Starting phenix.real_space_refine on Sat Aug 23 14:41:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ip3_35630/08_2025/8ip3_35630.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ip3_35630/08_2025/8ip3_35630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ip3_35630/08_2025/8ip3_35630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ip3_35630/08_2025/8ip3_35630.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ip3_35630/08_2025/8ip3_35630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ip3_35630/08_2025/8ip3_35630.map" } resolution = 2.6 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= 0.001 sd= 0.027 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 Mg 12 5.21 5 S 65 5.16 5 Cl 1 4.86 5 C 8275 2.51 5 N 2155 2.21 5 O 2360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12868 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2571 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CL': 1, ' MG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.15, per 1000 atoms: 0.17 Number of scatterers: 12868 At special positions: 0 Unit cell: (108.81, 106.95, 141.36, 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) Cl 1 17.00 S 65 16.00 Mg 12 11.99 O 2360 8.00 N 2155 7.00 C 8275 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: 0.85 Conformation dependent library (CDL) restraints added in 505.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3040 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 72.4% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.564A pdb=" N ARG A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 173 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 183 through 219 removed outlier: 3.625A pdb=" N ARG A 187 " --> pdb=" O PRO A 183 " (cutoff:3.500A) Proline residue: A 209 - end of helix Processing helix chain 'A' and resid 227 through 261 removed outlier: 4.050A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.516A pdb=" N LEU A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.932A pdb=" N ASP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 removed outlier: 4.099A pdb=" N LYS A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 359 Processing helix chain 'A' and resid 371 through 401 removed outlier: 4.425A pdb=" N TRP A 375 " --> pdb=" O HIS A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 114 through 119 removed outlier: 3.565A pdb=" N ARG B 119 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 173 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 183 through 219 removed outlier: 3.625A pdb=" N ARG B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Proline residue: B 209 - end of helix Processing helix chain 'B' and resid 227 through 261 removed outlier: 4.051A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.517A pdb=" N LEU B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 removed outlier: 3.932A pdb=" N ASP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 283 removed outlier: 4.099A pdb=" N LYS B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 359 Processing helix chain 'B' and resid 371 through 401 removed outlier: 4.424A pdb=" N TRP B 375 " --> pdb=" O HIS B 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.564A pdb=" N ARG C 119 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 173 Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 183 through 219 removed outlier: 3.625A pdb=" N ARG C 187 " --> pdb=" O PRO C 183 " (cutoff:3.500A) Proline residue: C 209 - end of helix Processing helix chain 'C' and resid 227 through 261 removed outlier: 4.051A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 269 removed outlier: 3.516A pdb=" N LEU C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.931A pdb=" N ASP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 removed outlier: 4.099A pdb=" N LYS C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 359 Processing helix chain 'C' and resid 371 through 401 removed outlier: 4.425A pdb=" N TRP C 375 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.565A pdb=" N ARG D 119 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 173 