Starting phenix.real_space_refine on Thu Mar 5 01:48:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c0e_16364/03_2026/8c0e_16364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c0e_16364/03_2026/8c0e_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_16364/03_2026/8c0e_16364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c0e_16364/03_2026/8c0e_16364.map" model { file = "/net/cci-nas-00/data/ceres_data/8c0e_16364/03_2026/8c0e_16364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c0e_16364/03_2026/8c0e_16364.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.89, per 1000 atoms: 0.21 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: 1.55 Conformation dependent library (CDL) restraints added in 788.1 milliseconds 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: 0.44 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: 2.96 Time building geometry restraints manager: 2.05 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.130 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.320 ------------------------------------------------------------------------------- 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 : 10.28 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG D 313 TYR 0.035 0.002 TYR H 115 PHE 0.014 0.001 PHE A 261 TRP 0.006 0.001 TRP B 202 HIS 0.004 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00366 (18737) covalent geometry : angle 0.71951 (25359) hydrogen bonds : bond 0.12034 ( 1290) hydrogen bonds : angle 5.69927 ( 3798) *********************** 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 : 0.646 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: 0.7403 (tt0) REVERT: A 227 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6927 (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: 0.7871 (mttt) REVERT: B 66 LYS cc_start: 0.8717 (ptpp) cc_final: 0.8343 (ptmm) REVERT: C 170 GLU cc_start: 0.7718 (tt0) cc_final: 0.7506 (tt0) REVERT: C 267 MET cc_start: 0.6856 (mmm) cc_final: 0.6282 (tpp) REVERT: C 320 LYS cc_start: 0.8208 (pttp) cc_final: 0.7926 (mttt) REVERT: D 66 LYS cc_start: 0.8718 (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: 0.7755 (tt0) cc_final: 0.7536 (tt0) REVERT: E 267 MET cc_start: 0.6439 (mmm) cc_final: 0.5822 (tpp) REVERT: E 292 MET cc_start: 0.8248 (mmm) cc_final: 0.8034 (tpp) REVERT: E 320 LYS cc_start: 0.8196 (pttp) cc_final: 0.7955 (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: 0.6138 (tpp) REVERT: G 320 LYS cc_start: 0.8150 (pttp) cc_final: 0.7927 (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: 0.1727 time to fit residues: 66.4542 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 : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 216 GLN D 307 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 = 0.4190 r_free = 0.4190 target = 0.203317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.159502 restraints weight = 18798.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.159502 restraints weight = 15409.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.159502 restraints weight = 15409.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.159502 restraints weight = 15409.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.159502 restraints weight = 15409.945| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18737 Z= 0.173 Angle : 0.621 7.882 25359 Z= 0.320 Chirality : 0.039 0.220 2771 Planarity : 0.008 0.125 3323 Dihedral : 4.603 36.289 2564 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.55 % Favored : 97.10 % Rotamer: Outliers : 3.66 % Allowed : 23.05 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 12.64 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.18), residues: 2277 helix: 2.36 (0.14), residues: 1479 sheet: -0.10 (0.34), residues: 216 loop : -1.21 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 131 TYR 0.016 0.002 TYR E 282 PHE 0.013 0.002 PHE H 90 TRP 0.017 0.002 TRP D 333 HIS 0.004 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00406 (18737) covalent geometry : angle 0.62119 (25359) hydrogen bonds : bond 0.04529 ( 1290) hydrogen bonds : angle 