Starting phenix.real_space_refine on Wed Sep 17 13:03:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdl_38280/09_2025/8xdl_38280.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdl_38280/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xdl_38280/09_2025/8xdl_38280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdl_38280/09_2025/8xdl_38280.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xdl_38280/09_2025/8xdl_38280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdl_38280/09_2025/8xdl_38280.map" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.23, per 1000 atoms: 0.25 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: 0.94 Conformation dependent library (CDL) restraints added in 336.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.30 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: 1.33 Time building geometry restraints manager: 1.10 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: 12.500 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.500 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B 28 TYR 0.008 0.001 TYR C 294 PHE 0.009 0.001 PHE A 255 TRP 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8937) covalent geometry : angle 0.77497 (12132) hydrogen bonds : bond 0.15560 ( 458) hydrogen bonds : angle 6.49953 ( 1152) *********************** 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 : 0.242 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: 0.6697 time to fit residues: 140.6674 Evaluate side-chains 128 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 C 92 ASN C 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130608 restraints weight = 8407.865| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.05 r_work: 0.3389 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2082 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= 0.154 Angle : 0.683 8.466 12132 Z= 0.339 Chirality : 0.047 0.199 1349 Planarity : 0.005 0.045 1550 Dihedral : 8.124 93.966 1262 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.99 % Allowed : 15.08 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.25), residues: 1094 helix: 1.33 (0.25), residues: 441 sheet: 0.50 (0.35), residues: 205 loop : 1.12 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 256 TYR 0.011 0.001 TYR C 166 PHE 0.012 0.002 PHE A 31 TRP 0.011 0.002 TRP B 79 HIS 0.006 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8937) covalent geometry : angle 0.68253 (12132) hydrogen bonds : bond 0.04612 ( 458) hydrogen bonds : angle 4.92919 ( 1152) *********************** 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 162 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.362 Fit side-chains REVERT: A 44 MET cc_start: 0.2102 (mmm) cc_final: 0.1819 (mmm) REVERT: A 284 LYS cc_start: 0.7676 (mptt) cc_final: 0.7418 (mmpt) REVERT: B 64 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8814 (pt) REVERT: B 314 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: B 336 LYS cc_start: 0.7889 (mtpt) cc_final: 0.7677 (mttp) REVERT: B 355 MET cc_start: 0.8192 (mmt) cc_final: 0.7886 (mmm) REVERT: C 64 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8407 (pp) REVERT: C 100 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6609 (mt-10) REVERT: C 119 MET cc_start: 0.7954 (mtp) cc_final: 0.7737 (mtp) REVERT: C 211 ASP cc_start: 0.8250 (t70) cc_final: 0.8023 (t70) REVERT: C 354 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7540 (pt0) outliers start: 28 outliers final: 9 residues processed: 152 average time/residue: 0.6634 time to fit residues: 106.4794 Evaluate side-chains 134 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 236 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 64 ILE 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 276 GLU 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 15 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124013 restraints weight = 8547.648| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 0.99 r_work: 0.3284 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2538 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= 0.190 Angle : 0.721 8.253 12132 Z= 0.357 Chirality : 0.049 0.218 1349 Planarity : 0.006 0.055 1550 Dihedral : 7.913 100.521 1245 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.85 % Allowed : 14.65 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.25), residues: 1094 helix: 1.24 (0.25), residues: 440 sheet: 0.47 (0.35), residues: 193 loop : 0.96 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 256 TYR 0.013 0.001 TYR C 166 PHE 0.013 0.002 PHE A 31 TRP 0.013 0.002 TRP B 340 HIS 0.006 0.002 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 8937) covalent geometry : angle 0.72096 (12132) hydrogen bonds : bond 0.05313 ( 458) hydrogen bonds : angle 4.86042 ( 1152) *********************** 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: 36 poor density : 124 time to evaluate : 0.322 Fit side-chains REVERT: A 47 MET cc_start: 0.4010 (mpt) cc_final: 0.3520 (mmt) REVERT: A 215 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7573 (tppp) REVERT: A 227 MET cc_start: 0.8893 (mmm) cc_final: 0.8389 (mmm) REVERT: A 314 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: A 326 LYS cc_start: 