Proline residue: D 168 - end of helix Processing helix chain 'D' and resid 183 through 219 removed outlier: 3.625A pdb=" N ARG D 187 " --> pdb=" O PRO D 183 " (cutoff:3.500A) Proline residue: D 209 - end of helix Processing helix chain 'D' and resid 227 through 261 removed outlier: 4.050A pdb=" N GLU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 removed outlier: 3.517A pdb=" N LEU D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.932A pdb=" N ASP D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 283 removed outlier: 4.099A pdb=" N LYS D 281 " --> pdb=" O GLN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 359 Processing helix chain 'D' and resid 371 through 401 removed outlier: 4.425A pdb=" N TRP D 375 " --> pdb=" O HIS D 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 114 through 119 removed outlier: 3.565A pdb=" N ARG E 119 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 173 Proline residue: E 168 - end of helix Processing helix chain 'E' and resid 183 through 219 removed outlier: 3.625A pdb=" N ARG E 187 " --> pdb=" O PRO E 183 " (cutoff:3.500A) Proline residue: E 209 - end of helix Processing helix chain 'E' and resid 227 through 261 removed outlier: 4.051A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 269 removed outlier: 3.517A pdb=" N LEU E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS E 269 " --> pdb=" O LEU E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 removed outlier: 3.932A pdb=" N ASP E 275 " --> pdb=" O SER E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 283 removed outlier: 4.099A pdb=" N LYS E 281 " --> pdb=" O GLN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 359 Processing helix chain 'E' and resid 371 through 401 removed outlier: 4.424A pdb=" N TRP E 375 " --> pdb=" O HIS E 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103 removed outlier: 4.191A pdb=" N LYS A 141 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 103 removed outlier: 4.192A pdb=" N LYS B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 103 removed outlier: 4.192A pdb=" N LYS C 141 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 103 removed outlier: 4.192A pdb=" N LYS D 141 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 103 removed outlier: 4.192A pdb=" N LYS E 141 " --> pdb=" O LEU E 152 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 2970 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: 1.67 Time building geometry restraints manager: 1.09 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: 4210 1.34 - 1.46: 2437 1.46 - 1.58: 6318 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 13085 Sorted by residual: bond pdb=" C SER B 348 " pdb=" O SER B 348 " ideal model delta sigma weight residual 1.237 1.245 -0.008 1.17e-02 7.31e+03 5.01e-01 bond pdb=" C SER E 348 " pdb=" O SER E 348 " ideal model delta sigma weight residual 1.237 1.245 -0.008 1.17e-02 7.31e+03 4.74e-01 bond pdb=" CA LEU D 354 " pdb=" C LEU D 354 " ideal model delta sigma weight residual 1.523 1.515 0.008 1.30e-02 5.92e+03 4.19e-01 bond pdb=" CA LEU C 354 " pdb=" C LEU C 354 " ideal model delta sigma weight residual 1.523 1.515 0.008 1.30e-02 5.92e+03 4.11e-01 bond pdb=" C SER D 348 " pdb=" O SER D 348 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.17e-02 7.31e+03 4.03e-01 ... (remaining 13080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 17215 1.04 - 2.09: 375 2.09 - 3.13: 55 3.13 - 4.17: 20 4.17 - 5.21: 20 Bond angle restraints: 17685 Sorted by residual: angle pdb=" C LEU E 351 " pdb=" N PHE E 352 " pdb=" CA PHE E 352 " ideal model delta sigma weight residual 121.14 117.47 3.67 1.75e+00 3.27e-01 4.41e+00 angle pdb=" C LEU C 351 " pdb=" N PHE C 352 " pdb=" CA PHE C 352 " ideal model delta sigma weight residual 121.14 117.47 3.67 1.75e+00 3.27e-01 4.39e+00 angle pdb=" C LEU B 351 " pdb=" N PHE B 352 " pdb=" CA PHE B 352 " ideal model delta sigma weight residual 121.14 117.47 3.67 1.75e+00 3.27e-01 4.39e+00 angle pdb=" C LEU A 351 " pdb=" N PHE A 352 " pdb=" CA PHE A 352 " ideal model delta sigma weight residual 121.14 117.47 3.67 1.75e+00 3.27e-01 