Starting phenix.real_space_refine on Mon Jun 16 04:25:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c0e_16364/06_2025/8c0e_16364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c0e_16364/06_2025/8c0e_16364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c0e_16364/06_2025/8c0e_16364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c0e_16364/06_2025/8c0e_16364.map" model { file = "/net/cci-nas-00/data/ceres_data/8c0e_16364/06_2025/8c0e_16364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c0e_16364/06_2025/8c0e_16364.cif" } resolution = 3.6 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= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 11582 2.51 5 N 3210 2.21 5 O 3533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18385 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "B" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2203 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 10, 'TRANS': 264} Chain breaks: 1 Chain: "C" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "D" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2214 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 10, 'TRANS': 265} Chain breaks: 1 Chain: "E" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "F" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2218 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Chain: "G" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "H" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2218 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Time building chain proxies: 10.32, per 1000 atoms: 0.56 Number of scatterers: 18385 At special positions: 0 Unit cell: (119.78, 119.78, 144.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 3533 8.00 N 3210 7.00 C 11582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.99 Conformation dependent library (CDL) restraints added in 2.4 seconds 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 8 sheets defined 70.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 39 through 54 Processing helix chain 'A' and resid 69 through 72 Processing helix chain 'A' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.519A pdb=" N GLY A 337 " --> pdb=" O TRP A 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 54 Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 125 through 130 removed outlier: 3.527A pdb=" N LYS B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 278 Processing helix chain 'B' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY B 337 " --> pdb=" O TRP B 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 Processing helix chain 'C' and resid 69 through 72 Processing helix chain 'C' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 82 " --> pdb=" O GLN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 99 through 113 Processing helix chain 'C' and resid 114 through 125 Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS C 129 " --> pdb=" O THR C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY C 337 " --> pdb=" O TRP C 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 54 Processing helix chain 'D' and resid 69 through 72 Processing helix chain 'D' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 114 through 125 Processing helix chain 'D' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS D 129 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 241 removed outlier: 3.642A pdb=" N LEU D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 283 through 298 removed outlier: 3.730A pdb=" N ASP D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY D 337 " --> pdb=" O TRP D 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 54 Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 73 through 84 removed outlier: 4.306A pdb=" N SER E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU E 82 " --> pdb=" O GLN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 99 through 113 Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 125 through 130 removed outlier: 3.525A pdb=" N LYS E 129 " --> pdb=" O THR E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 241 removed outlier: 3.640A pdb=" N LEU E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 263 removed outlier: 3.759A pdb=" N LEU E 263 " --> pdb=" O MET E 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 260 through 263' Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY E 337 " --> pdb=" O TRP E 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 54 Processing helix chain 'F' and resid 69 through 72 Processing helix chain 'F' and resid 73 through 84 removed outlier: 4.306A pdb=" N SER F 77 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU F 82 " --> pdb=" O GLN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 99 through 113 Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS F 129 " --> pdb=" O THR F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE F 150 " --> pdb=" O LEU F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU F 179 " --> pdb=" O SER F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 278 Processing helix chain 'F' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY F 337 " --> pdb=" O TRP F 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 54 Processing helix chain 'G' and resid 69 through 72 Processing helix chain 'G' and resid 73 through 84 removed outlier: 4.306A pdb=" N SER G 77 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU G 82 " --> pdb=" O GLN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 92 Processing helix chain 'G' and resid 99 through 113 Processing helix chain 'G' and resid 114 through 125 Processing helix chain 'G' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS G 129 " --> pdb=" O THR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU G 179 " --> pdb=" O SER G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 278 Processing helix chain 'G' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP G 287 " --> pdb=" O GLU G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY G 337 " --> pdb=" O TRP G 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 54 Processing helix chain 'H' and resid 69 through 72 Processing helix chain 'H' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU H 82 " --> pdb=" O GLN H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 92 Processing helix chain 'H' and resid 99 through 113 Processing helix chain 'H' and resid 114 through 125 Processing helix chain 'H' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS H 129 " --> pdb=" O THR H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 150 removed outlier: 3.791A pdb=" N ILE H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU H 179 " --> pdb=" O SER H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 278 Processing helix chain 'H' and resid 283 through 298 removed outlier: 3.730A pdb=" N ASP H 287 " --> pdb=" O GLU H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY H 337 " --> pdb=" O TRP H 333 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP A 163 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP A 65 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR A 311 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.842A pdb=" N ASP B 163 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP B 65 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N TYR B 311 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP C 163 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP C 65 " --> pdb=" O TYR C 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR C 311 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP D 163 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP D 65 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR D 311 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP E 163 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP E 65 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR E 311 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 151 through 153 removed outlier: 3.842A pdb=" N ASP F 163 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP F 65 " --> pdb=" O TYR F 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR F 311 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP G 163 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP G 65 " --> pdb=" O TYR G 311 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR G 311 " --> pdb=" O ASP G 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP H 163 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP H 65 " --> pdb=" O TYR H 311 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR H 311 " --> pdb=" O ASP H 65 " (cutoff:3.500A) 1290 hydrogen bonds defined for protein. 3798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.57 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6170 1.34 - 1.46: 3246 1.46 - 1.57: 9201 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 18737 Sorted by residual: bond pdb=" C ILE A 255 " pdb=" N PRO A 256 " ideal model delta sigma weight residual 1.331 1.354 -0.023 1.21e-02 6.83e+03 3.55e+00 bond pdb=" C ARG H 265 " pdb=" N PRO H 266 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.15e+00 bond pdb=" C ARG D 265 " pdb=" N PRO D 266 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.20e-02 6.94e+03 2.89e+00 bond pdb=" C ILE E 255 " pdb=" N PRO E 256 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.21e-02 6.83e+03 2.36e+00 bond pdb=" C ARG A 265 " pdb=" N PRO A 266 " ideal model delta sigma weight residual 1.334 1.356 -0.021 1.51e-02 4.39e+03 2.00e+00 ... (remaining 18732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 25032 2.53 - 5.06: 257 5.06 - 7.60: 42 7.60 - 10.13: 10 10.13 - 12.66: 18 Bond angle restraints: 25359 Sorted by residual: angle pdb=" CB ARG G 313 " pdb=" CG ARG G 313 " pdb=" CD ARG G 313 " ideal model delta sigma weight residual 111.30 123.96 -12.66 2.30e+00 1.89e-01 3.03e+01 angle pdb=" CB ARG H 313 " pdb=" CG ARG H 313 " pdb=" CD ARG H 313 " ideal model delta sigma weight residual 111.30 123.94 -12.64 2.30e+00 1.89e-01 3.02e+01 angle pdb=" CB ARG F 313 " pdb=" CG ARG F 313 " pdb=" CD ARG F 313 " ideal model delta sigma weight residual 111.30 123.94 -12.64 2.30e+00 1.89e-01 3.02e+01 angle pdb=" CB ARG C 313 " pdb=" CG ARG C 313 " pdb=" CD ARG C 313 " ideal model delta sigma weight residual 111.30 123.93 -12.63 2.30e+00 1.89e-01 3.01e+01 angle pdb=" CB ARG B 313 " pdb=" CG ARG B 313 " pdb=" CD ARG B 313 " ideal model delta sigma weight residual 111.30 123.92 -12.62 2.30e+00 1.89e-01 3.01e+01 ... (remaining 25354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9468 17.95 - 35.91: 1448 35.91 - 53.86: 412 53.86 - 71.81: 42 71.81 - 89.76: 32 Dihedral angle restraints: 11402 sinusoidal: 4627 harmonic: 6775 Sorted by residual: dihedral pdb=" CA THR A 250 " pdb=" C THR A 250 " pdb=" N PRO A 251 " pdb=" CA PRO A 251 " ideal model delta harmonic sigma weight residual 180.00 144.06 35.94 0 5.00e+00 4.00e-02 5.17e+01 dihedral pdb=" CA ASP E 249 " pdb=" C ASP E 249 " pdb=" N THR E 250 " pdb=" CA THR E 250 " ideal model delta harmonic sigma weight residual 180.00 144.74 35.26 0 5.00e+00 4.00e-02 4.97e+01 dihedral pdb=" CA THR E 250 " pdb=" C THR E 250 " pdb=" N PRO E 251 " pdb=" CA PRO E 251 " ideal model delta harmonic sigma weight residual 180.00 147.08 32.92 0 5.00e+00 4.00e-02 4.34e+01 ... (remaining 11399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2076 0.041 - 0.081: 572 0.081 - 0.122: 92 0.122 - 0.162: 21 0.162 - 0.203: 10 Chirality restraints: 2771 Sorted by residual: chirality pdb=" CA PRO C 324 " pdb=" N PRO C 324 " pdb=" C PRO C 324 " pdb=" CB PRO C 324 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA PRO B 324 " pdb=" N PRO B 324 " pdb=" C PRO B 324 " pdb=" CB PRO B 324 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA PRO F 324 " pdb=" N PRO F 324 " pdb=" C PRO F 324 " pdb=" CB PRO F 324 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2768 not shown) Planarity restraints: 3323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 241 " 0.051 2.00e-02 2.50e+03 1.04e-01 1.08e+02 pdb=" C GLN C 241 " -0.180 2.00e-02 2.50e+03 pdb=" O GLN C 241 " 0.070 2.00e-02 2.50e+03 pdb=" N GLY C 242 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 241 " -0.026 2.00e-02 2.50e+03 5.18e-02 2.69e+01 pdb=" C GLN E 241 " 0.090 2.00e-02 2.50e+03 pdb=" O GLN E 241 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY E 242 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 241 " -0.025 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C GLN A 241 " 0.086 2.00e-02 2.50e+03 pdb=" O GLN A 241 " -0.032 2.00e-02 2.50e+03 pdb=" N GLY A 242 " -0.029 2.00e-02 2.50e+03 ... (remaining 3320 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 549 2.71 - 3.26: 18529 3.26 - 3.81: 31020 3.81 - 4.35: 33628 4.35 - 4.90: 61068 Nonbonded interactions: 144794 Sorted by model distance: nonbonded pdb=" OG1 THR G 171 " pdb=" OD2 ASP G 174 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR E 171 " pdb=" OD2 ASP E 174 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR C 171 " pdb=" OD2 ASP C 174 " model vdw 2.167 3.040 nonbonded pdb=" OG1 THR A 171 " pdb=" OD2 ASP A 174 " model vdw 2.167 3.040 nonbonded pdb=" OG1 THR D 171 " pdb=" OD2 ASP D 174 " model vdw 2.167 3.040 ... (remaining 144789 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 39 through 241 or resid 266 through 337)) selection = chain 'B' selection = (chain 'C' and (resid 39 through 241 or resid 266 through 337)) selection = (chain 'D' and (resid 39 through 241 or resid 266 through 337)) selection = (chain 'E' and (resid 39 through 241 or resid 266 through 337)) selection = (chain 'F' and (resid 39 through 241 or resid 266 through 337)) selection = (chain 'G' and (resid 39 through 241 or resid 266 through 337)) selection = (chain 'H' and (resid 39 