848 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= 0.199 Angle : 0.632 7.570 12132 Z= 0.307 Chirality : 0.046 0.212 1349 Planarity : 0.005 0.034 1550 Dihedral : 7.525 96.341 1245 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.10 % Allowed : 17.22 % Favored : 79.68 % 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: 1.48 (0.25), residues: 1094 helix: 1.24 (0.25), residues: 452 sheet: 0.47 (0.35), residues: 208 loop : 1.24 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 340 HIS 0.004 0.001 HIS A 161 PHE 0.012 0.001 PHE C 255 TYR 0.008 0.001 TYR C 166 ARG 0.006 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 160 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5151 (mpt) cc_final: 0.4470 (mmt) REVERT: A 237 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8152 (mt-10) REVERT: A 314 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: A 326 LYS cc_start: 0.7744 (mmmt) cc_final: 0.7095 (mmpt) REVERT: B 39 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7260 (mtm180) REVERT: B 44 MET cc_start: 0.5597 (mmm) cc_final: 0.5305 (mtp) REVERT: B 72 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: B 314 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: B 326 LYS cc_start: 0.7964 (mptt) cc_final: 0.7649 (mmpt) REVERT: B 334 GLU cc_start: 0.7649 (pm20) cc_final: 0.7376 (pm20) REVERT: B 355 MET cc_start: 0.8336 (mmt) cc_final: 0.8082 (mmm) REVERT: C 95 ARG cc_start: 0.8065 (mmt180) cc_final: 0.7856 (mtt90) REVERT: C 100 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6894 (tt0) REVERT: C 125 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: C 211 ASP cc_start: 0.8400 (t70) cc_final: 0.8004 (t70) outliers start: 29 outliers final: 13 residues processed: 151 average time/residue: 1.6015 time to fit residues: 254.7730 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 : 1.070 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 0.0040 chunk 95 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.143266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125332 restraints weight = 8533.840| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.07 r_work: 0.3335 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8937 Z= 0.290 Angle : 0.707 8.613 12132 Z= 0.347 Chirality : 0.049 0.236 1349 Planarity : 0.005 0.051 1550 Dihedral : 7.809 98.618 1245 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.57 % Allowed : 17.75 % Favored : 79.68 % 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: 1.24 (0.25), residues: 1094 helix: 1.08 (0.24), residues: 452 sheet: 0.37 (0.36), residues: 198 loop : 1.04 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 86 HIS 0.005 0.001 HIS A 161 PHE 0.013 0.002 PHE C 255 TYR 0.010 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 148 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5254 (mpt) cc_final: 0.4550 (mmt) REVERT: A 237 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: A 314 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7761 (tt0) REVERT: A 326 LYS cc_start: 0.7786 (mmmt) cc_final: 0.7242 (mmpt) REVERT: A 354 GLN cc_start: 0.7680 (mp10) cc_final: 0.7286 (pm20) REVERT: A 355 MET cc_start: 0.7312 (mpt) cc_final: 0.7053 (mmt) REVERT: B 39 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7266 (mtm180) REVERT: B 44 MET cc_start: 0.5675 (mmm) cc_final: 0.5414 (mtp) REVERT: B 72 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: B 314 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: B 355 MET cc_start: 0.8393 (mmt) cc_final: 0.8173 (mmm) REVERT: C 100 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7011 (tt0) REVERT: C 125 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: C 211 ASP cc_start: 0.8338 (t70) cc_final: 0.8026 (t70) outliers start: 24 outliers final: 14 residues processed: 141 average time/residue: 1.6071 time to fit residues: 238.1931 Evaluate side-chains 142 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 65 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.146007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128448 restraints weight = 8497.081| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.05 r_work: 0.3394 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8937 Z= 0.249 Angle : 0.679 8.200 12132 Z= 0.333 Chirality : 0.048 0.228 1349 Planarity : 0.005 0.043 1550 Dihedral : 7.679 97.682 1245 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.67 % Allowed : 17.86 % 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: 1.28 (0.25), residues: 1094 helix: 1.14 (0.24), residues: 452 sheet: 0.37 (0.36), residues: 198 loop : 1.04 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 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 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 150 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5406 (mpt) cc_final: 0.4761 (mmt) REVERT: A 237 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: A 314 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: A 326 LYS cc_start: 0.7734 (mmmt) cc_final: 0.7134 (mmpt) REVERT: A 354 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: A 355 MET cc_start: 0.7234 (mpt) cc_final: 0.6965 (mmt) REVERT: B 39 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7272 (mtm180) REVERT: B 44 MET cc_start: 0.5586 (mmm) cc_final: 0.5354 (mtp) REVERT: B 72 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: B 314 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: B 355 MET cc_start: 0.8309 (mmt) cc_final: 0.8084 (mmm) REVERT: C 100 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: C 125 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: C 211 ASP cc_start: 0.8293 (t70) cc_final: 0.7939 (t70) outliers start: 25 outliers final: 15 residues processed: 143 average time/residue: 1.5866 time to fit residues: 238.8447 Evaluate side-chains 145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 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 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 20 optimal weight: 0.5980 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: 0.5980 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.145276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127619 restraints weight = 8493.954| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.06 r_work: 0.3383 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8937 Z= 0.279 Angle : 0.706 8.303 12132 Z= 0.347 Chirality : 0.049 0.229 1349 Planarity : 0.005 0.050 1550 Dihedral : 7.756 98.456 1245 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.67 % Allowed : 17.97 % Favored : 79.36 % 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: 1.20 (0.25), residues: 1094 helix: 1.07 (0.24), residues: 452 sheet: 0.33 (0.36), residues: 198 loop : 0.98 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 86 HIS 0.005 0.001 HIS A 161 PHE 0.014 0.002 PHE C 255 TYR 0.009 0.001 TYR C 166 ARG 0.007 0.001 ARG A 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7830.84 seconds wall clock time: 139 minutes 5.50 seconds (8345.50 seconds total)