4.38036 ( 3798) *********************** 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 238 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 167 time to evaluate : 0.650 Fit side-chains REVERT: A 197 GLU cc_start: 0.6922 (tt0) cc_final: 0.6658 (mt-10) REVERT: A 227 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6892 (mt-10) REVERT: A 241 GLN cc_start: 0.5839 (OUTLIER) cc_final: 0.5506 (mp10) REVERT: A 267 MET cc_start: 0.7006 (mmm) cc_final: 0.6729 (tpp) REVERT: A 332 MET cc_start: 0.4909 (mmm) cc_final: 0.3536 (mmm) REVERT: B 43 PHE cc_start: 0.2574 (OUTLIER) cc_final: 0.1875 (m-10) REVERT: B 66 LYS cc_start: 0.8824 (ptpp) cc_final: 0.8525 (ptmm) REVERT: B 157 ASP cc_start: 0.7286 (m-30) cc_final: 0.6891 (m-30) REVERT: C 267 MET cc_start: 0.7112 (mmm) cc_final: 0.6460 (tpp) REVERT: C 332 MET cc_start: 0.4756 (mmm) cc_final: 0.3695 (tmm) REVERT: D 43 PHE cc_start: 0.2509 (OUTLIER) cc_final: 0.1810 (m-10) REVERT: D 66 LYS cc_start: 0.8809 (ptpp) cc_final: 0.8533 (ptmm) REVERT: D 157 ASP cc_start: 0.7326 (m-30) cc_final: 0.6995 (m-30) REVERT: E 267 MET cc_start: 0.6789 (mmm) cc_final: 0.6438 (tpp) REVERT: E 292 MET cc_start: 0.8455 (mmm) cc_final: 0.8179 (tpp) REVERT: E 332 MET cc_start: 0.5167 (mmm) cc_final: 0.3588 (tmm) REVERT: F 43 PHE cc_start: 0.2574 (OUTLIER) cc_final: 0.1882 (m-10) REVERT: F 66 LYS cc_start: 0.8838 (ptpp) cc_final: 0.8539 (ptmm) REVERT: F 267 MET cc_start: 0.5541 (ptp) cc_final: 0.5318 (ptp) REVERT: G 236 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7841 (tttt) REVERT: G 241 GLN cc_start: 0.5605 (OUTLIER) cc_final: 0.5385 (mp10) REVERT: G 267 MET cc_start: 0.6915 (mmm) cc_final: 0.6166 (tpp) REVERT: G 332 MET cc_start: 0.4981 (mmm) cc_final: 0.3789 (tmm) REVERT: H 43 PHE cc_start: 0.2412 (OUTLIER) cc_final: 0.1830 (m-10) REVERT: H 66 LYS cc_start: 0.8821 (ptpp) cc_final: 0.8555 (ptmm) REVERT: H 157 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.7006 (m-30) REVERT: H 267 MET cc_start: 0.5675 (ptp) cc_final: 0.5159 (ptp) outliers start: 71 outliers final: 19 residues processed: 232 average time/residue: 0.1475 time to fit residues: 51.3981 Evaluate side-chains 175 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 314 THR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 298 VAL 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 298 VAL Chi-restraints excluded: chain E residue 168 VAL 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 298 VAL Chi-restraints excluded: chain F residue 314 THR 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 157 ASP Chi-restraints excluded: chain H residue 298 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 41 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 90 optimal weight: 0.0770 chunk 110 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 170 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 240 GLN E 241 GLN G 240 GLN G 276 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.203713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.173866 restraints weight = 18809.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.158949 restraints weight = 32340.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.161342 restraints weight = 19586.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.162197 restraints weight = 14594.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.162818 restraints weight = 12836.556| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 18737 Z= 0.125 Angle : 0.548 8.039 25359 Z= 0.284 Chirality : 0.036 0.220 2771 Planarity : 0.007 0.126 3323 Dihedral : 4.456 33.153 2564 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.99 % Favored : 96.66 % Rotamer: Outliers : 2.48 % Allowed : 24.34 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.49 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.18), residues: 2277 helix: 2.56 (0.14), residues: 1479 sheet: -0.09 (0.34), residues: 216 loop : -1.25 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 131 TYR 0.010 0.001 TYR E 282 PHE 0.008 0.001 PHE B 90 TRP 0.009 0.001 TRP H 333 HIS 0.002 0.001 HIS G 193 Details of bonding