Starting phenix.real_space_refine on Sat Dec 28 16:29:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdl_38280/12_2024/8xdl_38280.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdl_38280/12_2024/8xdl_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_38280/12_2024/8xdl_38280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdl_38280/12_2024/8xdl_38280.map" model { file = "/net/cci-nas-00/data/ceres_data/8xdl_38280/12_2024/8xdl_38280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdl_38280/12_2024/8xdl_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 2.51 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: 1.36 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: 2.75 Time building geometry restraints manager: 2.86 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: 8.320 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: 0.100 Process input model: 26.860 Find NCS groups from input model: 0.410 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.520 ------------------------------------------------------------------------------- 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 : 0.987 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: 1.5276 time to fit residues: 321.8821 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 : 1.042 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 1.037 Fit side-chains REVERT: A 215 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7355 (tppp) REVERT: A 227 MET cc_start: 0.8692 (mmm) cc_final: 0.8156 (mmm) REVERT: A 314 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: B 72 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: B 314 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: B 355 MET cc_start: 0.7880 (mmt) cc_final: 0.7610 (mmm) REVERT: C 64 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8429 (pp) REVERT: C 100 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6720 (mt-10) REVERT: C 119 MET cc_start: 0.7494 (mtp) cc_final: 0.7275 (mtp) REVERT: C 211 ASP cc_start: 0.7785 (t70) cc_final: 0.7565 (t70) REVERT: C 313 MET cc_start: 0.8532 (tpt) cc_final: 0.8158 (tpt) outliers start: 28 outliers final: 11 residues processed: 153 average time/residue: 1.5321 time to fit residues: 246.7998 Evaluate side-chains 138 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 162 ASN A 225 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8937 Z= 0.326 Angle : 0.747 9.129 12132 Z= 0.371 Chirality : 0.050 0.226 1349 Planarity : 0.006 0.062 1550 Dihedral : 8.086 101.997 1245 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.74 % Allowed : 15.19 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1094 helix: 1.14 (0.25), residues: 440 sheet: 0.39 (0.35), residues: 194 loop : 0.92 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 340 HIS 0.006 0.002 HIS B 161 PHE 0.014 0.002 PHE A 31 TYR 0.011 0.002 TYR C 166 ARG 0.006 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.970 Fit side-chains REVERT: A 47 MET cc_start: 0.4035 (mpt) cc_final: 0.3648 (mmt) REVERT: A 215 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7324 (tppp) REVERT: A 227 MET cc_start: 0.8707 (mmm) cc_final: 0.8233 (mmm) REVERT: A 237 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: A 314 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7632 (tt0) REVERT: A 326 LYS cc_start: 0.7551 (mmmt) cc_final: 0.7221 (mmpt) REVERT: A 354 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7280 (mp10) REVERT: B 72 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7239 (mt-10) REVERT: B 314 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: B 355 MET cc_start: 0.7969 (mmt) cc_final: 0.7734 (mmm) REVERT: C 64 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8481 (pp) REVERT: C 100 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7034 (mt-10) REVERT: C 211 ASP cc_start: 0.7796 (t70) cc_final: 0.7573 (t70) REVERT: C 314 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7980 (tt0) outliers start: 35 outliers final: 13 residues processed: 151 average time/residue: 1.5622 time to fit residues: 248.0868 Evaluate side-chains 141 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 A residue 354 GLN 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 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 350 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 225 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8937 Z= 0.338 Angle : 0.750 9.009 12132 Z= 0.372 Chirality : 0.051 0.223 1349 Planarity : 0.006 0.062 1550 Dihedral : 8.045 99.947 1245 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.96 % Allowed : 15.40 % 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: 1.07 (0.25), residues: 1094 helix: 0.94 (0.24), residues: 452 sheet: 0.32 (0.35), residues: 198 loop : 0.91 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 340 HIS 0.006 0.002 HIS A 161 PHE 0.014 0.002 PHE C 31 TYR 0.010 0.002 TYR B 133 ARG 0.006 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 162 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.972 Fit side-chains REVERT: A 47 MET cc_start: 0.4710 (mpt) cc_final: 0.4391 (mmt) REVERT: A 215 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7300 (tppp) REVERT: A 237 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: A 314 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7632 (tt0) REVERT: A 326 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7280 (mmpt) REVERT: B 39 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7240 (mtm180) REVERT: B 72 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: B 314 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: C 64 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8471 (pp) REVERT: C 100 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: C 125 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: C 211 ASP cc_start: 0.7802 (t70) cc_final: 0.7562 (t70) outliers start: 37 outliers final: 16 residues processed: 151 average time/residue: 1.5621 time to fit residues: 248.3600 Evaluate side-chains 141 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 326 LYS 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 314 GLN Chi-restraints excluded: chain B residue 351 THR 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 125 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 192 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 0.0970 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 225 ASN B 12 ASN C 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2824 