Starting phenix.real_space_refine on Fri May 23 13:44:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ts3_41589/05_2025/8ts3_41589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ts3_41589/05_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_41589/05_2025/8ts3_41589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ts3_41589/05_2025/8ts3_41589.map" model { file = "/net/cci-nas-00/data/ceres_data/8ts3_41589/05_2025/8ts3_41589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ts3_41589/05_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-5687/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: 11.31, per 1000 atoms: 0.47 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: 5.72 Conformation dependent library (CDL) restraints added in 1.7 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: 1.52 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: 7.88 Time building geometry restraints manager: 6.90 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: 0.700 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: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 46.200 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.760 ------------------------------------------------------------------------------- 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 : 1.921 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: 0.4030 time to fit residues: 56.5378 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 : 1.838 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.054330 restraints weight = 98312.611| |-----------------------------------------------------------------------------| 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 : 2.108 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: 0.4179 time to fit residues: 49.2987 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 : 2.040 ------------------------------------------------------------------------------- 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: 0.0050 chunk 80 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- 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 = 0.069675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.050090 restraints weight = 99547.039| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.33 r_work: 0.2742 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12225 Z= 0.221 Angle : 0.533 5.019 16520 Z= 0.295 Chirality : 0.036 0.143 1940 Planarity : 0.003 0.023 2070 Dihedral : 3.503 13.722 1605 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.99 % Allowed : 12.21 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.11 (0.22), residues: 1475 helix: 3.60 (0.15), residues: 1010 sheet: 2.02 (0.41), residues: 145 loop : -0.07 (0.40), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 162 HIS 0.003 0.001 HIS D 232 PHE 0.011 0.001 PHE E 352 TYR 0.018 0.002 TYR D 299 ARG 0.002 0.000 ARG D 187 Details of bonding type rmsd hydrogen bonds : bond 0.06613 ( 955) hydrogen bonds : angle 4.30849 ( 2820) covalent geometry : bond 0.00496 (12225) covalent geometry : angle 0.53312 (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 86 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 383 MET cc_start: 0.9119 (mmp) cc_final: 0.8902 (mmp) REVERT: E 383 MET cc_start: 0.9107 (mmp) cc_final: 0.8857 (mmp) outliers start: 13 outliers final: 4 residues processed: 79 average time/residue: 0.4105 time to fit residues: 52.7010 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 : 1.895 ------------------------------------------------------------------------------- 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: 2.9990 chunk 114 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.069220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.049679 restraints weight = 100793.538| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.36 r_work: 0.2739 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 12225 Z= 0.203 Angle : 0.506 4.297 16520 Z= 0.279 Chirality : 0.035 0.147 1940 Planarity : 0.003 0.023 2070 Dihedral : 3.493 13.706 1605 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.45 % Allowed : 12.90 % 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: 4.05 (0.22), residues: 1475 helix: 3.58 (0.15), residues: 1010 sheet: 1.90 (0.41), residues: 145 loop : -0.17 (0.39), residues: 320 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 B 352 TYR 0.016 0.001 TYR B 299 ARG 0.002 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.06479 ( 955) hydrogen bonds : angle 4.22094 ( 2820) covalent geometry : bond 0.00451 (12225) covalent geometry : angle 0.50579 (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 92 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 137 MET cc_start: 0.8927 (mmt) cc_final: 0.8665 (mmt) REVERT: E 361 MET cc_start: 0.7761 (tpt) cc_final: 0.7358 (tpp) outliers start: 19 outliers final: 4 residues processed: 82 average time/residue: 0.4117 time to fit residues: 54.8400 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 : 1.979 ------------------------------------------------------------------------------- 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: 0.6980 chunk 128 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 