4.39e+00 angle pdb=" C LEU D 351 " pdb=" N PHE D 352 " pdb=" CA PHE D 352 " ideal model delta sigma weight residual 121.14 117.48 3.66 1.75e+00 3.27e-01 4.37e+00 ... (remaining 17680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 7428 17.51 - 35.03: 462 35.03 - 52.54: 35 52.54 - 70.05: 5 70.05 - 87.57: 5 Dihedral angle restraints: 7935 sinusoidal: 3270 harmonic: 4665 Sorted by residual: dihedral pdb=" CB GLU E 147 " pdb=" CG GLU E 147 " pdb=" CD GLU E 147 " pdb=" OE1 GLU E 147 " ideal model delta sinusoidal sigma weight residual 0.00 87.57 -87.57 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU D 147 " pdb=" CG GLU D 147 " pdb=" CD GLU D 147 " pdb=" OE1 GLU D 147 " ideal model delta sinusoidal sigma weight residual 0.00 87.54 -87.54 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU B 147 " pdb=" CG GLU B 147 " pdb=" CD GLU B 147 " pdb=" OE1 GLU B 147 " ideal model delta sinusoidal sigma weight residual 0.00 87.54 -87.54 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 7932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1379 0.029 - 0.058: 420 0.058 - 0.086: 156 0.086 - 0.115: 75 0.115 - 0.144: 20 Chirality restraints: 2050 Sorted by residual: chirality pdb=" CA LEU A 167 " pdb=" N LEU A 167 " pdb=" C LEU A 167 " pdb=" CB LEU A 167 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA LEU C 167 " pdb=" N LEU C 167 " pdb=" C LEU C 167 " pdb=" CB LEU C 167 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA LEU B 167 " pdb=" N LEU B 167 " pdb=" C LEU B 167 " pdb=" CB LEU B 167 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 2047 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 163 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C LEU B 163 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU B 163 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE B 164 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 163 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C LEU E 163 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU E 163 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE E 164 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 163 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C LEU A 163 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU A 163 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 164 " 0.012 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2582 2.78 - 3.31: 13000 3.31 - 3.84: 21592 3.84 - 4.37: 25684 4.37 - 4.90: 45039 Nonbonded interactions: 107897 Sorted by model distance: nonbonded pdb=" OG SER D 99 " pdb=" OH TYR D 154 " model vdw 2.255 3.040 nonbonded pdb=" OG SER E 99 " pdb=" OH TYR E 154 " model vdw 2.255 3.040 nonbonded pdb=" OG SER C 99 " pdb=" OH TYR C 154 " model vdw 2.255 3.040 nonbonded pdb=" OG SER B 99 " pdb=" OH TYR B 154 " model vdw 2.255 3.040 nonbonded pdb=" OG SER A 99 " pdb=" OH TYR A 154 " model vdw 2.256 3.040 ... (remaining 107892 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 83 through 401 or resid 502)) selection = (chain 'B' and (resid 83 through 401 or resid 502)) selection = (chain 'C' and (resid 83 through 401 or resid 502)) selection = (chain 'D' and (resid 83 through 401 or resid 502)) selection = (chain 'E' and (resid 83 through 401 or resid 502)) } 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: 1.610 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 9.770 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 0.002 0.018 13085 Z= 0.116 Angle : 0.425 5.214 17685 Z= 0.224 Chirality : 0.037 0.144 2050 Planarity : 0.003 0.029 2235 Dihedral : 10.758 87.566 4895 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.79 (0.21), residues: 1585 helix: 3.32 (0.15), residues: 1040 sheet: 2.16 (0.38), residues: 145 loop : 0.33 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 136 TYR 0.012 0.001 TYR E 299 PHE 0.016 0.001 PHE D 352 TRP 0.008 0.001 TRP A 162 HIS 0.001 0.000 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00236 (13085) covalent geometry : angle 0.42491 (17685) hydrogen bonds : bond 0.08434 ( 1015) hydrogen bonds : angle 4.40704 ( 