Starting phenix.real_space_refine on Fri Jun 20 23:42:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ts3_41589/06_2025/8ts3_41589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ts3_41589/06_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_41589/06_2025/8ts3_41589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ts3_41589/06_2025/8ts3_41589.map" model { file = "/net/cci-nas-00/data/ceres_data/8ts3_41589/06_2025/8ts3_41589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ts3_41589/06_2025/8ts3_41589.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} 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: 11.76, per 1000 atoms: 0.49 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: 5.90 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.58 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: 7.99 Time building geometry restraints manager: 7.20 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 399 or resid 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: 1.160 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: 0.390 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 48.460 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.880 ------------------------------------------------------------------------------- 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 : 3.82 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.004 0.001 TRP B 375 HIS 0.001 0.000 HIS A 288 PHE 0.010 0.001 PHE D 352 TYR 0.004 0.001 TYR C 299 ARG 0.002 0.000 ARG C 136 Details of bonding type rmsd hydrogen bonds : bond 0.08483 ( 955) hydrogen bonds : angle 4.62217 ( 2820) covalent geometry : bond 0.00201 (12225) covalent geometry : angle 0.45237 (16520) *********************** 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 : 2.205 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: 0.4144 time to fit residues: 58.3326 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 : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.073531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.054329 restraints weight = 98312.650| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.37 r_work: 0.2853 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12225 Z= 0.174 Angle : 0.513 6.985 16520 Z= 0.275 Chirality : 0.036 0.143 1940 Planarity : 0.003 0.027 2070 Dihedral : 3.261 12.515 1605 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.61 % Allowed : 11.45 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.29 (0.22), residues: 1475 helix: 3.71 (0.15), residues: 1010 sheet: 2.12 (0.42), residues: 145 loop : 0.06 (0.40), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 273 HIS 0.002 0.001 HIS A 232 PHE 0.009 0.001 PHE E 352 TYR 0.014 0.001 TYR B 299 ARG 0.002 0.000 ARG D 311 Details of bonding type rmsd hydrogen bonds : bond 0.05643 ( 955) hydrogen bonds : angle 4.15365 ( 2820) covalent geometry : bond 0.00390 (12225) covalent geometry : angle 0.51274 (16520) *********************** 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 81 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 73 average time/residue: 0.4186 time to fit residues: 49.6711 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 : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 127 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.068679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.049073 restraints weight = 100236.499| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.33 r_work: 0.2715 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 12225 Z= 0.264 Angle : 0.571 5.136 16520 Z= 0.318 Chirality : 0.037 0.143 1940 Planarity : 0.003 0.023 2070 Dihedral : 3.629 14.040 1605 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.15 % Allowed : 12.29 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.22), residues: 1475 helix: 3.39 (0.15), residues: 1025 sheet: 1.96 (0.40), residues: 145 loop : -0.08 (0.41), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 162 HIS 0.003 0.001 HIS A 232 PHE 0.011 0.001 PHE E 352 TYR 0.019 0.002 TYR A 299 ARG 0.002 0.000 ARG E 332 Details of bonding type rmsd hydrogen bonds : bond 0.06919 ( 955) hydrogen bonds : angle 4.45717 ( 2820) covalent geometry : bond 0.00598 (12225) covalent geometry : angle 0.57138 (16520) *********************** 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 87 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 383 MET cc_start: 0.9089 (mmp) cc_final: 0.8862 (mmp) REVERT: E 383 MET cc_start: 0.9066 (mmp) cc_final: 0.8784 (mmp) outliers start: 15 outliers final: 4 residues processed: 78 average time/residue: 0.6975 time to fit residues: 90.1526 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 : 3.034 ------------------------------------------------------------------------------- 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 142 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.068920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.049410 restraints weight = 100839.663| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.36 r_work: 0.2731 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 12225 Z= 0.205 Angle : 0.509 4.313 16520 Z= 0.280 Chirality : 0.036 0.148 1940 Planarity : 0.003 0.024 2070 Dihedral : 3.545 13.829 1605 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.30 % Allowed : 12.