type rmsd covalent geometry : bond 0.00304 (18737) covalent geometry : angle 0.54814 (25359) hydrogen bonds : bond 0.04201 ( 1290) hydrogen bonds : angle 4.23141 ( 3798) *********************** 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 203 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 0.648 Fit side-chains REVERT: A 227 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6916 (mt-10) REVERT: A 267 MET cc_start: 0.7123 (mmm) cc_final: 0.6597 (tpp) REVERT: A 332 MET cc_start: 0.5209 (mmm) cc_final: 0.3676 (mmm) REVERT: B 157 ASP cc_start: 0.7141 (m-30) cc_final: 0.6731 (m-30) REVERT: B 311 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: C 88 ARG cc_start: 0.7214 (mtt180) cc_final: 0.6928 (mtt90) REVERT: C 267 MET cc_start: 0.7217 (mmm) cc_final: 0.6756 (tpp) REVERT: C 332 MET cc_start: 0.5112 (mmm) cc_final: 0.3967 (tmm) REVERT: D 157 ASP cc_start: 0.7231 (m-30) cc_final: 0.6859 (m-30) REVERT: D 311 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: E 88 ARG cc_start: 0.7173 (mtt180) cc_final: 0.6956 (mtt90) REVERT: E 110 MET cc_start: 0.7868 (ttm) cc_final: 0.7460 (ttm) REVERT: E 267 MET cc_start: 0.6984 (mmm) cc_final: 0.6515 (tpp) REVERT: E 332 MET cc_start: 0.5319 (mmm) cc_final: 0.3780 (tmm) REVERT: F 157 ASP cc_start: 0.7201 (m-30) cc_final: 0.6825 (m-30) REVERT: F 267 MET cc_start: 0.5808 (ptp) cc_final: 0.5414 (ptt) REVERT: F 311 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: G 88 ARG cc_start: 0.7209 (mtt180) cc_final: 0.6906 (mtt90) REVERT: G 267 MET cc_start: 0.7023 (mmm) cc_final: 0.6715 (tpp) REVERT: G 332 MET cc_start: 0.5037 (mmm) cc_final: 0.3885 (tmm) REVERT: H 157 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: H 311 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7416 (m-80) outliers start: 48 outliers final: 19 residues processed: 197 average time/residue: 0.1367 time to fit residues: 41.4021 Evaluate side-chains 165 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 314 THR 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 C residue 99 SER Chi-restraints excluded: chain C residue 298 VAL 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 E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 298 VAL 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 G residue 99 SER Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 185 optimal weight: 0.9980 chunk 141 optimal weight: 40.0000 chunk 146 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 222 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.198419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3714 r_free = 0.3714 target = 0.157134 restraints weight = 18464.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.157469 restraints weight = 15977.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.158210 restraints weight = 14112.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.158215 restraints weight = 12898.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.158444 restraints weight = 12873.271| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 18737 Z= 0.204 Angle : 0.618 8.368 25359 Z= 0.319 Chirality : 0.039 0.210 2771 Planarity : 0.008 0.131 3323 Dihedral : 4.559 34.817 2564 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.90 % Favored : 96.75 % Rotamer: Outliers : 4.44 % Allowed : 23.16 % Favored : 72.41 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.18), residues: 2277 helix: 2.22 (0.13), residues: 1511 sheet: 0.05 (0.36), residues: 200 loop : -1.36 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 313 TYR 0.014 0.002 TYR C 282 PHE 0.011 0.001 PHE D 81 TRP 0.016 0.002 TRP D 202 HIS 0.004 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00478 (18737) covalent geometry : angle 0.61844 (25359) hydrogen bonds : bond 0.04764 ( 1290) hydrogen bonds : angle 4.12590 ( 3798) *********************** 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 310 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 224 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.6213 (OUTLIER) cc_final: 0.5975 (tt) REVERT: A 85 LEU cc_start: 0.4866 (OUTLIER) cc_final: 