2970) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.412 Fit side-chains REVERT: A 383 MET cc_start: 0.6980 (mmp) cc_final: 0.6550 (mtp) REVERT: C 383 MET cc_start: 0.6789 (mmp) cc_final: 0.6236 (mtm) REVERT: D 383 MET cc_start: 0.6884 (mmp) cc_final: 0.6458 (mtp) REVERT: E 383 MET cc_start: 0.7061 (mmp) cc_final: 0.6482 (mtp) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.5219 time to fit residues: 117.8764 Evaluate side-chains 152 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.079541 restraints weight = 19813.057| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.54 r_work: 0.2880 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 13085 Z= 0.259 Angle : 0.556 7.963 17685 Z= 0.288 Chirality : 0.043 0.227 2050 Planarity : 0.004 0.033 2235 Dihedral : 4.089 14.350 1720 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.06 % Allowed : 6.64 % Favored : 92.30 % 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: 3.40 (0.21), residues: 1585 helix: 3.09 (0.15), residues: 1020 sheet: 2.02 (0.39), residues: 145 loop : 0.15 (0.35), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 165 TYR 0.026 0.002 TYR C 299 PHE 0.023 0.002 PHE A 395 TRP 0.009 0.001 TRP E 196 HIS 0.003 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00605 (13085) covalent geometry : angle 0.55630 (17685) hydrogen bonds : bond 0.05398 ( 1015) hydrogen bonds : angle 4.17690 ( 2970) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.346 Fit side-chains REVERT: A 94 GLN cc_start: 0.8220 (mp10) cc_final: 0.7815 (mp10) REVERT: A 383 MET cc_start: 0.6983 (mmp) cc_final: 0.6322 (mtp) REVERT: C 350 SER cc_start: 0.8003 (t) cc_final: 0.7776 (m) REVERT: C 383 MET cc_start: 0.6948 (mmp) cc_final: 0.6265 (mtm) REVERT: D 350 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8097 (p) REVERT: D 383 MET cc_start: 0.6884 (mmp) cc_final: 0.6225 (mtp) REVERT: E 94 GLN cc_start: 0.8256 (mp10) cc_final: 0.7733 (mp10) REVERT: E 350 SER cc_start: 0.8154 (t) cc_final: 0.7940 (m) REVERT: E 355 MET cc_start: 0.7990 (ttm) cc_final: 0.7737 (ttm) REVERT: E 383 MET cc_start: 0.6984 (mmp) cc_final: 0.6193 (mtp) outliers start: 15 outliers final: 6 residues processed: 156 average time/residue: 0.4937 time to fit residues: 83.9460 Evaluate side-chains 142 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 355 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 128 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN D 121 GLN E 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.109637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.080884 restraints weight = 19944.318| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.54 r_work: 0.2908 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13085 Z= 0.179 Angle : 0.484 5.336 17685 Z= 0.256 Chirality : 0.040 0.213 2050 Planarity : 0.004 0.036 2235 Dihedral : 3.977 14.342 1720 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.77 % Allowed : 7.21 % Favored : 91.02 % 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: 3.42 (0.21), residues: 1585 helix: 2.86 (0.15), residues: 1050 sheet: 2.03 (0.40), residues: 145 loop : 0.68 (0.36), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 165 TYR 0.019 0.002 TYR C 299 PHE 0.020 0.002 PHE A 352 TRP 0.008 0.001 TRP B 375 HIS 0.002 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00408 (13085) covalent geometry : angle 0.48351 (17685) hydrogen bonds : bond 0.04998 ( 1015) hydrogen bonds : angle 4.03670 ( 2970) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.488 Fit side-chains REVERT: A 94 GLN cc_start: 0.8177 (mp10) cc_final: 0.7767 (mp10) REVERT: A 359 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7653 (t80) REVERT: A 383 MET cc_start: 0.6811 (mmp) cc_final: 0.6198 (mtp) REVERT: B 355 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7772 (ttp) REVERT: B 359 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7806 (t80) REVERT: C 383 MET cc_start: 0.6919 (mmp) cc_final: 0.6197 (mtm) REVERT: D 359 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7689 (t80) REVERT: D 383 MET cc_start: 0.6867 (mmp) cc_final: 0.6237 (mtp) REVERT: D 391 