Starting phenix.real_space_refine on Mon Aug 25 01:06:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ts3_41589/08_2025/8ts3_41589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ts3_41589/08_2025/8ts3_41589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ts3_41589/08_2025/8ts3_41589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ts3_41589/08_2025/8ts3_41589.map" model { file = "/net/cci-nas-00/data/ceres_data/8ts3_41589/08_2025/8ts3_41589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ts3_41589/08_2025/8ts3_41589.cif" } resolution = 3.11 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= 0.005 sd= 0.050 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 Ca 7 9.91 5 S 65 5.16 5 C 7750 2.51 5 N 2015 2.21 5 O 2190 1.98 5 H 12055 0.53 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: 24082 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 4815 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 8, 'TRANS': 292} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 5.18, per 1000 atoms: 0.22 Number of scatterers: 24082 At special positions: 0 Unit cell: (111.1, 111.1, 138.6, 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) Ca 7 19.99 S 65 16.00 O 2190 8.00 N 2015 7.00 C 7750 6.00 H 12055 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 792.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2890 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 5 sheets defined 71.1% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 183 through 220 removed outlier: 3.855A pdb=" N ARG A 187 " --> pdb=" O PRO A 183 " (cutoff:3.500A) Proline residue: A 209 - end of helix removed outlier: 3.611A pdb=" N ASP A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 261 removed outlier: 3.635A pdb=" N ILE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.730A pdb=" N LEU A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 Processing helix chain 'A' and resid 287 through 360 removed outlier: 3.791A pdb=" N GLU A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 399 removed outlier: 3.764A pdb=" N GLY A 386 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'B' and resid 159 through 166 Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 183 through 220 removed outlier: 3.855A pdb=" N ARG B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Proline residue: B 209 - end of helix removed outlier: 3.611A pdb=" N ASP B 220 " --> pdb=" O ASP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 261 removed outlier: 3.634A pdb=" N ILE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.731A pdb=" N LEU B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 Processing helix chain 'B' and resid 287 through 360 removed outlier: 3.791A pdb=" N GLU B 291 " --> pdb=" O ASP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 399 removed outlier: 3.763A pdb=" N GLY B 386 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 111 Processing helix chain 'C' and resid 159 through 166 Processing helix chain 'C' and resid 166 through 172 Processing helix chain 'C' and resid 183 through 220 removed outlier: 3.855A pdb=" N ARG C 187 " --> pdb=" O PRO C 183 " (cutoff:3.500A) Proline residue: C 209 - end of helix removed outlier: 3.611A pdb=" N ASP C 220 " --> pdb=" O ASP C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 261 removed outlier: 3.634A pdb=" N ILE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 269 removed outlier: 3.732A pdb=" N LEU C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 Processing helix chain 'C' and resid 287 through 360 removed outlier: 3.791A pdb=" N GLU C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 399 removed outlier: 3.763A pdb=" N GLY C 386 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 111 Processing helix chain 'D' and resid 159 through 166 Processing helix chain 'D' and resid 166 through 172 Processing helix chain 'D' and resid 183 through 220 removed outlier: 3.856A pdb=" N ARG D 187 " --> pdb=" O PRO D 183 " (cutoff:3.500A) Proline residue: D 209 - end of helix removed outlier: 3.611A pdb=" N ASP D 220 " --> pdb=" O ASP D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 261 removed outlier: 3.634A pdb=" N ILE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 removed outlier: 3.730A pdb=" N LEU D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 Processing helix chain 'D' and resid 287 through 360 removed outlier: 3.791A pdb=" N GLU D 291 " --> pdb=" O ASP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 399 removed outlier: 3.764A pdb=" N GLY D 386 " --> pdb=" O PHE D 382 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 111 Processing helix chain 'E' and resid 159 through 166 Processing helix chain 'E' and resid 166 through 172 Processing helix chain 'E' and resid 183 through 220 removed outlier: 3.855A pdb=" N ARG E 187 " --> pdb=" O PRO E 183 " (cutoff:3.500A) Proline residue: E 209 - end of helix removed outlier: 3.611A pdb=" N ASP