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= 0.245 Angle : 0.677 7.764 12132 Z= 0.332 Chirality : 0.048 0.214 1349 Planarity : 0.005 0.044 1550 Dihedral : 7.791 97.894 1245 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.42 % Allowed : 15.83 % 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: 1.21 (0.25), residues: 1094 helix: 1.07 (0.25), residues: 452 sheet: 0.35 (0.35), residues: 197 loop : 0.99 (0.29), residues: 445 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 0.005 0.001 ARG A 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 153 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.046 Fit side-chains REVERT: A 47 MET cc_start: 0.4628 (mpt) cc_final: 0.4268 (mmt) REVERT: A 237 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: A 326 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7282 (mmpt) REVERT: B 39 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7223 (mtm180) REVERT: B 72 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: B 314 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: C 100 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7048 (tt0) REVERT: C 125 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: C 211 ASP cc_start: 0.7798 (t70) cc_final: 0.7571 (t70) REVERT: C 284 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7026 (tmtt) REVERT: C 314 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7991 (tt0) outliers start: 32 outliers final: 14 residues processed: 143 average time/residue: 1.6529 time to fit residues: 248.7515 Evaluate side-chains 141 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 326 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 276 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 C 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2896 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= 0.283 Angle : 0.706 8.460 12132 Z= 0.347 Chirality : 0.049 0.215 1349 Planarity : 0.005 0.051 1550 Dihedral : 7.842 98.707 1245 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.53 % Allowed : 16.36 % Favored : 80.11 % 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: 1.14 (0.25), residues: 1094 helix: 1.02 (0.24), residues: 452 sheet: 0.35 (0.36), residues: 198 loop : 0.94 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 340 HIS 0.005 0.001 HIS B 161 PHE 0.013 0.002 PHE C 255 TYR 0.011 0.001 TYR C 166 ARG 0.004 0.001 ARG B 256 *********************** 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 156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.062 Fit side-chains REVERT: A 47 MET cc_start: 0.4849 (mpt) cc_final: 0.4366 (mmt) REVERT: A 237 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: A 314 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: A 326 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7260 (mmpt) REVERT: B 39 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7246 (mtm180) REVERT: B 44 MET cc_start: 0.6007 (mmm) cc_final: 0.5668 (mtp) REVERT: B 72 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: B 100 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: B 314 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: B 355 MET cc_start: 0.7950 (mmt) cc_final: 0.7741 (mmm) REVERT: C 100 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: C 125 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: C 211 ASP cc_start: 0.7803 (t70) cc_final: 0.7560 (t70) REVERT: C 284 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7035 (tmtt) REVERT: C 314 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7997 (tt0) outliers start: 33 outliers final: 14 residues processed: 143 average time/residue: 1.6690 time to fit residues: 251.1481 Evaluate side-chains 143 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 237 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 326 LYS 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 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 125 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 276 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 11 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN B 12 ASN C 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8937 Z= 0.304 Angle : 0.725 8.972 12132 Z= 0.357 Chirality : 0.050 0.213 1349 Planarity : 0.005 0.055 1550 Dihedral : 7.862 98.611 1245 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.53 % Allowed : 16.58 % 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: 1.08 (0.25), residues: 1094 helix: 1.01 (0.24), residues: 452 sheet: 0.27 (0.36), residues: 198 loop : 0.87 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 340 HIS 0.005 0.001 HIS B 161 PHE 0.014 0.002 PHE C 255 TYR 0.011 0.001 TYR C 166 ARG 0.004 0.001 ARG B 256 *********************** 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 159 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.999 Fit side-chains REVERT: A 47 MET cc_start: 0.5034 (mpt) cc_final: 0.4346 (mmt) REVERT: A 237 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: A 314 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: A 326 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7264 (mmpt) REVERT: A 354 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: B 39 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7258 (mtm180) REVERT: B 44 MET cc_start: 0.6034 (mmm) cc_final: 0.5729 (mtp) REVERT: B 72 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: B 100 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7128 (mt-10) REVERT: B 314 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7606 (tt0) REVERT: B 326 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7513 (mmpt) REVERT: C 100 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7054 (tt0) REVERT: C 125 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: C 211 ASP cc_start: 0.7810 (t70) cc_final: 0.7564 (t70) outliers start: 33 outliers final: 15 residues processed: 147 average time/residue: 1.6009 time to fit residues: 247.3042 Evaluate side-chains 148 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 326 LYS 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 100 GLU 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 326 LYS 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 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 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 83 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN C 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8937 Z= 0.232 Angle : 0.668 8.442 12132 Z= 0.327 Chirality : 0.047 0.207 