0.7742 (mmmt) cc_final: 0.7309 (mmpt) REVERT: A 354 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7375 (mp-120) REVERT: B 47 MET cc_start: 0.4312 (OUTLIER) cc_final: 0.3594 (mmm) REVERT: B 64 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8929 (pt) REVERT: B 72 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: B 314 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: B 326 LYS cc_start: 0.8019 (tppt) cc_final: 0.7794 (mmtm) REVERT: B 355 MET cc_start: 0.8459 (mmt) cc_final: 0.8156 (mmm) REVERT: C 64 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8545 (pp) REVERT: C 100 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7030 (mt-10) REVERT: C 211 ASP cc_start: 0.8288 (t70) cc_final: 0.8026 (t70) REVERT: C 314 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: C 354 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7714 (pt0) outliers start: 36 outliers final: 12 residues processed: 150 average time/residue: 0.6835 time to fit residues: 107.9336 Evaluate side-chains 144 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 314 GLN 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 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 276 GLU Chi-restraints excluded: chain C residue 314 GLN 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 77 optimal weight: 1.9990 chunk 3 optimal weight: 0.0000 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.125335 restraints weight = 8617.265| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.02 r_work: 0.3299 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2614 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= 0.146 Angle : 0.655 7.581 12132 Z= 0.321 Chirality : 0.047 0.211 1349 Planarity : 0.005 0.038 1550 Dihedral : 7.608 95.412 1245 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.85 % Allowed : 15.29 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.25), residues: 1094 helix: 1.19 (0.25), residues: 452 sheet: 0.53 (0.34), residues: 209 loop : 1.10 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 28 TYR 0.009 0.001 TYR C 166 PHE 0.011 0.002 PHE C 255 TRP 0.013 0.002 TRP B 340 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8937) covalent geometry : angle 0.65528 (12132) hydrogen bonds : bond 0.04364 ( 458) hydrogen bonds : angle 4.68866 ( 1152) *********************** 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: 36 poor density : 126 time to evaluate : 0.430 Fit side-chains REVERT: A 47 MET cc_start: 0.4301 (mpt) cc_final: 0.4057 (mmt) REVERT: A 215 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7544 (tppp) REVERT: A 237 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8152 (mt-10) REVERT: A 314 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: A 326 LYS cc_start: 0.7701 (mmmt) cc_final: 0.7328 (mmpt) REVERT: A 354 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: B 39 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7256 (mtm180) REVERT: B 50 LYS cc_start: 0.8491 (mtmt) cc_final: 0.8281 (mtpt) REVERT: B 64 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8919 (pt) REVERT: B 72 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: B 314 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: B 355 MET cc_start: 0.8426 (mmt) cc_final: 0.8166 (mmm) REVERT: C 64 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8489 (pp) REVERT: C 100 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7039 (mt-10) REVERT: C 211 ASP cc_start: 0.8329 (t70) cc_final: 0.8103 (t70) REVERT: C 314 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: C 354 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7821 (pt0) outliers start: 36 outliers final: 13 residues processed: 151 average time/residue: 0.6900 time to fit residues: 109.7338 Evaluate side-chains 150 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 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 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 314 GLN Chi-restraints excluded: chain C residue 350 SER 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 104 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 50 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 B 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123783 restraints weight = 8536.527| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.02 r_work: 0.3276 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8937 Z= 0.177 Angle : 0.697 8.095 12132 Z= 0.344 Chirality : 0.049 0.214 1349 Planarity : 0.005 0.051 1550 Dihedral : 7.776 98.944 1245 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.42 % Allowed : 16.