Starting phenix.real_space_refine on Sat Jun 7 14:23:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdl_38280/06_2025/8xdl_38280.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdl_38280/06_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_38280/06_2025/8xdl_38280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdl_38280/06_2025/8xdl_38280.map" model { file = "/net/cci-nas-00/data/ceres_data/8xdl_38280/06_2025/8xdl_38280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdl_38280/06_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-5710/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: 7.56, 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.32 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: 2.77 Time building geometry restraints manager: 2.77 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: 7.630 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: 0.080 Process input model: 25.810 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 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:14.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.080 ------------------------------------------------------------------------------- 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= 0.167 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 Details of bonding type rmsd hydrogen bonds : bond 0.15560 ( 458) hydrogen bonds : angle 6.49953 ( 1152) covalent geometry : bond 0.00365 ( 8937) covalent geometry : angle 0.77497 (12132) *********************** 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 : 0.931 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: 1.4889 time to fit residues: 313.6896 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 : 1.021 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.145556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129028 restraints weight = 8435.060| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.04 r_work: 0.3369 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2118 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= 0.180 Angle : 0.719 8.741 12132 Z= 0.359 Chirality : 0.049 0.200 1349 Planarity : 0.006 0.051 1550 Dihedral : 8.361 98.071 1262 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.10 % Allowed : 15.08 % 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: 0.48 (0.36), residues: 194 loop : 1.02 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 79 HIS 0.007 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 Details of bonding type rmsd hydrogen bonds : bond 0.05169 ( 458) hydrogen bonds : angle 5.00404 ( 1152) covalent geometry : bond 0.00421 ( 8937) covalent geometry : angle 0.71919 (12132) *********************** 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 159 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.116 Fit side-chains REVERT: A 215 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7577 (tppp) REVERT: A 227 MET cc_start: 0.8850 (mmm) cc_final: 0.8318 (mmm) REVERT: A 314 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: B 64 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8836 (pt) REVERT: B 72 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: B 314 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: B 336 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7764 (mttp) REVERT: B 355 MET cc_start: 0.8268 (mmt) cc_final: 0.7968 (mmm) REVERT: C 64 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8420 (pp) REVERT: C 100 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6685 (mt-10) REVERT: C 119 MET cc_start: 0.7940 (mtp) cc_final: 0.7733 (mtp) REVERT: C 125 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: C 211 ASP cc_start: 0.8251 (t70) cc_final: 0.8003 (t70) REVERT: C 354 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7548 (pt0) outliers start: 29 outliers final: 10 residues processed: 149 average time/residue: 1.5462 time to fit residues: 242.6618 Evaluate side-chains 139 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 125 GLU 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: 0.8980 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 0.0170 chunk 21 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.141463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.124691 restraints weight = 8559.331| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.02 r_work: 0.3290 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2552 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= 0.172 Angle : 0.698 8.081 12132 Z= 0.345 Chirality : 0.048 0.214 1349 Planarity : 0.005 0.051 1550 Dihedral : 7.826 100.310 1245 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.17 % Allowed : 14.87 % 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: 1.35 (0.25), residues: 1094 helix: 1.24 (0.25), residues: 440 sheet: 0.44 (0.35), residues: 194 loop : 1.00 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.006 0.001 HIS B 161 PHE 0.012 0.002 PHE A 31 TYR 0.010 0.001 TYR C 166 ARG 0.004 0.001 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 458) hydrogen bonds : angle 4.80833 ( 1152) covalent geometry : bond 0.00405 ( 8937) covalent