through 241 or resid 266 through 337)) } 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 group one per residue 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: 0.850 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.890 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.090 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18737 Z= 0.156 Angle : 0.720 12.661 25359 Z= 0.368 Chirality : 0.039 0.203 2771 Planarity : 0.008 0.121 3323 Dihedral : 18.449 89.765 7028 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.12 % Favored : 96.53 % Rotamer: Outliers : 0.77 % Allowed : 28.16 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.05 % 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: 1.91 (0.18), residues: 2277 helix: 2.34 (0.14), residues: 1479 sheet: 0.25 (0.34), residues: 216 loop : -1.24 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 202 HIS 0.004 0.001 HIS F 193 PHE 0.014 0.001 PHE A 261 TYR 0.035 0.002 TYR H 115 ARG 0.007 0.001 ARG D 313 Details of bonding type rmsd hydrogen bonds : bond 0.12034 ( 1290) hydrogen bonds : angle 5.69927 ( 3798) covalent geometry : bond 0.00366 (18737) covalent geometry : angle 0.71951 (25359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLU cc_start: 0.7670 (tt0) cc_final: 0.7402 (tt0) REVERT: A 227 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6928 (mt-10) REVERT: A 267 MET cc_start: 0.6654 (mmm) cc_final: 0.6050 (tpp) REVERT: A 320 LYS cc_start: 0.8098 (pttp) cc_final: 0.7872 (mttt) REVERT: B 66 LYS cc_start: 0.8717 (ptpp) cc_final: 0.8343 (ptmm) REVERT: C 170 GLU cc_start: 0.7719 (tt0) cc_final: 0.7503 (tt0) REVERT: C 267 MET cc_start: 0.6856 (mmm) cc_final: 0.6283 (tpp) REVERT: C 320 LYS cc_start: 0.8208 (pttp) cc_final: 0.7925 (mttt) REVERT: D 66 LYS cc_start: 0.8719 (ptpp) cc_final: 0.8321 (ptmm) REVERT: E 106 ASP cc_start: 0.6900 (t0) cc_final: 0.6544 (m-30) REVERT: E 170 GLU cc_start: 0.7756 (tt0) cc_final: 0.7532 (tt0) REVERT: E 267 MET cc_start: 0.6439 (mmm) cc_final: 0.5822 (tpp) REVERT: E 292 MET cc_start: 0.8249 (mmm) cc_final: 0.8034 (tpp) REVERT: E 320 LYS cc_start: 0.8196 (pttp) cc_final: 0.7954 (mttt) REVERT: F 66 LYS cc_start: 0.8699 (ptpp) cc_final: 0.8320 (ptmm) REVERT: G 267 MET cc_start: 0.6595 (mmm) cc_final: 0.6139 (tpp) REVERT: G 320 LYS cc_start: 0.8150 (pttp) cc_final: 0.7926 (mttt) REVERT: H 66 LYS cc_start: 0.8716 (ptpp) cc_final: 0.8330 (ptmm) outliers start: 15 outliers final: 0 residues processed: 268 average time/residue: 0.3615 time to fit residues: 139.5093 Evaluate side-chains 145 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 307 GLN B 193 HIS B 307 GLN C 307 GLN D 193 HIS D 307 GLN E 240 GLN E 307 GLN F 193 HIS F 307 GLN G 307 GLN H 193 HIS H 307 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.194022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.151654 restraints weight = 18624.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.152180 restraints weight = 16101.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.154619 restraints weight = 14891.131| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 18737 Z= 0.251 Angle : 0.709 8.308 25359 Z= 0.367 Chirality : 0.043 0.221 2771 Planarity : 0.009 0.127 3323 Dihedral : 4.755 34.244 2564 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.81 % Favored : 96.84 % Rotamer: Outliers : 5.05 % Allowed : 23.52 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.49 % Twisted General : 0.05 % 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: 1.62 (0.18), residues: 2277 helix: 2.11 (0.13), residues: 1479 sheet: 0.00 (0.34), residues: 200 loop : -1.22 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP A 333 HIS 0.004 0.001 HIS A 193 PHE 0.021 0.002 PHE E 328 TYR 0.021 0.002 TYR E 282 ARG 0.009 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.05055 ( 1290) hydrogen bonds : angle 4.45513 ( 3798) covalent geometry : bond 0.00560 (18737) covalent geometry : angle 0.70875 (25359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 207 time to evaluate : 1.926 Fit side-chains REVERT: A 137 LYS cc_start: 0.7870 (tppt) cc_final: 0.7529 (mtmt) REVERT: A 227 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7008 (mt-10) REVERT: A 236 LYS cc_start: 0.8475 (tttm) cc_final: 0.8218 (tttt) REVERT: A 241 GLN cc_start: 0.6397 (OUTLIER) cc_final: 0.6128 (mp-120) REVERT: A 267 MET cc_start: 0.7156 (mmm) cc_final: 0.6420 (tpp) REVERT: B 43 PHE cc_start: 0.2640 (OUTLIER) cc_final: 0.1955 (m-10) REVERT: B 57 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6873 (mm-30) REVERT: B 157 ASP cc_start: 0.7290 (m-30) cc_final: 0.6922 (m-30) REVERT: B 311 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: C 267 MET cc_start: 0.7088 (mmm) cc_final: 0.6403 (tpp) REVERT: D 43 PHE cc_start: 0.2526 (OUTLIER) cc_final: 0.1855 (m-10) REVERT: D 57 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6850 (mm-30) REVERT: D 68 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7974 (m) REVERT: D 157 ASP cc_start: 0.7311 (m-30) cc_final: 0.6945 (m-30) REVERT: D 311 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: E 106 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: E 267 MET cc_start: 0.6792 (mmm) cc_final: 0.6122 (tpp) REVERT: F 43 PHE cc_start: 0.2640 (OUTLIER) cc_final: 0.1953 (m-10) REVERT: F 57 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6873 (mm-30) REVERT: F 267 MET cc_start: 0.5986 (ptp) cc_final: 0.5691 (ptp) REVERT: G 236 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8105 (tttt) REVERT: G 241 GLN cc_start: 0.6148 (OUTLIER) cc_final: 0.5911 (mp10) REVERT: G 267 MET cc_start: 0.7043 (mmm) cc_final: 0.6470 (tpp) REVERT: H 43 PHE cc_start: 0.2560 (OUTLIER) cc_final: 0.1870 (m-10) REVERT: H 57 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6866 (mm-30) REVERT: H 157 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.7030 (m-30) REVERT: H 311 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7418 (m-80) outliers start: 98 outliers final: 29 residues processed: 290 average time/residue: 0.2736 time to fit residues: 123.5371 Evaluate side-chains 198 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 236 LYS Chi-restraints excluded: chain G residue 241 GLN Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 48 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 217 optimal weight: 0.0270 chunk 166 optimal weight: 2.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN C 276 GLN E 240 GLN E 241 GLN E 276 GLN G 240 GLN G 276 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.189286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.149055 restraints weight = 18801.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.149628 restraints weight = 15185.