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.25), residues: 1094 helix: 1.08 (0.24), residues: 452 sheet: 0.42 (0.35), residues: 198 loop : 1.04 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 256 TYR 0.010 0.001 TYR C 166 PHE 0.012 0.002 PHE C 31 TRP 0.014 0.003 TRP B 340 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 8937) covalent geometry : angle 0.69685 (12132) hydrogen bonds : bond 0.05019 ( 458) hydrogen bonds : angle 4.78591 ( 1152) *********************** 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 157 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.332 Fit side-chains REVERT: A 47 MET cc_start: 0.4917 (mpt) cc_final: 0.4691 (mmt) REVERT: A 215 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7575 (tppp) REVERT: A 237 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: A 314 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: A 326 LYS cc_start: 0.7724 (mmmt) cc_final: 0.7294 (mmpt) REVERT: A 354 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7387 (mp10) REVERT: B 39 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7309 (mtm180) REVERT: B 47 MET cc_start: 0.4452 (mmt) cc_final: 0.3838 (mmm) REVERT: B 50 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8252 (mtpt) REVERT: B 64 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8975 (pt) REVERT: B 72 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: B 314 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: B 355 MET cc_start: 0.8433 (mmt) cc_final: 0.8194 (mmm) REVERT: C 64 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8552 (pp) REVERT: C 100 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: C 211 ASP cc_start: 0.8353 (t70) cc_final: 0.8072 (t70) REVERT: C 314 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8197 (tt0) outliers start: 32 outliers final: 15 residues processed: 148 average time/residue: 0.6895 time to fit residues: 107.4363 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 : 0.277 ------------------------------------------------------------------------------- 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 39 ARG Chi-restraints excluded: chain B residue 57 GLU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 0.0770 chunk 82 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 B 12 ASN C 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.124818 restraints weight = 8519.045| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.04 r_work: 0.3299 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8937 Z= 0.144 Angle : 0.648 7.368 12132 Z= 0.317 Chirality : 0.047 0.205 1349 Planarity : 0.005 0.039 1550 Dihedral : 7.601 97.050 1245 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.42 % Allowed : 16.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.25), residues: 1094 helix: 1.17 (0.25), residues: 452 sheet: 0.44 (0.34), residues: 208 loop : 1.20 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 28 TYR 0.008 0.001 TYR C 166 PHE 0.013 0.002 PHE C 255 TRP 0.013 0.002 TRP B 340 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8937) covalent geometry : angle 0.64845 (12132) hydrogen bonds : bond 0.04318 ( 458) hydrogen bonds : angle 4.66546 ( 1152) *********************** 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 160 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.295 Fit side-chains REVERT: A 47 MET cc_start: 0.5106 (mpt) cc_final: 0.4655 (mmt) REVERT: A 236 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7672 (mm) REVERT: A 237 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: A 314 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: A 326 LYS cc_start: 0.7721 (mmmt) cc_final: 0.7322 (mmpt) REVERT: A 354 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7381 (mp10) REVERT: B 39 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7327 (mtm180) REVERT: B 47 MET cc_start: 0.4276 (mmt) cc_final: 0.3749 (mmm) REVERT: B 64 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8935 (pt) REVERT: B 72 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: B 314 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: B 355 MET cc_start: 0.8401 (mmt) cc_final: 0.8189 (mmm) REVERT: C 100 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7072 (tt0) REVERT: C 125 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: C 211 ASP cc_start: 0.8367 (t70) cc_final: 0.8119 (t70) REVERT: C 284 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7019 (tmtt) REVERT: C 314 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8185 (tt0) outliers start: 32 outliers final: 12 residues processed: 151 average time/residue: 0.6612 time to fit residues: 105.0046 Evaluate side-chains 147 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 0.0470 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- 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 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124574 restraints weight = 8542.237| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.04 r_work: 0.3290 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2825 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= 0.150 Angle : 0.657 7.488 12132 Z= 0.322 Chirality : 0.047 0.207 1349 Planarity : 0.005 0.042 1550 Dihedral : 7.611 97.639 1245 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.32 % Allowed : 16.