geometry : angle 0.69809 (12132) *********************** 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 165 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 1.023 Fit side-chains REVERT: A 47 MET cc_start: 0.3861 (mpt) cc_final: 0.3406 (mmt) REVERT: A 215 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7537 (tppp) REVERT: A 227 MET cc_start: 0.8875 (mmm) cc_final: 0.8368 (mmm) REVERT: A 237 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: A 326 LYS cc_start: 0.7732 (mmmt) cc_final: 0.7335 (mmpt) REVERT: A 354 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7374 (mp-120) REVERT: B 47 MET cc_start: 0.4264 (OUTLIER) cc_final: 0.3636 (mmm) REVERT: B 64 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8919 (pt) REVERT: B 72 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: B 314 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: B 355 MET cc_start: 0.8466 (mmt) cc_final: 0.8176 (mmm) REVERT: C 100 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7028 (mt-10) REVERT: C 211 ASP cc_start: 0.8299 (t70) cc_final: 0.8032 (t70) REVERT: C 354 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7733 (pt0) outliers start: 39 outliers final: 12 residues processed: 152 average time/residue: 1.4389 time to fit residues: 230.7828 Evaluate side-chains 140 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 215 LYS 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 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 96 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 23 optimal weight: 0.0070 chunk 82 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 107 optimal weight: 0.0980 overall best weight: 0.3798 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.143386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126820 restraints weight = 8527.051| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.04 r_work: 0.3320 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8937 Z= 0.121 Angle : 0.618 7.226 12132 Z= 0.300 Chirality : 0.045 0.201 1349 Planarity : 0.004 0.033 1550 Dihedral : 7.422 92.846 1245 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.32 % Allowed : 15.94 % Favored : 80.75 % 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: 1.26 (0.25), residues: 453 sheet: 0.53 (0.34), residues: 205 loop : 1.14 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 340 HIS 0.004 0.001 HIS B 161 PHE 0.011 0.001 PHE C 255 TYR 0.008 0.001 TYR C 166 ARG 0.004 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 458) hydrogen bonds : angle 4.58920 ( 1152) covalent geometry : bond 0.00271 ( 8937) covalent geometry : angle 0.61794 (12132) *********************** 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 160 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.017 Fit side-chains REVERT: A 237 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: A 314 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: A 326 LYS cc_start: 0.7651 (mmmt) cc_final: 0.7301 (mmpt) REVERT: A 354 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7400 (mp10) REVERT: B 39 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7288 (mtm180) REVERT: B 47 MET cc_start: 0.4308 (mmt) cc_final: 0.3757 (mmm) REVERT: B 50 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8236 (mtpt) REVERT: B 64 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8892 (pt) REVERT: B 314 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: B 355 MET cc_start: 0.8414 (mmt) cc_final: 0.8158 (mmm) REVERT: C 100 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7056 (mt-10) REVERT: C 211 ASP cc_start: 0.8350 (t70) cc_final: 0.8092 (t70) REVERT: C 314 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: C 354 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7790 (pt0) outliers start: 31 outliers final: 9 residues processed: 151 average time/residue: 1.4349 time to fit residues: 228.7109 Evaluate side-chains 148 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 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 64 ILE Chi-restraints excluded: chain B residue 88 HIS 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 314 GLN Chi-restraints excluded: chain C residue 354 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 162 ASN A 225 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 = 0.3603 r_free = 0.3603 target = 0.142300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125498 restraints weight = 8480.702| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.05 r_work: 0.3302 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8937 Z= 0.141 Angle : 0.644 7.405 12132 Z= 0.314 Chirality : 0.047 0.205 1349 Planarity : 0.005 0.037 1550 Dihedral : 7.513 95.503 1245 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.99 % Allowed : 16.58 % 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: 1.47 (0.25), residues: 1094 helix: 1.25 (0.25), residues: 452 sheet: 0.55 (0.34), residues: 209 loop : 1.17 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.005 0.001 HIS B 161 PHE 0.011 0.002 PHE C 255 TYR 0.009 0.001 TYR C 166 ARG 0.004 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 