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.22), residues: 1475 helix: 3.48 (0.15), residues: 1010 sheet: 1.88 (0.40), residues: 145 loop : -0.22 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 273 HIS 0.002 0.001 HIS B 122 PHE 0.013 0.001 PHE B 352 TYR 0.016 0.001 TYR B 299 ARG 0.001 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.06578 ( 955) hydrogen bonds : angle 4.26184 ( 2820) covalent geometry : bond 0.00454 (12225) covalent geometry : angle 0.50856 (16520) *********************** 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 90 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 361 MET cc_start: 0.7588 (tpt) cc_final: 0.7124 (tpp) outliers start: 17 outliers final: 4 residues processed: 82 average time/residue: 0.4346 time to fit residues: 58.0323 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 : 2.028 ------------------------------------------------------------------------------- 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 42 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.070223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.050670 restraints weight = 100159.567| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.37 r_work: 0.2760 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12225 Z= 0.133 Angle : 0.461 5.002 16520 Z= 0.250 Chirality : 0.034 0.149 1940 Planarity : 0.003 0.025 2070 Dihedral : 3.401 13.389 1605 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.07 % Allowed : 13.13 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.25 (0.22), residues: 1475 helix: 3.76 (0.15), residues: 1010 sheet: 1.87 (0.41), residues: 145 loop : -0.18 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 162 HIS 0.001 0.000 HIS B 122 PHE 0.014 0.001 PHE B 352 TYR 0.013 0.001 TYR D 299 ARG 0.001 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.06210 ( 955) hydrogen bonds : angle 4.05363 ( 2820) covalent geometry : bond 0.00271 (12225) covalent geometry : angle 0.46133 (16520) *********************** 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: 14 poor density : 77 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 361 MET cc_start: 0.7667 (tpt) cc_final: 0.7249 (tpp) outliers start: 14 outliers final: 3 residues processed: 80 average time/residue: 0.4315 time to fit residues: 55.8571 Evaluate side-chains 78 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain D residue 349 LEU 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 1 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.069026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.049536 restraints weight = 100521.117| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.33 r_work: 0.2738 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12225 Z= 0.197 Angle : 0.500 5.114 16520 Z= 0.275 Chirality : 0.035 0.147 1940 Planarity : 0.003 0.027 2070 Dihedral : 3.456 13.878 1605 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.76 % Allowed : 13.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.17 (0.22), residues: 1475 helix: 3.66 (0.15), residues: 1025 sheet: 1.80 (0.41), residues: 145 loop : -0.22 (0.40), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 162 HIS 0.001 0.001 HIS A 122 PHE 0.013 0.001 PHE E 352 TYR 0.016 0.001 TYR A 299 ARG 0.002 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.06372 ( 955) hydrogen bonds : angle 4.18700 ( 2820) covalent geometry : bond 0.00440 (12225) covalent geometry : angle 0.50023 (16520) *********************** 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 86 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 137 MET cc_start: 0.8985 (mmt) cc_final: 0.8738 (mmt) REVERT: E 349 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9200 (mp) REVERT: E 361 MET cc_start: 0.7780 (tpt) cc_final: 0.7483 (tpp) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.4032 time to fit residues: 52.3969 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 : 1.940 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 387 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 33 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.069376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.049885 restraints weight = 100528.341| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.33 r_work: 0.2743 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3139 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= 0.163 Angle : 0.479 5.457 16520 Z= 0.261 Chirality : 0.035 0.148 1940 Planarity : 0.003 0.028 2070 Dihedral : 3.428 13.816 1605 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.69 % Allowed : 13.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.22), residues: 1475 helix: 3.72 (0.15), residues: 1025 sheet: 1.77 (0.41), residues: 145 loop : -0.21 (0.40), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 162 HIS 0.001 0.000 HIS B 122 PHE 0.013 0.001 PHE B 352 TYR 0.015 0.001 TYR A 299 ARG 0.001 0.000 ARG C 129 Details of bonding type rmsd hydrogen bonds : bond 0.06297 ( 955) hydrogen bonds : angle 4.11461 ( 2820) covalent geometry : bond 0.00351 (12225) covalent geometry : angle 0.47897 (16520) *********************** 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 84 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 137 MET cc_start: 0.8998 (mmt) cc_final: 0.8759 (mmt) REVERT: E 349 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9198 (mp) REVERT: E 361 MET cc_start: 0.7764 (tpt) cc_final: 0.7463 (tpp) outliers start: 9 outliers final: 6 residues processed: 78 average time/residue: 0.4162 time to fit residues: 52.8014 Evaluate side-chains 80 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 Chi-restraints excluded: chain E residue 387 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3308 r_free = 0.3308 target = 0.069139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.049650 restraints weight = 100241.747| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.32 r_work: 0.2735 