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.25), residues: 1094 helix: 1.14 (0.25), residues: 452 sheet: 0.44 (0.35), residues: 208 loop : 1.19 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 28 TYR 0.008 0.001 TYR C 166 PHE 0.013 0.002 PHE C 255 TRP 0.014 0.002 TRP B 340 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8937) covalent geometry : angle 0.65719 (12132) hydrogen bonds : bond 0.04504 ( 458) hydrogen bonds : angle 4.67426 ( 1152) *********************** 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: 31 poor density : 125 time to evaluate : 0.283 Fit side-chains REVERT: A 47 MET cc_start: 0.5017 (mpt) cc_final: 0.4441 (mmt) REVERT: A 99 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6971 (tp30) REVERT: A 237 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: A 314 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: A 326 LYS cc_start: 0.7726 (mmmt) cc_final: 0.7321 (mmpt) REVERT: A 354 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7375 (mp10) REVERT: B 39 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7330 (mtm180) REVERT: B 44 MET cc_start: 0.5751 (mmm) cc_final: 0.5292 (mtp) REVERT: B 47 MET cc_start: 0.4266 (mmt) cc_final: 0.3694 (mmm) REVERT: B 64 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8943 (pt) REVERT: B 72 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: B 314 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: C 100 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7103 (tt0) REVERT: C 125 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: C 211 ASP cc_start: 0.8371 (t70) cc_final: 0.8125 (t70) REVERT: C 314 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8202 (tt0) outliers start: 31 outliers final: 13 residues processed: 145 average time/residue: 0.6641 time to fit residues: 101.2505 Evaluate side-chains 145 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 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 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 314 GLN Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.145645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127982 restraints weight = 8536.715| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.06 r_work: 0.3387 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2897 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= 0.169 Angle : 0.687 8.837 12132 Z= 0.337 Chirality : 0.049 0.226 1349 Planarity : 0.005 0.049 1550 Dihedral : 7.721 98.782 1245 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.53 % Allowed : 16.68 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.25), residues: 1094 helix: 1.10 (0.24), residues: 452 sheet: 0.41 (0.35), residues: 198 loop : 1.04 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 28 TYR 0.009 0.001 TYR C 166 PHE 0.013 0.002 PHE C 255 TRP 0.015 0.003 TRP B 86 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8937) covalent geometry : angle 0.68719 (12132) hydrogen bonds : bond 0.04834 ( 458) hydrogen bonds : angle 4.72834 ( 1152) *********************** 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 159 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.372 Fit side-chains REVERT: A 47 MET cc_start: 0.5094 (mpt) cc_final: 0.4487 (mmt) REVERT: A 99 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6787 (tp30) REVERT: A 237 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: A 314 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: A 326 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7182 (mmpt) REVERT: A 355 MET cc_start: 0.7139 (mpt) cc_final: 0.6866 (mmt) REVERT: B 39 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7234 (mtm180) REVERT: B 44 MET cc_start: 0.5670 (mmm) cc_final: 0.5343 (mtp) REVERT: B 64 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8857 (pt) REVERT: B 72 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7592 (mt-10) REVERT: B 314 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: C 100 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6933 (tt0) REVERT: C 125 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: C 211 ASP cc_start: 0.8296 (t70) cc_final: 0.7930 (t70) REVERT: C 314 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8178 (tt0) outliers start: 33 outliers final: 14 residues processed: 148 average time/residue: 0.6684 time to fit residues: 104.0095 Evaluate side-chains 146 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 105 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 53 optimal weight: 0.0670 chunk 27 optimal weight: 0.8980 chunk 67 optimal weight: 0.0040 chunk 75 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.3930 ------------------------------------------------------------------------------- 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 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.147822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130356 restraints weight = 8543.745| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.06 r_work: 0.3417 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2875 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= 0.122 Angle : 0.622 7.696 12132 Z= 0.302 Chirality : 0.046 0.221 1349 Planarity : 0.004 0.034 1550 Dihedral : 7.452 96.264 1245 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.99 % Allowed : 17.22 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.25), residues: 1094 helix: 1.27 (0.25), residues: 453 sheet: 0.47 (0.35), residues: 208 loop : 1.19 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 28 TYR 0.008 0.001 TYR B 306 PHE 0.012 0.001 PHE C 255 TRP 0.014 0.002 TRP B 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8937) covalent geometry : angle 0.62181 (12132) hydrogen bonds : bond 0.03827 ( 458) hydrogen bonds : angle 4.54032 ( 1152) *********************** 