458) hydrogen bonds : angle 4.63604 ( 1152) covalent geometry : bond 0.00326 ( 8937) covalent geometry : angle 0.64350 (12132) *********************** 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 158 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.088 Fit side-chains REVERT: A 47 MET cc_start: 0.4537 (mpt) cc_final: 0.4060 (mmt) REVERT: A 314 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: A 326 LYS cc_start: 0.7709 (mmmt) cc_final: 0.7325 (mmpt) REVERT: A 354 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7427 (mp-120) REVERT: B 39 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7273 (mtm180) REVERT: B 47 MET cc_start: 0.4218 (mmt) cc_final: 0.3696 (mmm) REVERT: B 64 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8918 (pt) REVERT: B 314 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: B 355 MET cc_start: 0.8390 (mmt) cc_final: 0.8142 (mmm) REVERT: C 100 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6963 (tt0) REVERT: C 211 ASP cc_start: 0.8357 (t70) cc_final: 0.8115 (t70) REVERT: C 284 LYS cc_start: 0.7746 (mmtm) cc_final: 0.7003 (tmtt) REVERT: C 314 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8183 (tt0) outliers start: 28 outliers final: 11 residues processed: 149 average time/residue: 1.4093 time to fit residues: 221.7537 Evaluate side-chains 143 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 64 ILE Chi-restraints excluded: chain B residue 88 HIS 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 276 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.0570 chunk 74 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 162 ASN A 225 ASN B 12 ASN C 162 ASN C 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122732 restraints weight = 8408.540| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.03 r_work: 0.3263 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8937 Z= 0.218 Angle : 0.753 9.112 12132 Z= 0.373 Chirality : 0.051 0.230 1349 Planarity : 0.006 0.065 1550 Dihedral : 7.929 101.407 1245 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.53 % Allowed : 16.26 % Favored : 80.21 % 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: 1.03 (0.24), residues: 452 sheet: 0.37 (0.35), residues: 198 loop : 0.97 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 340 HIS 0.006 0.002 HIS B 161 PHE 0.014 0.002 PHE C 31 TYR 0.010 0.002 TYR C 166 ARG 0.006 0.001 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.05656 ( 458) hydrogen bonds : angle 4.87512 ( 1152) covalent geometry : bond 0.00526 ( 8937) covalent geometry : angle 0.75300 (12132) *********************** 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: 33 poor density : 126 time to evaluate : 1.882 Fit side-chains REVERT: A 47 MET cc_start: 0.4832 (mpt) cc_final: 0.4344 (mmt) REVERT: A 215 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7568 (tppp) REVERT: A 237 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: A 314 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7811 (tt0) REVERT: A 326 LYS cc_start: 0.7823 (mmmt) cc_final: 0.7356 (mmpt) REVERT: B 39 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7341 (mtm180) REVERT: B 64 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8981 (pt) REVERT: B 72 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: B 314 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: B 355 MET cc_start: 0.8454 (mmt) cc_final: 0.8244 (mmm) REVERT: C 100 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: C 211 ASP cc_start: 0.8373 (t70) cc_final: 0.8126 (t70) REVERT: C 314 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8208 (tt0) outliers start: 33 outliers final: 13 residues processed: 147 average time/residue: 1.6172 time to fit residues: 250.4820 Evaluate side-chains 142 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 B residue 39 ARG 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 96 VAL 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 276 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 45 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 162 ASN A 225 ASN B 12 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 = 0.3589 r_free = 0.3589 target = 0.141028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124297 restraints weight = 8448.996| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.03 r_work: 0.3286 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 : 0.004 0.038 8937 Z= 0.158 Angle : 0.671 7.698 12132 Z= 0.328 Chirality : 0.048 0.210 1349 Planarity : 0.005 0.044 1550 Dihedral : 7.685 98.215 1245 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.21 % Allowed : 16.26 % Favored : 80.53 % 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: 1.13 (0.25), residues: 452 sheet: 0.37 (0.35), residues: 198 loop : 1.00 (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 B 161 PHE 0.013 0.002 PHE C 255 TYR 0.008 0.001 TYR C 166 ARG 0.007 0.001 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 458) hydrogen bonds : angle 4.69410 ( 1152) covalent geometry : bond 0.00371 ( 8937) covalent geometry : angle 0.67061 (12132) *********************** 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 