1349 Planarity : 0.005 0.039 1550 Dihedral : 7.700 97.052 1245 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: 1.25 (0.25), residues: 1094 helix: 1.12 (0.25), residues: 452 sheet: 0.29 (0.35), residues: 207 loop : 1.05 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 340 HIS 0.005 0.001 HIS A 161 PHE 0.013 0.002 PHE C 255 TYR 0.009 0.001 TYR C 166 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.003 Fit side-chains REVERT: A 47 MET cc_start: 0.5065 (mpt) cc_final: 0.4379 (mmt) REVERT: A 237 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: A 314 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: A 326 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7186 (mmpt) REVERT: A 354 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: B 39 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7284 (mtm180) REVERT: B 44 MET cc_start: 0.6040 (mmm) cc_final: 0.5775 (mtp) REVERT: B 314 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: B 326 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7472 (mmpt) REVERT: C 125 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: C 211 ASP cc_start: 0.7814 (t70) cc_final: 0.7592 (t70) outliers start: 29 outliers final: 14 residues processed: 147 average time/residue: 1.5773 time to fit residues: 243.8716 Evaluate side-chains 145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 96 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 326 LYS 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 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 326 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 225 ASN B 12 ASN C 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8937 Z= 0.304 Angle : 0.722 8.502 12132 Z= 0.357 Chirality : 0.050 0.214 1349 Planarity : 0.005 0.056 1550 Dihedral : 7.846 98.608 1245 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.32 % Allowed : 17.11 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1094 helix: 1.00 (0.24), residues: 452 sheet: 0.27 (0.36), residues: 198 loop : 0.90 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 86 HIS 0.006 0.001 HIS A 161 PHE 0.014 0.002 PHE C 255 TYR 0.011 0.001 TYR C 166 ARG 0.005 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5200 (mpt) cc_final: 0.4511 (mmt) REVERT: A 237 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: A 314 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: A 326 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7208 (mmpt) REVERT: B 39 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7277 (mtm180) REVERT: B 44 MET cc_start: 0.6019 (mmm) cc_final: 0.5771 (mtp) REVERT: B 72 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: B 314 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: B 326 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7514 (mmpt) REVERT: B 355 MET cc_start: 0.8010 (mmt) cc_final: 0.7745 (mmm) REVERT: C 125 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6649 (mp0) REVERT: C 211 ASP cc_start: 0.7803 (t70) cc_final: 0.7562 (t70) outliers start: 31 outliers final: 17 residues processed: 139 average time/residue: 1.6283 time to fit residues: 237.9903 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 : 1.104 ------------------------------------------------------------------------------- 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 96 VAL 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 326 LYS 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 260 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 96 VAL 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 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 49 optimal weight: 0.0970 chunk 72 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 53 optimal weight: 0.5980 chunk 69 optimal weight: 0.0470 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.2676 ------------------------------------------------------------------------------- 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 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8937 Z= 0.155 Angle : 0.597 7.100 12132 Z= 0.291 Chirality : 0.044 0.171 1349 Planarity : 0.004 0.036 1550 Dihedral : 7.332 96.106 1245 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.35 % Allowed : 18.07 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1094 helix: 1.31 (0.25), residues: 453 sheet: 0.36 (0.35), residues: 207 loop : 1.19 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 340 HIS 0.003 0.001 HIS C 161 PHE 0.013 0.001 PHE C 255 TYR 0.007 0.001 TYR B 306 ARG 0.004 0.000 ARG C 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.084 Fit side-chains REVERT: A 47 MET cc_start: 0.5079 (mpt) cc_final: 0.4404 (mmt) REVERT: A 237 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: A 314 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: A 326 LYS cc_start: 0.7410 (mmmt) cc_final: 0.7184 (mmpt) REVERT: B 39 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7231 (mtm180) REVERT: B 44 MET cc_start: 0.5955 (mmm) cc_final: 0.5746 (mtp) REVERT: B 72 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: B 326 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7517 (mmpt) REVERT: B 355 MET cc_start: 0.7910 (mmt) cc_final: 0.7691 (mmm) outliers start: 22 outliers final: 9 residues processed: 147 average time/residue: 1.5414 time to fit residues: 238.9953 Evaluate side-chains 143 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 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 96 VAL Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 105 LEU 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 80 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.144942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.127402 restraints weight = 8425.383| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.04 r_work: 0.3379 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8937 Z= 0.313 Angle : 0.726 8.561 12132 Z= 0.359 Chirality : 0.050 0.229 1349 Planarity : 0.005 0.054 1550 Dihedral : 7.780 99.442 1245 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.14 % Allowed : 18.82 % Favored : 79.04 % 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: 1.09 (0.24), residues: 452 sheet: 0.29 (0.36), residues: 198 loop : 0.98 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 86 HIS 0.005 0.002 HIS B 161 PHE 0.014 0.002 PHE C 255 TYR 0.010 0.001 TYR C 166 ARG 0.008 0.001 ARG A 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4391.85 seconds wall clock time: 79 minutes 26.19 seconds (4766.19 seconds total)