E 220 " --> pdb=" O ASP E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 261 removed outlier: 3.635A pdb=" N ILE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 269 removed outlier: 3.732A pdb=" N LEU E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS E 269 " --> pdb=" O LEU E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 Processing helix chain 'E' and resid 287 through 360 removed outlier: 3.791A pdb=" N GLU E 291 " --> pdb=" O ASP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 399 removed outlier: 3.764A pdb=" N GLY E 386 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103 removed outlier: 4.237A 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: 4.236A 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: 4.235A 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: 4.237A 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: 4.237A pdb=" N LYS E 141 " --> pdb=" O LEU E 152 " (cutoff:3.500A) 955 hydrogen bonds defined for protein. 2820 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: 5.62 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12045 1.03 - 1.23: 10 1.23 - 1.42: 4980 1.42 - 1.61: 7125 1.61 - 1.81: 120 Bond restraints: 24280 Sorted by residual: bond pdb=" C SER B 348 " pdb=" O SER B 348 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.17e-02 7.31e+03 6.52e-01 bond pdb=" C SER D 348 " pdb=" O SER D 348 " ideal model delta sigma weight residual 1.237 1.245 -0.009 1.17e-02 7.31e+03 5.60e-01 bond pdb=" SD MET A 344 " pdb=" CE MET A 344 " ideal model delta sigma weight residual 1.791 1.772 0.019 2.50e-02 1.60e+03 5.60e-01 bond pdb=" SD MET E 344 " pdb=" CE MET E 344 " ideal model delta sigma weight residual 1.791 1.773 0.018 2.50e-02 1.60e+03 5.39e-01 bond pdb=" SD MET B 344 " pdb=" CE MET B 344 " ideal model delta sigma weight residual 1.791 1.773 0.018 2.50e-02 1.60e+03 5.38e-01 ... (remaining 24275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 43059 1.35 - 2.70: 811 2.70 - 4.05: 65 4.05 - 5.39: 10 5.39 - 6.74: 5 Bond angle restraints: 43950 Sorted by residual: angle pdb=" CB MET A 344 " pdb=" CG MET A 344 " pdb=" SD MET A 344 " ideal model delta sigma weight residual 112.70 119.44 -6.74 3.00e+00 1.11e-01 5.05e+00 angle pdb=" CB MET C 344 " pdb=" CG MET C 344 " pdb=" SD MET C 344 " ideal model delta sigma weight residual 112.70 119.43 -6.73 3.00e+00 1.11e-01 5.04e+00 angle pdb=" CB MET D 344 " pdb=" CG MET D 344 " pdb=" SD MET D 344 " ideal model delta sigma weight residual 112.70 119.42 -6.72 3.00e+00 1.11e-01 5.02e+00 angle pdb=" CB MET E 344 " pdb=" CG MET E 344 " pdb=" SD MET E 344 " ideal model delta sigma weight residual 112.70 119.42 -6.72 3.00e+00 1.11e-01 5.02e+00 angle pdb=" CB MET B 344 " pdb=" CG MET B 344 " pdb=" SD MET B 344 " ideal model delta sigma weight residual 112.70 119.39 -6.69 3.00e+00 1.11e-01 4.97e+00 ... (remaining 43945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 10038 17.24 - 34.48: 912 34.48 - 51.72: 230 51.72 - 68.96: 75 68.96 - 86.20: 25 Dihedral angle restraints: 11280 sinusoidal: 6150 harmonic: 5130 Sorted by residual: dihedral pdb=" CB GLU A 185 " pdb=" CG GLU A 185 " pdb=" CD GLU A 185 " pdb=" OE1 GLU A 185 " ideal model delta sinusoidal sigma weight residual 0.00 -86.20 86.20 1 3.00e+01 1.11e-03 9.96e+00 dihedral pdb=" CB GLU B 185 " pdb=" CG GLU B 185 " pdb=" CD GLU B 185 " pdb=" OE1 GLU B 185 " ideal model delta sinusoidal sigma weight residual 0.00 -86.20 86.20 1 3.00e+01 1.11e-03 9.96e+00 dihedral pdb=" CB GLU E 185 " pdb=" CG GLU E 185 " pdb=" CD GLU E 185 " pdb=" OE1 GLU E 185 " ideal model delta sinusoidal sigma weight residual 0.00 -86.19 86.19 1 3.00e+01 1.11e-03 9.96e+00 ... (remaining 11277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1415 0.028 - 0.056: 325 0.056 - 0.084: 118 0.084 - 0.112: 61 0.112 - 0.141: 21 Chirality restraints: 1940 Sorted by residual: chirality pdb=" CA ILE B 126 " pdb=" N ILE B 126 " pdb=" C ILE B 126 " pdb=" CB ILE B 126 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA ILE A 126 " pdb=" N ILE A 126 " pdb=" C ILE A 126 " pdb=" CB ILE A 126 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE E 126 " pdb=" N ILE E 126 " pdb=" C ILE E 126 " pdb=" CB ILE E 126 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 1937 not shown) Planarity restraints: 3525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 182 " -0.017 5.00e-02 4.00e+02 2.63e-02 1.11e+00 pdb=" N PRO E 183 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO E 183 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 183 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 182 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO B 183 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 182 " -0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO A 183 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 183 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 183 " -0.014 5.00e-02 4.00e+02 ... (remaining 