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.149757 restraints weight = 13697.917| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 18737 Z= 0.172 Angle : 0.598 7.521 25359 Z= 0.309 Chirality : 0.038 0.224 2771 Planarity : 0.007 0.128 3323 Dihedral : 4.585 34.287 2564 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.81 % Favored : 96.84 % Rotamer: Outliers : 3.61 % Allowed : 23.83 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.49 % Twisted General : 0.05 % 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: 1.87 (0.18), residues: 2277 helix: 2.35 (0.13), residues: 1483 sheet: -0.02 (0.36), residues: 200 loop : -1.26 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 202 HIS 0.004 0.001 HIS B 193 PHE 0.011 0.001 PHE B 90 TYR 0.013 0.002 TYR G 282 ARG 0.005 0.001 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 1290) hydrogen bonds : angle 4.24772 ( 3798) covalent geometry : bond 0.00422 (18737) covalent geometry : angle 0.59778 (25359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 166 time to evaluate : 1.834 Fit side-chains REVERT: A 85 LEU cc_start: 0.4926 (OUTLIER) cc_final: 0.4713 (mt) REVERT: A 137 LYS cc_start: 0.7854 (tppt) cc_final: 0.7533 (mtmt) REVERT: A 197 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6797 (mt-10) REVERT: A 227 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7035 (mt-10) REVERT: A 236 LYS cc_start: 0.8646 (tttm) cc_final: 0.8372 (tttt) REVERT: A 267 MET cc_start: 0.7273 (mmm) cc_final: 0.6927 (tpp) REVERT: A 332 MET cc_start: 0.5858 (mmp) cc_final: 0.3817 (ppp) REVERT: B 43 PHE cc_start: 0.2526 (OUTLIER) cc_final: 0.1888 (m-10) REVERT: B 57 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6866 (mm-30) REVERT: B 157 ASP cc_start: 0.7461 (m-30) cc_final: 0.7019 (m-30) REVERT: C 85 LEU cc_start: 0.4809 (OUTLIER) cc_final: 0.4600 (mt) REVERT: C 267 MET cc_start: 0.7287 (mmm) cc_final: 0.7075 (tpp) REVERT: C 332 MET cc_start: 0.5960 (mmp) cc_final: 0.3956 (tmm) REVERT: D 43 PHE cc_start: 0.2462 (OUTLIER) cc_final: 0.1810 (m-10) REVERT: D 57 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6863 (mm-30) REVERT: E 110 MET cc_start: 0.7818 (ttm) cc_final: 0.7508 (ttm) REVERT: E 137 LYS cc_start: 0.7584 (tppt) cc_final: 0.7368 (mtmt) REVERT: E 236 LYS cc_start: 0.8569 (tttm) cc_final: 0.8297 (tttt) REVERT: E 332 MET cc_start: 0.5772 (OUTLIER) cc_final: 0.3795 (tmm) REVERT: F 43 PHE cc_start: 0.2647 (OUTLIER) cc_final: 0.1973 (m-10) REVERT: F 57 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6872 (mm-30) REVERT: F 267 MET cc_start: 0.5864 (ptp) cc_final: 0.5439 (ptt) REVERT: F 311 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: G 241 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6443 (mp10) REVERT: G 332 MET cc_start: 0.5913 (mmp) cc_final: 0.3872 (tmm) REVERT: H 43 PHE cc_start: 0.2549 (OUTLIER) cc_final: 0.1885 (m-10) REVERT: H 157 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7168 (m-30) outliers start: 70 outliers final: 31 residues processed: 221 average time/residue: 0.3044 time to fit residues: 101.4542 Evaluate side-chains 189 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 241 GLN Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 197 optimal weight: 30.0000 chunk 203 optimal weight: 4.9990 chunk 56 optimal weight: 30.0000 chunk 23 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 240 GLN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 GLN ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.197977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.156509 restraints weight = 18546.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.157403 restraints weight = 15219.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.157885 restraints weight = 13655.901| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 18737 Z= 0.173 Angle : 0.580 7.306 25359 Z= 0.298 Chirality : 0.038 0.214 2771 Planarity : 0.007 0.130 3323 Dihedral : 4.505 34.625 2564 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.90 % Favored : 96.75 % Rotamer: Outliers : 4.80 % Allowed : 22.28 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.34 % Twisted General : 0.05 % 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: 1.94 (0.18), residues: 2277 helix: 2.40 (0.14), residues: 1490 sheet: -0.02 (0.37), residues: 200 loop : -1.26 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 202 HIS 0.002 0.001 HIS H 193 PHE 0.009 0.001 PHE D 306 TYR 0.011 0.002 TYR A 282 ARG 0.005 0.000 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 1290) hydrogen bonds : angle 4.12438 ( 3798) covalent geometry : bond 0.00415 (18737) covalent geometry : angle 0.58001 (25359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 187 time to evaluate : 1.987 Fit side-chains REVERT: A 85 LEU cc_start: 0.4910 (OUTLIER) cc_final: 0.4681 (mt) REVERT: A 227 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6995 (mt-10) REVERT: A 236 LYS cc_start: 0.8627 (tttm) cc_final: 0.8338 (tttt) REVERT: A 271 ARG cc_start: 0.6636 (tpt-90) cc_final: 0.6394 (tpp80) REVERT: A 332 MET cc_start: 0.5752 (mmp) cc_final: 0.3741 (ppp) REVERT: B 43 PHE cc_start: 0.2532 (OUTLIER) cc_final: 0.1870 (m-10) REVERT: B 57 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6954 (mm-30) REVERT: B 311 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: C 85 LEU cc_start: 0.4797 (OUTLIER) cc_final: 0.4590 (mt) REVERT: C 332 MET cc_start: 0.5796 (mmp) cc_final: 0.3768 (tmm) REVERT: D 43 PHE cc_start: 0.2443 (OUTLIER) cc_final: 0.1800 (m-10) REVERT: D 57 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6911 (mm-30) REVERT: D 199 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7904 (mptt) REVERT: D 311 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7971 (m-80) REVERT: E 85 LEU cc_start: 0.4840 (OUTLIER) cc_final: 0.4583 (mt) REVERT: E 110 MET cc_start: 0.7757 (ttm) cc_final: 0.7512 (ttm) REVERT: E 137 LYS cc_start: 0.7526 (tppt) cc_final: 0.7292 (mtmt) REVERT: E 236 LYS cc_start: 0.8521 (tttm) cc_final: 0.8269 (tttt) REVERT: E 267 MET cc_start: 0.6628 (tpp) cc_final: 0.6170 (tpp) REVERT: E 311 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: E 332 MET cc_start: 0.5625 (OUTLIER) cc_final: 0.3651 (tmm) REVERT: F 43 PHE cc_start: 0.2513 (OUTLIER) cc_final: 0.1867 (m-10) REVERT: F 57 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6962 (mm-30) REVERT: F 267 MET cc_start: 0.5910 (ptp) cc_final: 0.5439 (ptt) REVERT: F 311 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.7966 (m-80) REVERT: G 85 LEU cc_start: 0.4821 (OUTLIER) cc_final: 0.4572 (mt) REVERT: G 241 GLN cc_start: 0.6635 (OUTLIER) cc_final: 0.6185 (mp10) REVERT: G 267 MET cc_start: 0.6781 (tpp) cc_final: 0.6318 (tpp) REVERT: G 311 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8367 (m-80) REVERT: G 332 MET cc_start: 0.5793 (mmp) cc_final: 0.3804 (tmm) REVERT: H 43 PHE cc_start: 0.2417 (OUTLIER) cc_final: 0.1771 (m-10) REVERT: H 157 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: H 199 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7925 (mptt) REVERT: H 311 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7964 (m-80) outliers start: 93 outliers final: 43 residues processed: 267 average time/residue: 0.3788 time to fit residues: 141.8777 Evaluate side-chains 220 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 158 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 241 GLN Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 0 optimal weight: 30.0000 chunk 97 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 112 optimal weight: 30.0000 chunk 48 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 61 optimal weight: 0.0040 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 GLN ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.201703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.175920 restraints weight = 19233.