0.4636 (mt) REVERT: A 137 LYS cc_start: 0.7736 (tppt) cc_final: 0.7464 (mtmt) REVERT: A 227 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6989 (mt-10) REVERT: A 236 LYS cc_start: 0.8654 (tttm) cc_final: 0.8391 (tttt) REVERT: A 332 MET cc_start: 0.5848 (mmm) cc_final: 0.5600 (mmm) REVERT: B 43 PHE cc_start: 0.2565 (OUTLIER) cc_final: 0.1886 (m-10) REVERT: B 57 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6967 (mm-30) REVERT: B 157 ASP cc_start: 0.7436 (m-30) cc_final: 0.6972 (m-30) REVERT: B 311 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7736 (m-80) REVERT: C 214 LYS cc_start: 0.7925 (mmmm) cc_final: 0.7709 (mttt) REVERT: D 43 PHE cc_start: 0.2550 (OUTLIER) cc_final: 0.1859 (m-10) REVERT: D 57 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6937 (mm-30) REVERT: D 229 ARG cc_start: 0.7391 (ttp-110) cc_final: 0.6824 (ttp-110) REVERT: D 311 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: E 110 MET cc_start: 0.7803 (ttm) cc_final: 0.7513 (ttm) REVERT: E 137 LYS cc_start: 0.7543 (tppt) cc_final: 0.7280 (mtmt) REVERT: E 214 LYS cc_start: 0.7854 (mmmm) cc_final: 0.7648 (mttt) REVERT: E 236 LYS cc_start: 0.8463 (tttm) cc_final: 0.8248 (tttt) REVERT: F 43 PHE cc_start: 0.2588 (OUTLIER) cc_final: 0.1876 (m-10) REVERT: F 57 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6956 (mm-30) REVERT: F 267 MET cc_start: 0.5807 (ptp) cc_final: 0.5340 (ptt) REVERT: F 311 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: G 332 MET cc_start: 0.5364 (mmm) cc_final: 0.4155 (tmm) REVERT: H 43 PHE cc_start: 0.2607 (OUTLIER) cc_final: 0.1903 (m-10) REVERT: H 157 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7100 (m-30) REVERT: H 229 ARG cc_start: 0.7400 (ttp-110) cc_final: 0.6795 (ttp-110) REVERT: H 267 MET cc_start: 0.5832 (ptp) cc_final: 0.5325 (ptt) REVERT: H 311 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7744 (m-80) outliers start: 86 outliers final: 32 residues processed: 296 average time/residue: 0.1664 time to fit residues: 70.4380 Evaluate side-chains 211 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 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 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR 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 99 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain E residue 99 SER 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 F residue 43 PHE Chi-restraints excluded: chain F residue 99 SER 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 61 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 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 275 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 169 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 217 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN C 276 GLN D 148 ASN E 276 GLN F 148 ASN G 276 GLN H 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.196377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.154053 restraints weight = 18487.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.155226 restraints weight = 14846.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.155226 restraints weight = 12766.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.155226 restraints weight = 12766.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.155226 restraints weight = 12766.100| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4090 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= 0.173 Angle : 0.585 7.227 25359 Z= 0.302 Chirality : 0.038 0.216 2771 Planarity : 0.007 0.131 3323 Dihedral : 4.431 33.973 2564 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.99 % Favored : 96.66 % Rotamer: Outliers : 4.07 % Allowed : 23.10 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.18), residues: 2277 helix: 2.46 (0.14), residues: 1501 sheet: 0.04 (0.37), residues: 200 loop : -1.40 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 88 TYR 0.012 0.002 TYR H 115 PHE 0.013 0.001 PHE D 81 TRP 0.015 0.001 TRP D 202 HIS 0.003 0.001 HIS H 193 Details of bonding type rmsd covalent geometry : bond 0.00428 (18737) covalent geometry : angle 0.58548 (25359) hydrogen bonds : bond 0.04487 ( 1290) hydrogen bonds : angle 4.04335 ( 3798) *********************** 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 255 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 176 time to evaluate : 0.725 Fit side-chains REVERT: A 48 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6211 (tt) REVERT: A 85 LEU cc_start: 0.4997 (OUTLIER) cc_final: 0.4728 (mt) REVERT: A 227 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6891 (mt-10) REVERT: A 236 LYS cc_start: 0.8563 (tttm) cc_final: 0.8307 (tttt) REVERT: A 332 MET cc_start: 0.5837 (mmm) cc_final: 0.5584 (mmm) REVERT: B 43 PHE cc_start: 0.2371 (OUTLIER) cc_final: 0.1765 (m-10) REVERT: B 57 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6907 (mm-30) REVERT: B 311 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: B 320 LYS cc_start: 0.7302 (tttm) cc_final: 0.6962 (mmmt) REVERT: C 48 LEU cc_start: 0.6163 (tt) cc_final: 0.5685 (tt) REVERT: C 85 LEU cc_start: 0.4750 (OUTLIER) cc_final: 0.4502 (mt) REVERT: C 137 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6979 (mtmt) REVERT: C 214 LYS cc_start: 0.7857 (mmmm) cc_final: 0.7645 (mttt) REVERT: C 267 MET cc_start: 0.6634 (tpp) cc_final: 0.6356 (tpp) REVERT: C 311 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8491 (m-80) REVERT: C 332 MET cc_start: 0.5417 (mmm) cc_final: 0.3800 (tmm) REVERT: D 43 PHE cc_start: 0.2363 (OUTLIER) cc_final: 0.1756 (m-10) REVERT: D 57 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6925 (mm-30) REVERT: D 267 MET cc_start: 0.5679 (ptp) cc_final: 0.5209 (ptt) REVERT: D 311 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: E 85 LEU cc_start: 0.4749 (OUTLIER) cc_final: 0.4498 (mt) REVERT: E 110 MET cc_start: 0.7796 (ttm) cc_final: 0.7516 (ttm) REVERT: E 236 LYS cc_start: 0.8482 (tttm) cc_final: 0.8256 (tttt) REVERT: E 267 MET cc_start: 0.6812 (tpp) cc_final: 0.6480 (tpp) REVERT: E 311 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: E 332 MET cc_start: 0.5678 (mmp) cc_final: 0.3728 (tmm) REVERT: F 43 PHE cc_start: 0.2484 (OUTLIER) cc_final: 0.1876 (m-10) REVERT: F 57 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6924 (mm-30) REVERT: F 311 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: G 48 LEU cc_start: 0.6043 (tt) cc_final: 0.5529 (tt) REVERT: G 85 LEU cc_start: 0.4691 (OUTLIER) cc_final: 0.4457 (mt) REVERT: G 137 LYS cc_start: 0.7617 (tptt) cc_final: 0.6960 (mtmt) REVERT: G 267 MET cc_start: 0.6635 (tpp) cc_final: 0.6233 (tpp) REVERT: G 272 LEU cc_start: 0.8036 (tp) cc_final: 0.7763 (tp) REVERT: G 311 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: G 332 MET cc_start: 0.5488 (mmm) cc_final: 0.3855 (tmm) REVERT: H 43 PHE cc_start: 0.2227 (OUTLIER) cc_final: 0.1618 (m-10) REVERT: H 157 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: H 267 MET cc_start: 0.5902 (ptp) cc_final: 0.5377 (ptt) REVERT: H 311 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8000 (m-80) outliers start: 79 outliers final: 50 residues processed: 242 average time/residue: 0.1622 time to fit residues: 56.6762 Evaluate side-chains 222 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 154 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 295 THR 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 71 MET Chi-restraints excluded: chain B residue 84 ASN 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 68 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 137 LYS Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 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 228 VAL Chi-restraints excluded: chain E residue 241 GLN 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 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 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 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 235 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 21 optimal weight: 0.0270 chunk 104 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 chunk 82 optimal weight: 0.0050 chunk 65 optimal weight: 0.5980 chunk 176 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 overall best weight: 0.3652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 GLN E 240 GLN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4206 r_free = 0.4206 target = 0.205156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.179385 restraints weight = 18981.