3522 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 2857 2.26 - 2.84: 55099 2.84 - 3.43: 60482 3.43 - 4.01: 79848 4.01 - 4.60: 127101 Nonbonded interactions: 325387 Sorted by model distance: nonbonded pdb=" O LEU D 171 " pdb="HH21 ARG D 187 " model vdw 1.670 2.450 nonbonded pdb=" O LEU E 171 " pdb="HH21 ARG E 187 " model vdw 1.670 2.450 nonbonded pdb=" O LEU B 171 " pdb="HH21 ARG B 187 " model vdw 1.670 2.450 nonbonded pdb=" O LEU A 171 " pdb="HH21 ARG A 187 " model vdw 1.670 2.450 nonbonded pdb=" O LEU C 171 " pdb="HH21 ARG C 187 " model vdw 1.670 2.450 ... (remaining 325382 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 82 through 601) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.290 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.060 Find NCS groups from input model: 0.390 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 0.024 12225 Z= 0.108 Angle : 0.452 6.743 16520 Z= 0.244 Chirality : 0.034 0.141 1940 Planarity : 0.002 0.026 2070 Dihedral : 15.135 86.204 4530 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % 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: 4.66 (0.23), residues: 1475 helix: 3.89 (0.15), residues: 1040 sheet: 1.96 (0.41), residues: 145 loop : 0.35 (0.44), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 136 TYR 0.004 0.001 TYR C 299 PHE 0.010 0.001 PHE D 352 TRP 0.004 0.001 TRP B 375 HIS 0.001 0.000 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00201 (12225) covalent geometry : angle 0.45237 (16520) hydrogen bonds : bond 0.08483 ( 955) hydrogen bonds : angle 4.62217 ( 2820) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8147 (tpt) cc_final: 0.7846 (tpt) REVERT: A 361 MET cc_start: 0.6605 (tpt) cc_final: 0.6100 (mmm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1957 time to fit residues: 27.5458 Evaluate side-chains 74 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.075144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.056070 restraints weight = 98602.969| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.38 r_work: 0.2826 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12225 Z= 0.157 Angle : 0.497 7.143 16520 Z= 0.264 Chirality : 0.035 0.144 1940 Planarity : 0.003 0.028 2070 Dihedral : 3.225 12.162 1605 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.61 % Allowed : 11.76 % Favored : 87.63 % 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: 4.36 (0.22), residues: 1475 helix: 3.76 (0.15), residues: 1010 sheet: 2.13 (0.42), residues: 145 loop : 0.08 (0.40), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 116 TYR 0.013 0.001 TYR B 299 PHE 0.009 0.001 PHE E 352 TRP 0.007 0.001 TRP C 273 HIS 0.002 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00345 (12225) covalent geometry : angle 0.49698 (16520) hydrogen bonds : bond 0.05479 ( 955) hydrogen bonds : angle 4.07972 ( 2820) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 383 MET cc_start: 0.8983 (mmp) cc_final: 0.8779 (mmp) outliers start: 8 outliers final: 0 residues processed: 74 average time/residue: 0.1775 time to fit residues: 21.6168 Evaluate side-chains 71 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.069636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.050036 restraints weight = 100136.955| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.35 r_work: 0.2741 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12225 Z= 0.222 Angle : 0.548 5.479 16520 Z= 0.302 Chirality : 0.037 0.142 1940 Planarity : 0.003 0.023 2070 Dihedral : 3.510 13.832 1605 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.07 % Allowed : 12.06 % Favored : 86.87 % 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: 4.12 (0.22), residues: 1475 helix: 3.56 (0.15), residues: 1025 sheet: 2.06 (0.41), residues: 145 loop : -0.13 (0.41), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 332 TYR 0.018 0.002 TYR D 299 PHE 0.012 0.001 PHE E 352 TRP 0.007 0.001 TRP D 162 HIS 0.003 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00501 (12225) covalent geometry : angle 0.54755 (16520) hydrogen bonds : bond 0.06644 ( 955) hydrogen bonds : angle 4.30116 ( 2820) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8853 (mmt) cc_final: 0.8649 (mmt) outliers start: 14 outliers final: 4 residues processed: 78 average time/residue: 0.1690 time to fit residues: 21.4699 Evaluate side-chains 76 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain E residue 317 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.070341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.050820 restraints weight = 99910.151| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.38 r_work: 0.2765 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12225 Z= 0.149 Angle : 0.467 4.128 16520 Z= 0.255 Chirality : 0.034 0.147 1940 Planarity : 0.003 0.024 2070 Dihedral : 3.385 13.444 1605 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.22 % Allowed : 12.60 % Favored : 86.18 % 