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.155081 restraints weight = 38871.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.156136 restraints weight = 23615.887| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18737 Z= 0.158 Angle : 0.570 7.161 25359 Z= 0.292 Chirality : 0.037 0.218 2771 Planarity : 0.007 0.132 3323 Dihedral : 4.407 34.032 2564 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.90 % Favored : 96.75 % Rotamer: Outliers : 4.85 % Allowed : 22.54 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % 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: 2.02 (0.18), residues: 2277 helix: 2.44 (0.14), residues: 1513 sheet: 0.02 (0.37), residues: 200 loop : -1.33 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 202 HIS 0.003 0.001 HIS F 193 PHE 0.012 0.001 PHE F 81 TYR 0.010 0.001 TYR D 286 ARG 0.007 0.000 ARG G 88 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 1290) hydrogen bonds : angle 4.00394 ( 3798) covalent geometry : bond 0.00391 (18737) covalent geometry : angle 0.56981 (25359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 168 time to evaluate : 1.852 Fit side-chains REVERT: A 85 LEU cc_start: 0.5003 (OUTLIER) cc_final: 0.4758 (mt) REVERT: A 227 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6804 (mt-10) REVERT: A 311 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8507 (m-10) REVERT: A 332 MET cc_start: 0.5284 (mmp) cc_final: 0.3348 (tmm) REVERT: B 43 PHE cc_start: 0.2399 (OUTLIER) cc_final: 0.1845 (m-10) REVERT: B 57 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6821 (mm-30) REVERT: B 292 MET cc_start: 0.8688 (mmt) cc_final: 0.8486 (mmm) REVERT: B 311 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: B 320 LYS cc_start: 0.7271 (tttm) cc_final: 0.6894 (mmmt) REVERT: C 48 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5669 (tt) REVERT: C 85 LEU cc_start: 0.4712 (OUTLIER) cc_final: 0.4495 (mt) REVERT: C 137 LYS cc_start: 0.7326 (tptt) cc_final: 0.6587 (mtmt) REVERT: C 311 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: C 332 MET cc_start: 0.5252 (mmp) cc_final: 0.3310 (tmm) REVERT: D 43 PHE cc_start: 0.2199 (OUTLIER) cc_final: 0.1636 (m-10) REVERT: D 57 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6787 (mm-30) REVERT: D 199 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7953 (mptt) REVERT: D 311 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: E 48 LEU cc_start: 0.6042 (tt) cc_final: 0.5458 (tt) REVERT: E 85 LEU cc_start: 0.4768 (OUTLIER) cc_final: 0.4540 (mt) REVERT: E 110 MET cc_start: 0.7847 (ttm) cc_final: 0.7574 (ttm) REVERT: E 236 LYS cc_start: 0.8393 (tttm) cc_final: 0.8188 (tttt) REVERT: E 240 GLN cc_start: 0.6665 (tt0) cc_final: 0.6442 (tt0) REVERT: E 267 MET cc_start: 0.6924 (tpp) cc_final: 0.6558 (tpp) REVERT: E 311 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8376 (m-80) REVERT: E 332 MET cc_start: 0.5002 (OUTLIER) cc_final: 0.3273 (tmm) REVERT: F 43 PHE cc_start: 0.2374 (OUTLIER) cc_final: 0.1813 (m-10) REVERT: F 57 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6821 (mm-30) REVERT: F 311 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8083 (m-80) REVERT: F 320 LYS cc_start: 0.7235 (tttm) cc_final: 0.6881 (mmmt) REVERT: G 48 LEU cc_start: 0.5882 (tt) cc_final: 0.5465 (tt) REVERT: G 85 LEU cc_start: 0.4708 (OUTLIER) cc_final: 0.4474 (mt) REVERT: G 137 LYS cc_start: 0.7442 (tptt) cc_final: 0.6684 (mtmt) REVERT: G 267 MET cc_start: 0.6795 (tpp) cc_final: 0.6441 (tpp) REVERT: G 311 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8378 (m-80) REVERT: G 332 MET cc_start: 0.5259 (mmp) cc_final: 0.3328 (tmm) REVERT: H 43 PHE cc_start: 0.2208 (OUTLIER) cc_final: 0.1643 (m-10) REVERT: H 157 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7412 (m-30) REVERT: H 199 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7968 (mptt) REVERT: H 311 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8031 (m-80) outliers start: 94 outliers final: 56 residues processed: 253 average time/residue: 0.3355 time to fit residues: 124.4224 Evaluate side-chains 228 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 151 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.0050 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 76 optimal weight: 30.0000 chunk 109 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS C 193 HIS ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 GLN G 240 GLN G 241 GLN ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.196362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.165200 restraints weight = 18919.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.153972 restraints weight = 35498.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.153723 restraints weight = 22250.544| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 18737 Z= 0.166 Angle : 0.564 7.190 25359 Z= 0.290 Chirality : 0.037 0.216 2771 Planarity : 0.007 0.134 3323 Dihedral : 4.378 34.015 2564 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.85 % Favored : 96.79 % Rotamer: Outliers : 4.59 % Allowed : 22.38 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % 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: 2.08 (0.18), residues: 2277 helix: 2.48 (0.14), residues: 1513 sheet: 0.37 (0.39), residues: 184 loop : -1.37 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 202 HIS 0.004 0.001 HIS B 193 PHE 0.014 0.001 PHE H 81 TYR 0.011 0.002 TYR H 127 ARG 0.005 0.000 ARG G 88 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 1290) hydrogen bonds : angle 3.99197 ( 3798) covalent geometry : bond 0.00414 (18737) covalent geometry : angle 0.56404 (25359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 156 time to evaluate : 2.024 Fit side-chains REVERT: A 48 LEU cc_start: 0.6025 (tt) cc_final: 0.5261 (tt) REVERT: A 52 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6428 (t80) REVERT: A 85 LEU cc_start: 0.5051 (OUTLIER) cc_final: 0.4831 (mt) REVERT: A 227 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6890 (mt-10) REVERT: A 332 MET cc_start: 0.5584 (mmp) cc_final: 0.3617 (tmm) REVERT: B 43 PHE cc_start: 0.2425 (OUTLIER) cc_final: 0.1831 (m-10) REVERT: B 57 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6915 (mm-30) REVERT: B 311 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8054 (m-80) REVERT: B 320 LYS cc_start: 0.7269 (tttm) cc_final: 0.6937 (mmmt) REVERT: C 85 LEU cc_start: 0.4885 (OUTLIER) cc_final: 0.4648 (mt) REVERT: C 137 LYS cc_start: 0.7384 (tptt) cc_final: 0.6651 (mtmt) REVERT: C 311 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8492 (m-10) REVERT: C 332 MET cc_start: 0.5637 (mmp) cc_final: 0.3689 (tmm) REVERT: D 43 PHE cc_start: 0.2430 (OUTLIER) cc_final: 0.1780 (m-10) REVERT: D 57 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6904 (mm-30) REVERT: D 199 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7924 (mptt) REVERT: D 311 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: E 85 LEU cc_start: 0.4870 (OUTLIER) cc_final: 0.4629 (mt) REVERT: E 110 MET cc_start: 0.7779 (ttm) cc_final: 0.7547 (ttm) REVERT: E 137 LYS cc_start: 0.7513 (tptt) cc_final: 0.6801 (mtmt) REVERT: E 236 LYS cc_start: 0.8507 (tttm) cc_final: 0.8247 (tttt) REVERT: E 240 GLN cc_start: 0.6848 (tt0) cc_final: 0.6598 (tt0) REVERT: E 267 MET cc_start: 0.6621 (tpp) cc_final: 0.6275 (tpp) REVERT: E 311 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8523 (m-10) REVERT: E 332 MET cc_start: 0.5627 (OUTLIER) cc_final: 0.3795 (tmm) REVERT: F 43 PHE cc_start: 0.2530 (OUTLIER) cc_final: 0.1893 (m-10) REVERT: F 57 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6908 (mm-30) REVERT: F 311 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: G 85 LEU cc_start: 0.4855 (OUTLIER) cc_final: 0.4610 (mt) REVERT: G 137 LYS cc_start: 0.7365 (tptt) cc_final: 0.6649 (mtmt) REVERT: G 267 MET cc_start: 0.6703 (tpp) cc_final: 0.6439 (tpp) REVERT: G 311 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.8524 (m-10) REVERT: G 332 MET cc_start: 0.5587 (mmp) cc_final: 0.3632 (tmm) REVERT: H 43 PHE cc_start: 0.2185 (OUTLIER) cc_final: 0.1550 (m-10) REVERT: H 157 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: H 199 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7903 (mptt) REVERT: H 311 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8048 (m-80) outliers start: 89 outliers final: 54 residues processed: 233 average time/residue: 0.3214 time to fit residues: 111.8220 Evaluate side-chains 227 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 153 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 15 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 198 optimal weight: 0.7980 chunk 209 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 ASN C 276 GLN D 289 ASN F 289 ASN G 241 GLN ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.202312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.174634 restraints weight = 19019.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.154521 restraints weight = 36872.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.157971 restraints weight = 23835.031| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 18737 Z= 0.127 Angle : 0.530 7.925 25359 Z= 0.272 Chirality : 0.036 0.220 2771 Planarity : 0.007 0.134 3323 Dihedral : 4.224 33.393 2564 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.90 % Favored : 96.75 % Rotamer: Outliers : 3.46 % Allowed : 23.16 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % 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: 2.26 (0.19), residues: 2277 helix: 2.67 (0.14), residues: 1513 sheet: 0.08 (0.39), residues: 200 loop : -1.37 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 202 HIS 0.002 0.001 HIS D 193 PHE 0.013 0.001 PHE H 90 TYR 0.010 0.001 TYR B 127 ARG 0.005 0.000 ARG E 88 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 1290) hydrogen bonds : angle 3.91430 ( 3798) covalent geometry : bond 0.00321 (18737) covalent geometry : angle 0.52998 (25359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 154 time to evaluate : 1.817 Fit side-chains REVERT: A 52 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6436 (t80) REVERT: A 85 LEU cc_start: 0.4872 (OUTLIER) cc_final: 0.4648 (mt) REVERT: A 227 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6964 (mt-10) REVERT: A 311 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: A 332 MET cc_start: 0.5539 (mmp) cc_final: 0.3489 (tmm) REVERT: B 57 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6934 (mm-30) REVERT: B 63 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8551 (mt) REVERT: B 311 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: B 320 LYS cc_start: 0.7200 (tttm) cc_final: 0.6876 (mmmt) REVERT: C 85 LEU cc_start: 0.4844 (OUTLIER) cc_final: 0.4621 (mt) REVERT: C 137 LYS cc_start: 0.7267 (tptt) cc_final: 0.6514 (mtmt) REVERT: C 311 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8390 (m-80) REVERT: C 332 MET cc_start: 0.5404 (mmp) cc_final: 0.3474 (tmm) REVERT: D 57 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6926 (mm-30) REVERT: D 63 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8535 (mt) REVERT: D 199 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7931 (mptt) REVERT: D 311 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: E 52 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.6640 (t80) REVERT: E 85 LEU cc_start: 0.4873 (OUTLIER) cc_final: 0.4648 (mt) REVERT: E 110 MET cc_start: 0.7743 (ttm) cc_final: 0.7497 (ttm) REVERT: E 137 LYS cc_start: 0.7496 (tptt) cc_final: 0.6752 (mtmt) REVERT: E 236 LYS cc_start: 0.8473 (tttm) cc_final: 0.8226 (tttt) REVERT: E 240 GLN cc_start: 0.6783 (tt0) cc_final: 0.6512 (tt0) REVERT: E 311 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: E 332 MET cc_start: 0.5362 (OUTLIER) cc_final: 0.3722 (tmm) REVERT: F 57 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6918 (mm-30) REVERT: F 63 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8515 (mt) REVERT: F 311 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: G 85 LEU cc_start: 0.4738 (OUTLIER) cc_final: 0.4509 (mt) REVERT: G 137 LYS cc_start: 0.7311 (tptt) cc_final: 0.6581 (mtmt) REVERT: G 311 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8395 (m-80) REVERT: G 332 MET cc_start: 0.5386 (mmp) cc_final: 0.3490 (tmm) REVERT: H 63 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8533 (mt) REVERT: H 157 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7379 (m-30) REVERT: H 161 THR cc_start: 0.8238 (t) cc_final: 0.8021 (p) REVERT: H 199 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7907 (mptt) REVERT: H 311 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.7929 (m-80) outliers start: 67 outliers final: 33 residues processed: 213 average time/residue: 0.3253 time to fit residues: 103.9384 Evaluate side-chains 206 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 151 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 200 optimal weight: 0.0070 chunk 156 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN D 148 ASN F 148 ASN ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 GLN H 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.198099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.172259 restraints weight = 19080.