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 = 0.3332 r_free = 0.3332 target = 0.070437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.050886 restraints weight = 99926.119| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.36 r_work: 0.2770 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2862 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= 0.132 Angle : 0.459 5.164 16520 Z= 0.249 Chirality : 0.034 0.149 1940 Planarity : 0.003 0.025 2070 Dihedral : 3.374 13.376 1605 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.07 % Allowed : 13.05 % 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: 4.31 (0.22), residues: 1475 helix: 3.81 (0.15), residues: 1010 sheet: 1.89 (0.41), residues: 145 loop : -0.15 (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 0.013 0.001 PHE B 352 TYR 0.013 0.001 TYR D 299 ARG 0.001 0.000 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.06155 ( 955) hydrogen bonds : angle 4.02233 ( 2820) covalent geometry : bond 0.00269 (12225) covalent geometry : angle 0.45869 (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 92 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 344 MET cc_start: 0.9373 (mtm) cc_final: 0.9138 (mtp) REVERT: E 361 MET cc_start: 0.7650 (tpt) cc_final: 0.7223 (tpp) outliers start: 14 outliers final: 3 residues processed: 82 average time/residue: 0.4148 time to fit residues: 54.7710 Evaluate side-chains 77 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 1.941 ------------------------------------------------------------------------------- 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: 5.9990 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: 4.9990 chunk 111 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 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 = 0.3295 r_free = 0.3295 target = 0.068508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.048991 restraints weight = 100655.098| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.32 r_work: 0.2724 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12225 Z= 0.223 Angle : 0.522 5.059 16520 Z= 0.289 Chirality : 0.036 0.146 1940 Planarity : 0.003 0.026 2070 Dihedral : 3.510 14.141 1605 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.76 % Allowed : 13.21 % Favored : 86.03 % 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: 4.02 (0.22), residues: 1475 helix: 3.60 (0.15), residues: 1010 sheet: 1.81 (0.40), residues: 145 loop : -0.27 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.002 0.001 HIS A 232 PHE 0.012 0.001 PHE C 352 TYR 0.017 0.001 TYR B 299 ARG 0.002 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.06524 ( 955) hydrogen bonds : angle 4.25043 ( 2820) covalent geometry : bond 0.00503 (12225) covalent geometry : angle 0.52215 (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 83 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 137 MET cc_start: 0.9034 (mmt) cc_final: 0.8745 (mmt) REVERT: E 349 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9175 (mp) REVERT: E 361 MET cc_start: 0.7855 (tpt) cc_final: 0.7587 (tpp) outliers start: 10 outliers final: 7 residues processed: 78 average time/residue: 0.3993 time to fit residues: 50.3279 Evaluate side-chains 80 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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: 3.9990 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 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: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.069576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.050030 restraints weight = 100201.170| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.34 r_work: 0.2745 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.003 0.028 12225 Z= 0.151 Angle : 0.471 5.503 16520 Z= 0.256 Chirality : 0.035 0.148 1940 Planarity : 0.003 0.026 2070 Dihedral : 3.425 13.675 1605 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.76 % Allowed : 13.13 % 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 (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: 3.73 (0.15), residues: 1025 sheet: 1.78 (0.41), residues: 145 loop : -0.18 (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 0.014 0.001 PHE B 352 TYR 0.014 0.001 TYR A 299 ARG 0.001 0.000 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.06285 ( 955) hydrogen bonds : angle 4.08558 ( 2820) covalent geometry : bond 0.00320 (12225) covalent geometry : angle 0.47101 (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 85 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 137 MET cc_start: 0.8993 (mmt) cc_final: 0.8759 (mmt) REVERT: E 349 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9182 (mp) outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 0.4004 time to fit residues: 51.4005 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 : 1.814 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.069485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.049909 restraints weight = 100044.532| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.33 r_work: 0.2742 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12225 Z= 0.163 Angle : 0.483 5.913 16520 Z= 