156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.052 Fit side-chains REVERT: A 47 MET cc_start: 0.5135 (mpt) cc_final: 0.4633 (mmt) REVERT: A 99 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6967 (tp30) REVERT: A 236 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7637 (mm) REVERT: A 237 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: A 314 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: A 326 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7331 (mmpt) REVERT: B 39 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7340 (mtm180) REVERT: B 44 MET cc_start: 0.5733 (mmm) cc_final: 0.5344 (mtp) REVERT: B 47 MET cc_start: 0.4294 (mmt) cc_final: 0.3731 (mmm) REVERT: B 64 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8978 (pt) REVERT: B 72 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: B 314 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: C 100 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7099 (tt0) REVERT: C 211 ASP cc_start: 0.8364 (t70) cc_final: 0.8120 (t70) outliers start: 30 outliers final: 12 residues processed: 147 average time/residue: 1.4827 time to fit residues: 229.7951 Evaluate side-chains 146 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 64 ILE 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 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 276 GLU 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: 0.6980 chunk 78 optimal weight: 0.2980 chunk 105 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 97 optimal weight: 0.0870 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 0.0270 chunk 89 optimal weight: 0.5980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 162 ASN A 225 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 = 0.3782 r_free = 0.3782 target = 0.152255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133986 restraints weight = 8677.517| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.24 r_work: 0.3471 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8937 Z= 0.106 Angle : 0.591 7.490 12132 Z= 0.285 Chirality : 0.044 0.197 1349 Planarity : 0.004 0.035 1550 Dihedral : 7.297 95.351 1245 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.67 % Allowed : 17.33 % Favored : 80.00 % 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: 1.57 (0.25), residues: 1094 helix: 1.36 (0.25), residues: 453 sheet: 0.49 (0.34), residues: 208 loop : 1.24 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.003 0.001 HIS B 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 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 458) hydrogen bonds : angle 4.45224 ( 1152) covalent geometry : bond 0.00235 ( 8937) covalent geometry : angle 0.59074 (12132) *********************** 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 158 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.063 Fit side-chains REVERT: A 47 MET cc_start: 0.5126 (mpt) cc_final: 0.4519 (mmt) REVERT: A 99 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6745 (tp30) REVERT: A 237 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: A 314 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: B 39 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7266 (mtm180) REVERT: B 44 MET cc_start: 0.5545 (mmm) cc_final: 0.5124 (mtp) REVERT: B 47 MET cc_start: 0.4069 (mmt) cc_final: 0.3535 (mmm) REVERT: B 64 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8807 (pt) REVERT: C 100 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6860 (tt0) REVERT: C 211 ASP cc_start: 0.8347 (t70) cc_final: 0.7993 (t70) outliers start: 25 outliers final: 11 residues processed: 152 average time/residue: 1.6331 time to fit residues: 262.8265 Evaluate side-chains 144 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 64 ILE 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 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 276 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: 0.5980 chunk 109 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 30 optimal weight: 0.0670 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 0.0670 chunk 95 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 162 ASN A 225 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 = 0.3761 r_free = 0.3761 target = 0.150525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132115 restraints weight = 8658.076| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.24 r_work: 0.3446 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2880 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= 0.131 Angle : 0.633 7.045 12132 Z= 0.307 Chirality : 0.046 0.207 1349 Planarity : 0.004 0.034 1550 Dihedral : 7.389 95.648 1245 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: 1.53 (0.25), residues: 1094 helix: 1.33 (0.25), residues: 452 sheet: 0.47 (0.34), residues: 208 loop : 1.22 (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 0.002 PHE C 255 TYR 0.007 0.001 TYR C 166 ARG 0.005 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 458) hydrogen bonds : angle 4.54575 ( 1152) covalent geometry : bond 0.00300 ( 8937) covalent geometry : angle 