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.157014 restraints weight = 34516.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.161027 restraints weight = 23305.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.160792 restraints weight = 17112.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.162796 restraints weight = 15758.469| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 18737 Z= 0.115 Angle : 0.528 8.254 25359 Z= 0.274 Chirality : 0.035 0.219 2771 Planarity : 0.007 0.133 3323 Dihedral : 4.243 33.013 2564 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.90 % Favored : 96.75 % Rotamer: Outliers : 3.51 % Allowed : 23.00 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.18), residues: 2277 helix: 2.68 (0.14), residues: 1501 sheet: -0.12 (0.37), residues: 212 loop : -1.45 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 88 TYR 0.008 0.001 TYR F 115 PHE 0.013 0.001 PHE G 208 TRP 0.008 0.001 TRP D 202 HIS 0.002 0.000 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00288 (18737) covalent geometry : angle 0.52789 (25359) hydrogen bonds : bond 0.03914 ( 1290) hydrogen bonds : angle 3.94532 ( 3798) *********************** 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 222 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 154 time to evaluate : 0.671 Fit side-chains REVERT: A 85 LEU cc_start: 0.4768 (OUTLIER) cc_final: 0.4517 (mt) REVERT: A 137 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6864 (mtmt) REVERT: A 227 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6988 (mt-10) REVERT: A 236 LYS cc_start: 0.8322 (tttm) cc_final: 0.8101 (tttt) REVERT: A 311 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: A 332 MET cc_start: 0.5636 (mmm) cc_final: 0.3815 (tmm) REVERT: B 43 PHE cc_start: 0.2242 (OUTLIER) cc_final: 0.1713 (m-10) REVERT: B 57 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6930 (mm-30) REVERT: B 63 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8361 (mt) REVERT: B 311 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7521 (m-80) REVERT: C 48 LEU cc_start: 0.5887 (OUTLIER) cc_final: 0.5475 (tt) REVERT: C 52 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.6467 (t80) REVERT: C 85 LEU cc_start: 0.4608 (OUTLIER) cc_final: 0.4354 (mt) REVERT: C 137 LYS cc_start: 0.7653 (tptt) cc_final: 0.6938 (mtmt) REVERT: C 267 MET cc_start: 0.6675 (tpp) cc_final: 0.6448 (tpp) REVERT: C 311 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: C 332 MET cc_start: 0.5002 (mmm) cc_final: 0.3529 (tmm) REVERT: D 43 PHE cc_start: 0.2191 (OUTLIER) cc_final: 0.1609 (m-10) REVERT: D 57 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6899 (mm-30) REVERT: D 267 MET cc_start: 0.5504 (ptp) cc_final: 0.5064 (ptt) REVERT: D 311 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: E 85 LEU cc_start: 0.4651 (OUTLIER) cc_final: 0.4392 (mt) REVERT: E 110 MET cc_start: 0.7719 (ttm) cc_final: 0.7418 (ttm) REVERT: E 137 LYS cc_start: 0.7491 (tptt) cc_final: 0.6836 (mtmt) REVERT: E 236 LYS cc_start: 0.8377 (tttm) cc_final: 0.8140 (tttt) REVERT: E 267 MET cc_start: 0.6671 (tpp) cc_final: 0.6395 (tpp) REVERT: E 311 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: E 332 MET cc_start: 0.5463 (mmp) cc_final: 0.3561 (tmm) REVERT: F 43 PHE cc_start: 0.2233 (OUTLIER) cc_final: 0.1709 (m-10) REVERT: F 57 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6870 (mm-30) REVERT: F 63 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8366 (mt) REVERT: F 267 MET cc_start: 0.5794 (ptp) cc_final: 0.5318 (ptt) REVERT: F 311 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: G 48 LEU cc_start: 0.5825 (OUTLIER) cc_final: 0.5154 (tt) REVERT: G 52 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.6509 (t80) REVERT: G 85 LEU cc_start: 0.4486 (OUTLIER) cc_final: 0.4239 (mt) REVERT: G 