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: 4.24 (0.22), residues: 1475 helix: 3.75 (0.15), residues: 1010 sheet: 1.99 (0.42), residues: 145 loop : -0.18 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 332 TYR 0.014 0.001 TYR D 299 PHE 0.012 0.001 PHE B 352 TRP 0.005 0.001 TRP C 273 HIS 0.002 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00316 (12225) covalent geometry : angle 0.46658 (16520) hydrogen bonds : bond 0.06205 ( 955) hydrogen bonds : angle 4.06631 ( 2820) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 82 average time/residue: 0.1580 time to fit residues: 21.1470 Evaluate side-chains 74 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain E residue 317 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 129 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.070124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.050488 restraints weight = 99758.165| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.34 r_work: 0.2751 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12225 Z= 0.179 Angle : 0.492 4.961 16520 Z= 0.269 Chirality : 0.035 0.145 1940 Planarity : 0.003 0.026 2070 Dihedral : 3.407 13.712 1605 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.30 % Allowed : 12.60 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.21 (0.22), residues: 1475 helix: 3.75 (0.15), residues: 1010 sheet: 1.85 (0.41), residues: 145 loop : -0.22 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 228 TYR 0.015 0.001 TYR A 299 PHE 0.012 0.001 PHE B 352 TRP 0.006 0.001 TRP A 162 HIS 0.001 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00394 (12225) covalent geometry : angle 0.49224 (16520) hydrogen bonds : bond 0.06252 ( 955) hydrogen bonds : angle 4.11615 ( 2820) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 137 MET cc_start: 0.8937 (mmt) cc_final: 0.8693 (mmt) REVERT: E 383 MET cc_start: 0.9024 (mmp) cc_final: 0.8762 (mmp) outliers start: 17 outliers final: 7 residues processed: 78 average time/residue: 0.1613 time to fit residues: 20.5778 Evaluate side-chains 76 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 85 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.069511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.049994 restraints weight = 99998.122| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.34 r_work: 0.2751 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12225 Z= 0.178 Angle : 0.483 5.133 16520 Z= 0.265 Chirality : 0.035 0.147 1940 Planarity : 0.003 0.027 2070 Dihedral : 3.414 13.819 1605 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.99 % Allowed : 13.05 % Favored : 85.95 % 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: 4.22 (0.22), residues: 1475 helix: 3.70 (0.15), residues: 1025 sheet: 1.79 (0.42), residues: 145 loop : -0.20 (0.40), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 332 TYR 0.015 0.001 TYR A 299 PHE 0.012 0.001 PHE D 352 TRP 0.006 0.001 TRP A 162 HIS 0.001 0.000 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00391 (12225) covalent geometry : angle 0.48315 (16520) hydrogen bonds : bond 0.06279 ( 955) hydrogen bonds : angle 4.10967 ( 2820) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 137 MET cc_start: 0.8976 (mmt) cc_final: 0.8733 (mmt) outliers start: 13 outliers final: 5 residues processed: 73 average time/residue: 0.1751 time to fit residues: 21.2287 Evaluate side-chains 74 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 146 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 142 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.069563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.050076 restraints weight = 100018.929| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.33 r_work: 0.2750 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 12225 Z= 0.166 Angle : 0.478 6.613 16520 Z= 0.261 Chirality : 0.035 0.148 1940 Planarity : 0.003 0.026 2070 Dihedral : 3.408 13.833 1605 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.53 % Allowed : 13.59 % Favored : 85.88 % 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: 4.26 (0.22), residues: 1475 helix: 3.74 (0.15), residues: 1025 sheet: 1.76 (0.42), residues: 145 loop : -0.20 (0.40), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 332 TYR 0.015 0.001 TYR A 299 PHE 0.013 0.001 PHE B 352 TRP 0.006 0.001 TRP A 162 HIS 0.001 0.000 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00360 (12225) covalent geometry : angle 0.47786 (16520) hydrogen bonds : bond 0.06240 ( 955) hydrogen bonds : angle 4.08743 ( 2820) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 137 MET cc_start: 0.9001 (mmt) cc_final: 0.8763 (mmt) outliers start: 7 outliers final: 4 residues processed: 77 average time/residue: 0.1966 time to fit residues: 24.7565 Evaluate side-chains 74 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.071459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.052033 restraints weight = 