0.63305 (12132) *********************** 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 153 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5226 (mpt) cc_final: 0.4645 (mmt) REVERT: A 237 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: A 314 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: A 355 MET cc_start: 0.7177 (mpt) cc_final: 0.6888 (mmt) REVERT: B 39 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7273 (mtm180) REVERT: B 44 MET cc_start: 0.5464 (mmm) cc_final: 0.5063 (mtp) REVERT: B 47 MET cc_start: 0.4121 (mmt) cc_final: 0.3567 (mmm) REVERT: B 64 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8824 (pt) REVERT: B 72 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7645 (mt-10) REVERT: B 355 MET cc_start: 0.8399 (mmt) cc_final: 0.8174 (mmm) REVERT: C 100 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6857 (tt0) REVERT: C 211 ASP cc_start: 0.8357 (t70) cc_final: 0.8026 (t70) outliers start: 25 outliers final: 12 residues processed: 145 average time/residue: 1.5303 time to fit residues: 233.6999 Evaluate side-chains 142 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 64 ILE 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 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 276 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: 0.9990 chunk 65 optimal weight: 0.3980 chunk 53 optimal weight: 0.0670 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 0.0570 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 162 ASN A 225 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 = 0.3771 r_free = 0.3771 target = 0.151423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133122 restraints weight = 8592.154| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.24 r_work: 0.3459 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2898 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= 0.117 Angle : 0.610 7.063 12132 Z= 0.295 Chirality : 0.045 0.183 1349 Planarity : 0.004 0.034 1550 Dihedral : 7.245 94.092 1245 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.46 % Allowed : 18.18 % 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: 1.60 (0.25), residues: 1094 helix: 1.39 (0.25), residues: 452 sheet: 0.50 (0.34), residues: 208 loop : 1.26 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 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 0.005 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 458) hydrogen bonds : angle 4.47144 ( 1152) covalent geometry : bond 0.00264 ( 8937) covalent geometry : angle 0.60988 (12132) ********************** 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 151 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5258 (mpt) cc_final: 0.4708 (mmt) REVERT: A 237 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: A 314 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: A 354 GLN cc_start: 0.7630 (mp10) cc_final: 0.7209 (pm20) REVERT: A 355 MET cc_start: 0.7137 (mpt) cc_final: 0.6865 (mmt) REVERT: B 39 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7258 (mtm180) REVERT: B 47 MET cc_start: 0.4082 (mmt) cc_final: 0.3574 (mmm) REVERT: B 64 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8808 (pt) REVERT: B 72 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: B 326 LYS cc_start: 0.8005 (mptt) cc_final: 0.7668 (mmpt) REVERT: B 355 MET cc_start: 0.8368 (mmt) cc_final: 0.8137 (mmm) REVERT: C 100 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6853 (tt0) REVERT: C 211 ASP cc_start: 0.8348 (t70) cc_final: 0.7976 (t70) outliers start: 23 outliers final: 13 residues processed: 143 average time/residue: 1.5559 time to fit residues: 234.0212 Evaluate side-chains 144 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 64 ILE 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 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 276 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: 0.6980 chunk 108 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 162 ASN A 225 ASN B 12 ASN C 162 ASN C 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.144764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127169 restraints weight = 8495.118| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.04 r_work: 0.3377 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8937 Z= 0.205 Angle : 0.734 8.818 12132 Z= 0.361 Chirality : 0.051 0.238 1349 Planarity : 0.005 0.059 1550 Dihedral : 7.760 100.138 1245 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.78 % Allowed : 17.86 % 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: 1.25 (0.25), residues: 1094 helix: 1.13 (0.24), residues: 452 sheet: 0.34 (0.35), residues: 198 loop : 1.01 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 86 HIS 0.006 0.002 HIS B 161 PHE 0.014 0.002 PHE C 31 TYR 0.010 0.001 TYR C 166 ARG 0.006 0.001 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.05353 ( 458) hydrogen bonds : angle 4.77652 ( 1152) covalent geometry : bond 0.00494 ( 8937) covalent geometry : angle 0.73375 (12132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8250.95 seconds wall clock time: 141 minutes 48.81 seconds (8508.81 seconds total)