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 155 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5365 (mpt) cc_final: 0.4768 (mmt) REVERT: A 237 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: A 314 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7767 (tt0) REVERT: A 326 LYS cc_start: 0.7655 (mmmt) cc_final: 0.7155 (mmpt) REVERT: A 355 MET cc_start: 0.7008 (mpt) cc_final: 0.6730 (mmt) REVERT: B 39 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7262 (mtm180) REVERT: B 44 MET cc_start: 0.5523 (mmm) cc_final: 0.5262 (mtp) REVERT: B 64 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8797 (pt) REVERT: B 72 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7621 (mt-10) REVERT: B 314 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: C 100 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6947 (tt0) REVERT: C 125 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: C 211 ASP cc_start: 0.8303 (t70) cc_final: 0.7950 (t70) outliers start: 28 outliers final: 13 residues processed: 147 average time/residue: 0.6899 time to fit residues: 106.6593 Evaluate side-chains 144 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 B residue 314 GLN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU 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 47 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 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 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 = 0.3681 r_free = 0.3681 target = 0.145229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127581 restraints weight = 8484.841| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.06 r_work: 0.3382 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2951 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= 0.191 Angle : 0.716 8.523 12132 Z= 0.352 Chirality : 0.050 0.233 1349 Planarity : 0.005 0.054 1550 Dihedral : 7.761 99.361 1245 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.89 % Allowed : 17.54 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.25), residues: 1094 helix: 1.09 (0.24), residues: 452 sheet: 0.36 (0.36), residues: 198 loop : 0.99 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 28 TYR 0.009 0.001 TYR C 166 PHE 0.013 0.002 PHE C 31 TRP 0.018 0.003 TRP B 86 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 8937) covalent geometry : angle 0.71558 (12132) hydrogen bonds : bond 0.05140 ( 458) hydrogen bonds : angle 4.75997 ( 1152) ********************** 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: 27 poor density : 124 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5259 (mpt) cc_final: 0.4537 (mmt) REVERT: A 237 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: A 314 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: A 326 LYS cc_start: 0.7761 (mmmt) cc_final: 0.7182 (mmpt) REVERT: A 354 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7308 (pm20) REVERT: A 355 MET cc_start: 0.7078 (mpt) cc_final: 0.6797 (mmt) REVERT: B 39 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7246 (mtm180) REVERT: B 44 MET cc_start: 0.5564 (mmm) cc_final: 0.5329 (mtp) REVERT: B 64 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8865 (pt) REVERT: B 72 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: B 314 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: B 355 MET cc_start: 0.8403 (mmt) cc_final: 0.8134 (mmm) REVERT: C 100 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: C 125 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: C 211 ASP cc_start: 0.8306 (t70) cc_final: 0.7975 (t70) REVERT: C 334 GLU cc_start: 0.7811 (pm20) cc_final: 0.7495 (pm20) outliers start: 27 outliers final: 14 residues processed: 143 average time/residue: 0.7075 time to fit residues: 106.2891 Evaluate side-chains 146 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 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 105 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU 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 6 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 78 optimal weight: 0.0020 chunk 40 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.146296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128759 restraints weight = 8494.505| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.04 r_work: 0.3398 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2941 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= 0.156 Angle : 0.674 8.211 12132 Z= 0.329 Chirality : 0.048 0.225 1349 Planarity : 0.005 0.043 1550 Dihedral : 7.654 97.681 1245 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.78 % Allowed : 17.43 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.25), residues: 1094 helix: 1.17 (0.25), residues: 452 sheet: 0.37 (0.36), residues: 198 loop : 1.01 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 28 TYR 0.008 0.001 TYR C 166 PHE 0.013 0.002 PHE C 255 TRP 0.018 0.002 TRP B 86 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8937) covalent geometry : angle 0.67356 (12132) hydrogen bonds : bond 0.04522 ( 458) hydrogen bonds : angle 4.66391 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3813.63 seconds wall clock time: 65 minutes 40.08 seconds (3940.08 seconds total)