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6559 (ttp-170) REVERT: E 94 GLN cc_start: 0.8212 (mp10) cc_final: 0.7778 (mp10) REVERT: E 355 MET cc_start: 0.8001 (ttm) cc_final: 0.7771 (ttm) REVERT: E 383 MET cc_start: 0.6948 (mmp) cc_final: 0.6163 (mtp) outliers start: 25 outliers final: 7 residues processed: 162 average time/residue: 0.5135 time to fit residues: 90.3834 Evaluate side-chains 160 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 391 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 20 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 0.1980 chunk 144 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN E 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.109548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.080862 restraints weight = 19890.864| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.55 r_work: 0.2909 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13085 Z= 0.178 Angle : 0.487 9.097 17685 Z= 0.255 Chirality : 0.041 0.232 2050 Planarity : 0.004 0.038 2235 Dihedral : 3.953 14.267 1720 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.41 % Allowed : 8.76 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.29 (0.21), residues: 1585 helix: 2.77 (0.15), residues: 1070 sheet: 2.00 (0.40), residues: 145 loop : 0.47 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 165 TYR 0.021 0.002 TYR C 299 PHE 0.020 0.002 PHE A 352 TRP 0.008 0.001 TRP B 375 HIS 0.002 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00408 (13085) covalent geometry : angle 0.48700 (17685) hydrogen bonds : bond 0.04986 ( 1015) hydrogen bonds : angle 4.00367 ( 2970) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.501 Fit side-chains REVERT: A 94 GLN cc_start: 0.8194 (mp10) cc_final: 0.7779 (mp10) REVERT: A 359 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7716 (t80) REVERT: A 383 MET cc_start: 0.6852 (mmp) cc_final: 0.6211 (mtp) REVERT: B 355 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7796 (ttp) REVERT: B 359 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7690 (t80) REVERT: C 383 MET cc_start: 0.6928 (mmp) cc_final: 0.6213 (mtm) REVERT: D 359 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7858 (t80) REVERT: D 383 MET cc_start: 0.6828 (mmp) cc_final: 0.6199 (mtp) REVERT: D 391 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6515 (ttp-170) REVERT: E 94 GLN cc_start: 0.8204 (mp10) cc_final: 0.7762 (mp10) REVERT: E 355 MET cc_start: 0.7894 (ttm) cc_final: 0.7688 (ttm) REVERT: E 383 MET cc_start: 0.6923 (mmp) cc_final: 0.6136 (mtp) outliers start: 20 outliers final: 10 residues processed: 165 average time/residue: 0.4992 time to fit residues: 89.9308 Evaluate side-chains 165 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 23 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 ASN D 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.110567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.082135 restraints weight = 19810.666| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.52 r_work: 0.2929 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13085 Z= 0.140 Angle : 0.454 5.255 17685 Z= 0.241 Chirality : 0.039 0.220 2050 Planarity : 0.003 0.039 2235 Dihedral : 3.855 14.361 1720 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.55 % Allowed : 9.19 % Favored : 89.26 % 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: 3.38 (0.21), residues: 1585 helix: 2.84 (0.15), residues: 1070 sheet: 1.99 (0.40), residues: 145 loop : 0.50 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 372 TYR 0.019 0.002 TYR C 299 PHE 0.020 0.001 PHE A 352 TRP 0.008 0.001 TRP E 162 HIS 0.002 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00306 (13085) covalent geometry : angle 0.45364 (17685) hydrogen bonds : bond 0.04746 ( 1015) hydrogen bonds : angle 3.93185 ( 2970) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.519 Fit side-chains REVERT: A 94 GLN cc_start: 0.8186 (mp10) cc_final: 0.7728 (mp10) REVERT: A 359 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7694 (t80) REVERT: A 383 MET cc_start: 0.6721 (mmp) cc_final: 0.6098 (mtp) REVERT: B 344 MET cc_start: 0.8680 (mtm) cc_final: 0.8478 (mtp) REVERT: B 355 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7815 (ttp) REVERT: B 362 ASN cc_start: 0.7920 (m110) cc_final: 0.7655 (m-40) REVERT: C 383 MET cc_start: 0.6822 (mmp) cc_final: 0.6118 (mtm) REVERT: D 359 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7805 (t80) REVERT: D 383 MET cc_start: 0.6777 (mmp) cc_final: 0.6154 (mtp) REVERT: D 391 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6517 (ttp-170) REVERT: E 94 GLN cc_start: 0.8200 (mp10) cc_final: 0.7689 (mp10) REVERT: E 355 MET cc_start: 0.7809 (ttm) cc_final: 0.7567 (ttm) REVERT: E 383 MET cc_start: 0.6805 (mmp) cc_final: 0.6018 (mtp) outliers start: 22 outliers final: 10 residues processed: 166 average time/residue: 0.5053 time to fit residues: 91.4845 Evaluate side-chains 166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 359 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.081713 restraints weight = 19604.290| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.51 r_work: 0.2921 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13085 Z= 0.156 Angle : 0.475 9.424 17685 Z= 0.249 Chirality : 0.040 0.210 2050 Planarity : 0.003 0.038 2235 Dihedral : 3.867 14.366 1720 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.55 % Allowed : 9.61 % Favored : 88.83 % 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: 3.39 (0.21), residues: 1585 helix: 2.84 (0.15), residues: 1070 sheet: 1.96 (0.40), residues: 145 loop : 0.55 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 372 TYR 0.021 0.002 TYR C 299 PHE 0.020 0.002 PHE D 352 TRP 0.008 0.001 TRP B 375 HIS 0.002 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00350 (13085) covalent geometry : angle 0.47491 (17685) hydrogen bonds : bond 0.04835 ( 1015) hydrogen bonds : angle 3.94241 ( 2970) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.448 Fit side-chains REVERT: A 94 GLN cc_start: 0.8206 (mp10) cc_final: 0.7740 (mp10) REVERT: A 359 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7802 (t80) REVERT: A 383 MET cc_start: 0.6751 (mmp) cc_final: 0.6141 (mtp) REVERT: B 344 MET cc_start: 0.8681 (mtm) cc_final: 0.8420 (mtp) REVERT: B 359 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7486 (t80) REVERT: C 383 MET cc_start: 0.6889 (mmp) cc_final: 0.6156 (mtm) REVERT: D 383 MET cc_start: 0.6781 (mmp) cc_final: 0.6141 (mtp) REVERT: D 391 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6547 (ttp-170) REVERT: E 94 GLN cc_start: 0.8221 (mp10) cc_final: 0.7674 (mp10) REVERT: E 355 MET cc_start: 0.7849 (ttm) cc_final: 0.7617 (ttm) REVERT: E 383 MET cc_start: 0.6866 (mmp) cc_final: 0.6101 (mtp) outliers start: 22 outliers final: 10 residues processed: 166 average time/residue: 0.4945 time to fit residues: 89.5433 Evaluate side-chains 163 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 15 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 79 optimal weight: 0.1980 chunk 132 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 117 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.084558 restraints weight = 19562.214| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.51 r_work: 0.2982 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13085 Z= 0.109 Angle : 0.427 5.160 17685 Z= 0.228 Chirality : 0.039 0.233 2050 Planarity : 0.003 0.039 2235 Dihedral : 3.692 14.795 1720 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.48 % Allowed : 10.18 % Favored : 88.34 % 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: 3.59 (0.21), residues: 1585 helix: 3.00 (0.15), residues: 1070 sheet: 1.99 (0.39), residues: 145 loop : 0.61 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 372 TYR 0.018 0.001 TYR C 299 PHE 0.020 0.001 PHE D 352 TRP 0.010 0.001 TRP E 162 HIS 0.001 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00215 (13085) covalent geometry : angle 0.42721 (17685) hydrogen bonds : bond 0.04446 ( 1015) hydrogen bonds : angle 3.78284 ( 2970) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.425 Fit side-chains REVERT: A 94 GLN cc_start: 0.8183 (mp10) cc_final: 0.7721 (mp10) REVERT: A 383 MET cc_start: 0.6802 (mmp) cc_final: 0.6150 (mtp) REVERT: C 124 MET cc_start: 0.8712 (tpt) cc_final: 0.8485 (tpp) REVERT: C 383 MET cc_start: 0.6617 (mmp) cc_final: 0.5913 (mtm) REVERT: D 359 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7345 (t80) REVERT: D 383 MET cc_start: 0.6729 (mmp) cc_final: 0.6080 (mtp) REVERT: E 94 GLN cc_start: 0.8258 (mp10) cc_final: 0.7795 (mp10) REVERT: E 124 MET cc_start: 0.8711 (tpt) cc_final: 0.8398 (tpp) REVERT: E 350 SER cc_start: 0.7941 (m) cc_final: 0.7511 (p) REVERT: E 355 MET cc_start: 0.7918 (ttm) cc_final: 0.7613 (ttm) REVERT: E 383 MET cc_start: 0.6747 (mmp) cc_final: 0.5973 (mtp) outliers start: 21 outliers final: 5 residues processed: 176 average time/residue: 0.4790 time to fit residues: 91.8612 Evaluate side-chains 160 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 154 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 359 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 114 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.110228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.081753 restraints weight = 19560.232| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.51 r_work: 0.2920 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13085 Z= 0.165 Angle : 0.492 10.383 17685 Z= 0.255 Chirality : 0.040 0.221 2050 Planarity : 0.003 0.038 2235 Dihedral : 3.813 14.301 1720 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.13 % Allowed : 11.10 % Favored : 87.77 % 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: 3.46 (0.21), residues: 1585 helix: 2.88 (0.15), residues: 1070 sheet: 2.00 (0.40), residues: 145 loop : 0.63 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.017 0.002 TYR D 299 PHE 0.021 0.002 PHE D 352 TRP 0.008 0.001 TRP B 375 HIS 0.001 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00373 (13085) covalent geometry : angle 0.49196 (17685) hydrogen bonds : bond 0.04842 ( 1015) hydrogen bonds : angle 3.91505 ( 2970) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.496 Fit side-chains REVERT: A 94 GLN cc_start: 0.8190 (mp10) cc_final: 0.7720 (mp10) REVERT: A 383 MET cc_start: 0.6846 (mmp) cc_final: 0.6189 (mtp) REVERT: B 94 GLN cc_start: 0.8288 (mp10) cc_final: 0.7733 (mp10) REVERT: C 336 MET cc_start: 0.9042 (ttp) cc_final: 0.8816 (ttm) REVERT: C 383 MET cc_start: 0.6804 (mmp) cc_final: 0.6114 (mtm) REVERT: D 359 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7334 (t80) REVERT: D 383 MET cc_start: 0.6744 (mmp) cc_final: 0.6144 (mtp) REVERT: E 94 GLN cc_start: 0.8213 (mp10) cc_final: 0.7770 (mp10) REVERT: E 355 MET cc_start: 0.7844 (ttm) cc_final: 0.7615 (ttm) REVERT: E 383 MET cc_start: 0.6863 (mmp) cc_final: 0.6106 (mtp) outliers start: 16 outliers final: 8 residues processed: 161 average time/residue: 0.4931 time to fit residues: 86.3728 Evaluate side-chains 156 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 154 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 126 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN D 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.083318 restraints weight = 19800.941| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.54 r_work: 0.2959 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13085 Z= 0.123 Angle : 0.447 5.193 17685 Z= 0.238 Chirality : 0.039 0.206 2050 Planarity : 0.003 0.038 2235 Dihedral : 3.717 14.816 1720 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.06 % Allowed : 11.02 % Favored : 87.92 % 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: 3.56 (0.21), residues: 1585 helix: 2.98 (0.15), residues: 1070 sheet: 1.98 (0.39), residues: 145 loop : 0.60 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 155 TYR 0.016 0.001 TYR C 299 PHE 0.020 0.001 PHE D 352 TRP 0.009 0.001 TRP E 162 HIS 0.001 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00260 (13085) covalent geometry : angle 0.44691 (17685) hydrogen bonds : bond 0.04577 ( 1015) hydrogen bonds : angle 3.83720 ( 2970) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.350 Fit side-chains REVERT: A 94 GLN cc_start: 0.8203 (mp10) cc_final: 0.7743 (mp10) REVERT: A 383 MET cc_start: 0.6838 (mmp) cc_final: 0.6159 (mtp) REVERT: B 94 GLN cc_start: 0.8189 (mp10) cc_final: 0.7623 (mp10) REVERT: C 124 MET cc_start: 0.8728 (tpt) cc_final: 0.8499 (tpp) REVERT: C 336 MET cc_start: 0.9030 (ttp) cc_final: 0.8798 (ttm) REVERT: C 383 MET cc_start: 0.6654 (mmp) cc_final: 0.5909 (mtm) REVERT: D 359 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7232 (t80) REVERT: D 383 MET cc_start: 0.6746 (mmp) cc_final: 0.6104 (mtp) REVERT: E 94 GLN cc_start: 0.8212 (mp10) cc_final: 0.7697 (mp10) REVERT: E 355 MET cc_start: 0.7874 (ttm) cc_final: 0.7638 (ttm) REVERT: E 383 MET cc_start: 0.6819 (mmp) cc_final: 0.6063 (mtp) outliers start: 15 outliers final: 5 residues processed: 159 average time/residue: 0.4751 time to fit residues: 82.6944 Evaluate side-chains 155 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 0.7980 chunk 137 optimal weight: 0.5980 chunk 98 optimal weight: 0.0980 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 125 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.112509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.084068 restraints weight = 19697.457| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.54 r_work: 0.2972 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13085 Z= 0.114 Angle : 0.451 10.827 17685 Z= 0.236 Chirality : 0.039 0.203 2050 Planarity : 0.003 0.038 2235 Dihedral : 3.649 14.944 1720 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.78 % Allowed : 11.02 % Favored : 88.20 % 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: 3.65 (0.21), residues: 1585 helix: 3.06 (0.15), residues: 1070 sheet: 1.94 (0.39), residues: 145 loop : 0.65 (0.38), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 155 TYR 0.013 0.001 TYR C 299 PHE 0.021 0.001 PHE E 352 TRP 0.010 0.001 TRP E 162 HIS 0.001 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00231 (13085) covalent geometry : angle 0.45128 (17685) hydrogen bonds : bond 0.04484 ( 1015) hydrogen bonds : angle 3.77885 ( 2970) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.314 Fit side-chains REVERT: A 94 GLN cc_start: 0.8185 (mp10) cc_final: 0.7721 (mp10) REVERT: A 147 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7972 (mm-30) REVERT: A 383 MET cc_start: 0.6885 (mmp) cc_final: 0.6202 (mtp) REVERT: B 94 GLN cc_start: 0.8169 (mp10) cc_final: 0.7507 (mp10) REVERT: C 124 MET cc_start: 0.8768 (tpt) cc_final: 0.8548 (tpp) REVERT: C 383 MET cc_start: 0.6615 (mmp) cc_final: 0.5855 (mtm) REVERT: D 359 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7091 (t80) REVERT: D 383 MET cc_start: 0.6735 (mmp) cc_final: 0.6099 (mtp) REVERT: E 94 GLN cc_start: 0.8218 (mp10) cc_final: 0.7737 (mp10) REVERT: E 355 MET cc_start: 0.7816 (ttm) cc_final: 0.7570 (ttm) REVERT: E 383 MET cc_start: 0.6804 (mmp) cc_final: 0.6035 (mtp) outliers start: 11 outliers final: 6 residues processed: 162 average time/residue: 0.4703 time to fit residues: 83.2590 Evaluate side-chains 152 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 122 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.083353 restraints weight = 19594.419| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.54 r_work: 0.2961 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13085 Z= 0.126 Angle : 0.451 5.253 17685 Z= 0.240 Chirality : 0.039 0.198 2050 Planarity : 0.003 0.037 2235 Dihedral : 3.675 14.878 1720 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.57 % Allowed : 11.31 % Favored : 88.13 % 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: 3.66 (0.21), residues: 1585 helix: 3.06 (0.15), residues: 1070 sheet: 1.95 (0.39), residues: 145 loop : 0.64 (0.38), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 155 TYR 0.017 0.001 TYR C 299 PHE 0.032 0.001 PHE E 395 TRP 0.010 0.001 TRP E 162 HIS 0.001 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00268 (13085) covalent geometry : angle 0.45067 (17685) hydrogen bonds : bond 0.04567 ( 1015) hydrogen bonds : angle 3.79727 ( 2970) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2980.04 seconds wall clock time: 51 minutes 40.06 seconds (3100.06 seconds total)