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3234 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= 0.175 Angle : 0.490 5.937 16520 Z= 0.268 Chirality : 0.035 0.152 1940 Planarity : 0.003 0.026 2070 Dihedral : 3.437 13.879 1605 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.76 % Allowed : 13.66 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.21 (0.22), residues: 1475 helix: 3.71 (0.15), residues: 1025 sheet: 1.74 (0.41), residues: 145 loop : -0.26 (0.40), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 162 HIS 0.001 0.000 HIS A 122 PHE 0.014 0.001 PHE C 352 TYR 0.015 0.001 TYR A 299 ARG 0.001 0.000 ARG E 228 Details of bonding type rmsd hydrogen bonds : bond 0.06322 ( 955) hydrogen bonds : angle 4.14004 ( 2820) covalent geometry : bond 0.00383 (12225) covalent geometry : angle 0.48965 (16520) *********************** 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 83 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 349 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9198 (mp) REVERT: E 361 MET cc_start: 0.7857 (tpt) cc_final: 0.7635 (tpp) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.4439 time to fit residues: 56.0611 Evaluate side-chains 81 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 387 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 Chi-restraints excluded: chain E residue 387 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.070158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.050582 restraints weight = 100344.343| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.38 r_work: 0.2756 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12225 Z= 0.134 Angle : 0.460 6.118 16520 Z= 0.248 Chirality : 0.035 0.150 1940 Planarity : 0.003 0.027 2070 Dihedral : 3.347 13.515 1605 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.53 % Allowed : 13.89 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.38 (0.22), residues: 1475 helix: 3.86 (0.15), residues: 1025 sheet: 1.73 (0.42), residues: 145 loop : -0.22 (0.40), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 162 HIS 0.001 0.000 HIS B 122 PHE 0.014 0.001 PHE C 352 TYR 0.013 0.001 TYR D 299 ARG 0.001 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.06075 ( 955) hydrogen bonds : angle 4.00266 ( 2820) covalent geometry : bond 0.00276 (12225) covalent geometry : angle 0.45976 (16520) *********************** 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 81 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 349 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9224 (mp) REVERT: E 361 MET cc_start: 0.7784 (tpt) cc_final: 0.7523 (tpp) outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 0.4278 time to fit residues: 51.9309 Evaluate side-chains 78 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 2.172 ------------------------------------------------------------------------------- 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 135 MET Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 387 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 25 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.071278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.051655 restraints weight = 99853.644| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.37 r_work: 0.2747 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12225 Z= 0.141 Angle : 0.465 5.643 16520 Z= 0.252 Chirality : 0.035 0.159 1940 Planarity : 0.003 0.027 2070 Dihedral : 3.329 13.514 1605 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.53 % Allowed : 13.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.38 (0.22), residues: 1475 helix: 3.87 (0.14), residues: 1025 sheet: 1.72 (0.42), residues: 145 loop : -0.25 (0.40), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 162 HIS 0.001 0.000 HIS A 122 PHE 0.013 0.001 PHE C 352 TYR 0.014 0.001 TYR D 299 ARG 0.003 0.000 ARG E 391 Details of bonding type rmsd hydrogen bonds : bond 0.06021 ( 955) hydrogen bonds : angle 4.00807 ( 2820) covalent geometry : bond 0.00296 (12225) covalent geometry : angle 0.46537 (16520) ********************** 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 80 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 361 MET cc_start: 0.7816 (tpt) cc_final: 0.7586 (tpp) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.4140 time to fit residues: 49.0021 Evaluate side-chains 79 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 135 MET Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 387 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.070800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.051165 restraints weight = 99634.674| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.33 r_work: 0.2723 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12225 Z= 0.173 Angle : 0.484 5.855 16520 Z= 0.265 Chirality : 0.035 0.149 1940 Planarity : 0.003 0.027 2070 Dihedral : 3.398 13.919 1605 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.46 % Allowed : 13.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.25 (0.22), residues: 1475 helix: 3.77 (0.14), residues: 1025 sheet: 1.68 (0.41), residues: 145 loop : -0.29 (0.39), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 162 HIS 0.001 0.001 HIS A 122 PHE 0.012 0.001 PHE C 352 TYR 0.016 0.001 TYR B 299 ARG 0.001 0.000 ARG E 228 Details of bonding type rmsd hydrogen bonds : bond 0.06229 ( 955) hydrogen bonds : angle 4.10767 ( 2820) covalent geometry : bond 0.00377 (12225) covalent geometry : angle 0.48412 (16520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8889.30 seconds wall clock time: 155 minutes 1.44 seconds (9301.44 seconds total)