0.263 Chirality : 0.035 0.149 1940 Planarity : 0.003 0.026 2070 Dihedral : 3.420 13.773 1605 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.61 % Allowed : 13.59 % 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: 3.73 (0.15), residues: 1025 sheet: 1.78 (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 0.000 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 B 332 Details of bonding type rmsd hydrogen bonds : bond 0.06261 ( 955) hydrogen bonds : angle 4.10699 ( 2820) covalent geometry : bond 0.00353 (12225) covalent geometry : angle 0.48332 (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 82 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 PHE cc_start: 0.8782 (t80) cc_final: 0.8454 (t80) REVERT: E 349 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9232 (mp) REVERT: E 361 MET cc_start: 0.7609 (tpt) cc_final: 0.7039 (tpp) outliers start: 8 outliers final: 6 residues processed: 76 average time/residue: 0.4348 time to fit residues: 53.6762 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 : 1.962 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 92 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.070656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.051149 restraints weight = 99683.066| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.34 r_work: 0.2775 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3198 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= 0.126 Angle : 0.452 6.051 16520 Z= 0.244 Chirality : 0.034 0.150 1940 Planarity : 0.003 0.027 2070 Dihedral : 3.306 13.318 1605 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.38 % Allowed : 13.82 % 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: 4.39 (0.22), residues: 1475 helix: 3.92 (0.15), residues: 1010 sheet: 1.76 (0.42), residues: 145 loop : -0.24 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 162 HIS 0.001 0.000 HIS B 223 PHE 0.015 0.001 PHE C 352 TYR 0.012 0.001 TYR D 299 ARG 0.001 0.000 ARG D 136 Details of bonding type rmsd hydrogen bonds : bond 0.05930 ( 955) hydrogen bonds : angle 3.95385 ( 2820) covalent geometry : bond 0.00257 (12225) covalent geometry : angle 0.45195 (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 78 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 73 average time/residue: 0.4200 time to fit residues: 49.5091 Evaluate side-chains 77 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 2.038 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 100 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.070846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.051190 restraints weight = 100222.275| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.34 r_work: 0.2725 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3304 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= 0.179 Angle : 0.491 5.505 16520 Z= 0.269 Chirality : 0.035 0.148 1940 Planarity : 0.003 0.027 2070 Dihedral : 3.396 13.759 1605 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.38 % Allowed : 13.74 % 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: 4.26 (0.22), residues: 1475 helix: 3.76 (0.14), residues: 1025 sheet: 1.72 (0.41), residues: 145 loop : -0.26 (0.39), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 162 HIS 0.002 0.001 HIS A 122 PHE 0.011 0.001 PHE C 352 TYR 0.016 0.001 TYR A 299 ARG 0.001 0.000 ARG E 332 Details of bonding type rmsd hydrogen bonds : bond 0.06204 ( 955) hydrogen bonds : angle 4.11538 ( 2820) covalent geometry : bond 0.00394 (12225) covalent geometry : angle 0.49061 (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 78 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 PHE cc_start: 0.8766 (t80) cc_final: 0.8556 (t80) REVERT: B 349 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9206 (mp) REVERT: E 349 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9191 (mp) outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 0.4144 time to fit residues: 49.0425 Evaluate side-chains 78 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 1.917 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 6 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.070724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.051013 restraints weight = 99635.637| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.40 r_work: 0.2737 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12225 Z= 0.143 Angle : 0.463 5.486 16520 Z= 0.251 Chirality : 0.035 0.149 1940 Planarity : 0.003 0.028 2070 Dihedral : 3.343 13.552 1605 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.38 % Allowed : 13.66 % 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: 4.35 (0.22), residues: 1475 helix: 3.84 (0.14), residues: 1025 sheet: 1.71 (0.41), residues: 145 loop : -0.25 (0.39), 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 0.014 0.001 PHE E 352 TYR 0.014 0.001 TYR D 299 ARG 0.001 0.000 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.06050 ( 955) hydrogen bonds : angle 4.01526 ( 2820) covalent geometry : bond 0.00303 (12225) covalent geometry : angle 0.46288 (16520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7868.71 seconds wall clock time: 135 minutes 52.81 seconds (8152.81 seconds total)