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.152020 restraints weight = 37597.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.153743 restraints weight = 24046.316| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 18737 Z= 0.162 Angle : 0.561 6.975 25359 Z= 0.288 Chirality : 0.037 0.217 2771 Planarity : 0.007 0.135 3323 Dihedral : 4.291 33.658 2564 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.94 % Favored : 96.71 % Rotamer: Outliers : 3.51 % Allowed : 23.26 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % 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: 2.15 (0.18), residues: 2277 helix: 2.57 (0.14), residues: 1513 sheet: 0.13 (0.39), residues: 192 loop : -1.38 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 202 HIS 0.005 0.001 HIS C 193 PHE 0.011 0.001 PHE H 90 TYR 0.011 0.002 TYR H 127 ARG 0.003 0.000 ARG G 88 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 1290) hydrogen bonds : angle 3.94448 ( 3798) covalent geometry : bond 0.00406 (18737) covalent geometry : angle 0.56066 (25359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 157 time to evaluate : 1.823 Fit side-chains revert: symmetry clash REVERT: A 52 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.6460 (t80) REVERT: A 85 LEU cc_start: 0.5010 (OUTLIER) cc_final: 0.4784 (mt) REVERT: A 227 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6994 (mt-10) REVERT: A 332 MET cc_start: 0.5505 (mmp) cc_final: 0.3471 (tmm) REVERT: B 57 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6953 (mm-30) REVERT: B 311 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8041 (m-80) REVERT: B 320 LYS cc_start: 0.7243 (tttm) cc_final: 0.6890 (mmmt) REVERT: C 85 LEU cc_start: 0.4980 (OUTLIER) cc_final: 0.4752 (mt) REVERT: C 137 LYS cc_start: 0.7349 (tptt) cc_final: 0.6572 (mtmt) REVERT: C 311 TYR cc_start: 0.8891 (OUTLIER) cc_final: 0.8511 (m-10) REVERT: C 332 MET cc_start: 0.5386 (mmp) cc_final: 0.3501 (tmm) REVERT: D 57 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6926 (mm-30) REVERT: D 199 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7923 (mptt) REVERT: D 311 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: D 320 LYS cc_start: 0.7247 (tttm) cc_final: 0.6904 (mmmt) REVERT: E 52 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.6673 (t80) REVERT: E 85 LEU cc_start: 0.5004 (OUTLIER) cc_final: 0.4747 (mt) REVERT: E 110 MET cc_start: 0.7765 (ttm) cc_final: 0.7522 (ttm) REVERT: E 137 LYS cc_start: 0.7530 (tptt) cc_final: 0.6786 (mtmt) REVERT: E 197 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6787 (mt-10) REVERT: E 236 LYS cc_start: 0.8401 (tttm) cc_final: 0.8131 (tttt) REVERT: E 240 GLN cc_start: 0.6824 (tt0) cc_final: 0.6535 (tt0) REVERT: E 332 MET cc_start: 0.5373 (OUTLIER) cc_final: 0.3666 (tmm) REVERT: F 43 PHE cc_start: 0.2184 (OUTLIER) cc_final: 0.1555 (m-10) REVERT: F 57 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6986 (mm-30) REVERT: F 311 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: F 320 LYS cc_start: 0.7320 (tttm) cc_final: 0.6925 (mmmt) REVERT: G 85 LEU cc_start: 0.4968 (OUTLIER) cc_final: 0.4692 (mt) REVERT: G 137 LYS cc_start: 0.7319 (tptt) cc_final: 0.6547 (mtmt) REVERT: G 311 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: G 332 MET cc_start: 0.5357 (mmp) cc_final: 0.3479 (tmm) REVERT: H 157 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: H 199 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7916 (mptt) REVERT: H 311 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.8031 (m-80) REVERT: H 320 LYS cc_start: 0.7227 (tttm) cc_final: 0.6892 (mmmt) outliers start: 68 outliers final: 45 residues processed: 219 average time/residue: 0.3203 time to fit residues: 104.1506 Evaluate side-chains 211 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 149 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 188 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 214 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 GLN H 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.196048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.153107 restraints weight = 18682.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.153317 restraints weight = 17454.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.153922 restraints weight = 14828.424| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18737 Z= 0.142 Angle : 0.544 9.306 25359 Z= 0.278 Chirality : 0.037 0.224 2771 Planarity : 0.007 0.136 3323 Dihedral : 4.249 33.438 2564 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.85 % Favored : 96.79 % Rotamer: Outliers : 3.71 % Allowed : 23.16 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % 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: 2.24 (0.18), residues: 2277 helix: 2.64 (0.14), residues: 1513 sheet: 0.32 (0.40), residues: 184 loop : -1.38 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 202 HIS 0.002 0.001 HIS C 193 PHE 0.010 0.001 PHE H 90 TYR 0.011 0.001 TYR H 127 ARG 0.004 0.000 ARG F 271 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 1290) hydrogen bonds : angle 3.90909 ( 3798) covalent geometry : bond 0.00361 (18737) covalent geometry : angle 0.54361 (25359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 153 time to evaluate : 1.861 Fit side-chains revert: symmetry clash REVERT: A 52 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6500 (t80) REVERT: A 85 LEU cc_start: 0.5026 (OUTLIER) cc_final: 0.4770 (mt) REVERT: A 332 MET cc_start: 0.5667 (mmp) cc_final: 0.3636 (tmm) REVERT: B 43 PHE cc_start: 0.2154 (OUTLIER) cc_final: 0.1474 (m-10) REVERT: B 57 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7078 (mm-30) REVERT: B 267 MET cc_start: 0.5521 (ptp) cc_final: 0.4744 (ppp) REVERT: B 311 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.8069 (m-80) REVERT: B 320 LYS cc_start: 0.7228 (tttm) cc_final: 0.6960 (mmmt) REVERT: C 85 LEU cc_start: 0.5027 (OUTLIER) cc_final: 0.4769 (mt) REVERT: C 137 LYS cc_start: 0.7388 (tptt) cc_final: 0.6643 (mtmt) REVERT: C 311 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.8439 (m-80) REVERT: C 332 MET cc_start: 0.5528 (mmp) cc_final: 0.3653 (tmm) REVERT: D 43 PHE cc_start: 0.2066 (OUTLIER) cc_final: 0.1425 (m-10) REVERT: D 57 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7096 (mm-30) REVERT: D 199 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7907 (mptt) REVERT: D 311 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: D 320 LYS cc_start: 0.7214 (tttm) cc_final: 0.6951 (mmmt) REVERT: E 52 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.6600 (t80) REVERT: E 85 LEU cc_start: 0.5068 (OUTLIER) cc_final: 0.4815 (mt) REVERT: E 137 LYS cc_start: 0.7530 (tptt) cc_final: 0.6847 (mtmt) REVERT: E 236 LYS cc_start: 0.8488 (tttm) cc_final: 0.8196 (tttt) REVERT: E 240 GLN cc_start: 0.6890 (tt0) cc_final: 0.6629 (tt0) REVERT: E 311 TYR cc_start: 0.8866 (OUTLIER) cc_final: 0.8529 (m-10) REVERT: E 332 MET cc_start: 0.5511 (OUTLIER) cc_final: 0.3870 (tmm) REVERT: F 311 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: F 320 LYS cc_start: 0.7235 (tttm) cc_final: 0.6956 (mmmt) REVERT: G 85 LEU cc_start: 0.5034 (OUTLIER) cc_final: 0.4761 (mt) REVERT: G 137 LYS cc_start: 0.7388 (tptt) cc_final: 0.6661 (mtmt) REVERT: G 311 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.8439 (m-80) REVERT: G 332 MET cc_start: 0.5491 (mmp) cc_final: 0.3606 (tmm) REVERT: H 43 PHE cc_start: 0.1961 (OUTLIER) cc_final: 0.1297 (m-10) REVERT: H 157 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: H 199 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7890 (mptt) REVERT: H 311 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: H 320 LYS cc_start: 0.7196 (tttm) cc_final: 0.6944 (mmmt) outliers start: 72 outliers final: 47 residues processed: 217 average time/residue: 0.3223 time to fit residues: 105.5397 Evaluate side-chains 218 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 151 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN D 148 ASN G 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.197373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.171836 restraints weight = 19161.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.151097 restraints weight = 33926.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.153068 restraints weight = 21967.293| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 18737 Z= 0.182 Angle : 0.575 8.160 25359 Z= 0.293 Chirality : 0.038 0.236 2771 Planarity : 0.007 0.136 3323 Dihedral : 4.324 33.762 2564 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.81 % Favored : 96.84 % Rotamer: Outliers : 3.61 % Allowed : 23.36 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % 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: 2.09 (0.18), residues: 2277 helix: 2.54 (0.13), residues: 1513 sheet: -0.17 (0.38), residues: 200 loop : -1.34 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 202 HIS 0.004 0.001 HIS C 193 PHE 0.011 0.001 PHE B 81 TYR 0.012 0.002 TYR E 115 ARG 0.011 0.000 ARG D 88 Details of bonding type rmsd hydrogen bonds : bond 0.04499 ( 1290) hydrogen bonds : angle 3.94400 ( 3798) covalent geometry : bond 0.00453 (18737) covalent geometry : angle 0.57460 (25359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 171 time to evaluate : 1.986 Fit side-chains REVERT: A 52 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.6568 (t80) REVERT: A 85 LEU cc_start: 0.5173 (OUTLIER) cc_final: 0.4913 (mt) REVERT: A 332 MET cc_start: 0.5434 (mmp) cc_final: 0.3396 (tmm) REVERT: B 43 PHE cc_start: 0.1956 (OUTLIER) cc_final: 0.1374 (m-10) REVERT: B 57 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6940 (mm-30) REVERT: B 214 LYS cc_start: 0.7895 (mmmm) cc_final: 0.7685 (mptt) REVERT: B 267 MET cc_start: 0.5486 (ptp) cc_final: 0.4663 (ppp) REVERT: B 311 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8180 (m-80) REVERT: B 320 LYS cc_start: 0.7248 (tttm) cc_final: 0.6915 (mmmt) REVERT: C 85 LEU cc_start: 0.4974 (OUTLIER) cc_final: 0.4729 (mt) REVERT: C 311 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.8540 (m-10) REVERT: C 332 MET cc_start: 0.5394 (mmp) cc_final: 0.3537 (tmm) REVERT: D 43 PHE cc_start: 0.1709 (OUTLIER) cc_final: 0.1119 (m-10) REVERT: D 57 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6952 (mm-30) REVERT: D 214 LYS cc_start: 0.7804 (mmmm) cc_final: 0.7580 (mptt) REVERT: D 311 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: D 320 LYS cc_start: 0.7253 (tttm) cc_final: 0.6910 (mmmt) REVERT: E 52 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.6734 (t80) REVERT: E 85 LEU cc_start: 0.4986 (OUTLIER) cc_final: 0.4733 (mt) REVERT: E 137 LYS cc_start: 0.7481 (tptt) cc_final: 0.6728 (mtmt) REVERT: E 236 LYS cc_start: 0.8272 (tttm) cc_final: 0.7998 (tttt) REVERT: E 240 GLN cc_start: 0.6845 (tt0) cc_final: 0.6548 (tt0) REVERT: E 311 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8549 (m-10) REVERT: E 332 MET cc_start: 0.5194 (OUTLIER) cc_final: 0.3557 (tmm) REVERT: F 214 LYS cc_start: 0.7902 (mmmm) cc_final: 0.7663 (mptt) REVERT: F 227 GLU cc_start: 0.7912 (tp30) cc_final: 0.7688 (tp30) REVERT: F 271 ARG cc_start: 0.7446 (ttp80) cc_final: 0.6750 (mtp-110) REVERT: F 311 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: F 320 LYS cc_start: 0.7271 (tttm) cc_final: 0.6944 (mmmt) REVERT: G 85 LEU cc_start: 0.5197 (OUTLIER) cc_final: 0.4885 (mt) REVERT: G 311 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8536 (m-10) REVERT: G 332 MET cc_start: 0.5257 (mmp) cc_final: 0.3379 (tmm) REVERT: H 43 PHE cc_start: 0.1752 (OUTLIER) cc_final: 0.1175 (m-10) REVERT: H 214 LYS cc_start: 0.7903 (mmmm) cc_final: 0.7674 (mptt) REVERT: H 311 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: H 320 LYS cc_start: 0.7235 (tttm) cc_final: 0.6919 (mmmt) outliers start: 70 outliers final: 48 residues processed: 233 average time/residue: 0.3568 time to fit residues: 118.8097 Evaluate side-chains 224 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 159 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 125 optimal weight: 0.3980 chunk 218 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 194 optimal weight: 0.0980 chunk 77 optimal weight: 0.0170 chunk 119 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.194761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.168568 restraints weight = 18672.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.148475 restraints weight = 35188.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.151494 restraints weight = 23972.237| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 18737 Z= 0.201 Angle : 0.754 59.200 25359 Z= 0.428 Chirality : 0.042 1.044 2771 Planarity : 0.008 0.136 3323 Dihedral : 4.340 33.718 2564 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.90 % Favored : 96.75 % Rotamer: Outliers : 3.35 % Allowed : 23.21 % Favored : 73.44 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % 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: 2.12 (0.18), residues: 2277 helix: 2.56 (0.14), residues: 1513 sheet: -0.17 (0.38), residues: 200 loop : -1.35 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 202 HIS 0.006 0.001 HIS C 193 PHE 0.010 0.001 PHE B 81 TYR 0.011 0.002 TYR H 127 ARG 0.011 0.000 ARG D 88 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 1290) hydrogen bonds : angle 3.96390 ( 3798) covalent geometry : bond 0.00443 (18737) covalent geometry : angle 0.75356 (25359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5480.57 seconds wall clock time: 95 minutes 51.28 seconds (5751.28 seconds total)