99298.544| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.35 r_work: 0.2796 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12225 Z= 0.111 Angle : 0.450 7.855 16520 Z= 0.239 Chirality : 0.035 0.151 1940 Planarity : 0.003 0.027 2070 Dihedral : 3.272 13.072 1605 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.38 % Allowed : 13.89 % Favored : 85.73 % 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: 4.49 (0.22), residues: 1475 helix: 4.00 (0.15), residues: 1010 sheet: 1.80 (0.43), residues: 145 loop : -0.20 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 136 TYR 0.009 0.001 TYR A 299 PHE 0.016 0.001 PHE E 352 TRP 0.005 0.000 TRP A 162 HIS 0.001 0.000 HIS B 223 Details of bonding type rmsd covalent geometry : bond 0.00213 (12225) covalent geometry : angle 0.44974 (16520) hydrogen bonds : bond 0.05803 ( 955) hydrogen bonds : angle 3.88244 ( 2820) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 74 average time/residue: 0.1724 time to fit residues: 21.0362 Evaluate side-chains 75 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 76 optimal weight: 0.0980 chunk 91 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.071894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.052476 restraints weight = 99774.323| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.37 r_work: 0.2808 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12225 Z= 0.110 Angle : 0.444 7.488 16520 Z= 0.236 Chirality : 0.035 0.150 1940 Planarity : 0.002 0.028 2070 Dihedral : 3.185 12.791 1605 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.31 % Allowed : 14.05 % Favored : 85.65 % 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: 4.58 (0.22), residues: 1475 helix: 4.08 (0.15), residues: 1010 sheet: 1.80 (0.43), residues: 145 loop : -0.19 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 332 TYR 0.010 0.001 TYR A 299 PHE 0.014 0.001 PHE E 352 TRP 0.005 0.000 TRP A 162 HIS 0.001 0.000 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00216 (12225) covalent geometry : angle 0.44390 (16520) hydrogen bonds : bond 0.05576 ( 955) hydrogen bonds : angle 3.81507 ( 2820) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 137 MET cc_start: 0.8778 (mmt) cc_final: 0.8312 (mmt) outliers start: 4 outliers final: 4 residues processed: 73 average time/residue: 0.2095 time to fit residues: 24.8598 Evaluate side-chains 75 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 146 optimal weight: 0.0370 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.070440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.050900 restraints weight = 100348.293| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.33 r_work: 0.2763 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 12225 Z= 0.162 Angle : 0.483 7.246 16520 Z= 0.261 Chirality : 0.035 0.150 1940 Planarity : 0.003 0.028 2070 Dihedral : 3.291 13.490 1605 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.38 % Allowed : 13.89 % Favored : 85.73 % 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: 4.42 (0.22), residues: 1475 helix: 3.90 (0.14), residues: 1025 sheet: 1.72 (0.42), residues: 145 loop : -0.21 (0.40), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 129 TYR 0.016 0.001 TYR A 299 PHE 0.011 0.001 PHE A 352 TRP 0.005 0.001 TRP A 162 HIS 0.002 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00354 (12225) covalent geometry : angle 0.48259 (16520) hydrogen bonds : bond 0.05964 ( 955) hydrogen bonds : angle 4.01218 ( 2820) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue ALA 83 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue ILE 373 is missing expected H atoms. Skipping. Residue LEU 376 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.2071 time to fit residues: 24.0295 Evaluate side-chains 75 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 45 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.071550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.051993 restraints weight = 98682.746| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.32 r_work: 0.2740 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12225 Z= 0.158 Angle : 0.477 8.505 16520 Z= 0.257 Chirality : 0.035 0.148 1940 Planarity : 0.003 0.028 2070 Dihedral : 3.309 13.718 1605 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.31 % Allowed : 14.05 % Favored : 85.65 % 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: 4.40 (0.22), residues: 1475 helix: 3.88 (0.14), residues: 1025 sheet: 1.68 (0.42), residues: 145 loop : -0.20 (0.39), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 228 TYR 0.015 0.001 TYR D 299 PHE 0.013 0.001 PHE C 352 TRP 0.005 0.001 TRP A 162 HIS 0.001 0.000 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00341 (12225) covalent geometry : angle 0.47712 (16520) hydrogen bonds : bond 0.06033 ( 955) hydrogen bonds : angle 4.01937 ( 2820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4167.58 seconds wall clock time: 71 minutes 40.33 seconds (4300.33 seconds total)