137 LYS cc_start: 0.7638 (tptt) cc_final: 0.6947 (mtmt) REVERT: G 267 MET cc_start: 0.6552 (tpp) cc_final: 0.6288 (tpp) REVERT: G 311 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: G 332 MET cc_start: 0.5267 (mmm) cc_final: 0.3690 (tmm) REVERT: H 43 PHE cc_start: 0.2042 (OUTLIER) cc_final: 0.1469 (m-10) REVERT: H 157 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: H 311 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7527 (m-80) outliers start: 68 outliers final: 32 residues processed: 211 average time/residue: 0.1607 time to fit residues: 49.4732 Evaluate side-chains 207 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 151 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 137 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 63 ILE 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 48 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 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 240 GLN Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 99 SER 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 48 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 228 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 181 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.195603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3671 r_free = 0.3671 target = 0.153694 restraints weight = 18569.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.155062 restraints weight = 14672.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.155062 restraints weight = 12735.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.155062 restraints weight = 12735.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.155062 restraints weight = 12735.955| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4459 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= 0.168 Angle : 0.562 7.689 25359 Z= 0.290 Chirality : 0.037 0.217 2771 Planarity : 0.007 0.134 3323 Dihedral : 4.294 33.459 2564 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.90 % Favored : 96.75 % Rotamer: Outliers : 3.97 % Allowed : 21.66 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.18), residues: 2277 helix: 2.62 (0.14), residues: 1501 sheet: 0.03 (0.38), residues: 200 loop : -1.44 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 88 TYR 0.011 0.002 TYR C 115 PHE 0.010 0.001 PHE H 81 TRP 0.012 0.001 TRP D 202 HIS 0.002 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00417 (18737) covalent geometry : angle 0.56207 (25359) hydrogen bonds : bond 0.04321 ( 1290) hydrogen bonds : angle 3.94475 ( 3798) *********************** 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 230 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 153 time to evaluate : 0.654 Fit side-chains REVERT: A 85 LEU cc_start: 0.4944 (OUTLIER) cc_final: 0.4689 (mt) REVERT: A 137 LYS cc_start: 0.7680 (tptt) cc_final: 0.6977 (mtmt) REVERT: A 227 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7071 (mt-10) REVERT: A 236 LYS cc_start: 0.8469 (tttm) cc_final: 0.8211 (tttt) REVERT: A 332 MET cc_start: 0.5796 (mmm) cc_final: 0.3971 (tmm) REVERT: B 43 PHE cc_start: 0.2209 (OUTLIER) cc_final: 0.1597 (m-10) REVERT: B 292 MET cc_start: 0.8665 (mmt) cc_final: 0.8459 (mmm) REVERT: B 311 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: C 48 LEU cc_start: 0.5931 (OUTLIER) cc_final: 0.5546 (tt) REVERT: C 52 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6522 (t80) REVERT: C 85 LEU cc_start: 0.4793 (OUTLIER) cc_final: 0.4550 (mt) REVERT: C 137 LYS cc_start: 0.7705 (tptt) cc_final: 0.7020 (mtmt) REVERT: C 267 MET cc_start: 0.6673 (tpp) cc_final: 0.6403 (tpp) REVERT: C 332 MET cc_start: 0.5188 (mmm) cc_final: 0.3640 (tmm) REVERT: D 43 PHE cc_start: 0.2253 (OUTLIER) cc_final: 0.1614 (m-10) REVERT: D 57 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6954 (mm-30) REVERT: D 267 MET cc_start: 0.5526 (ptp) cc_final: 0.5078 (ptt) REVERT: D 311 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.7839 (m-80) REVERT: E 48 LEU cc_start: 0.6206 (tt) cc_final: 0.5747 (tt) REVERT: E 85 LEU cc_start: 0.4809 (OUTLIER) cc_final: 0.4566 (mt) REVERT: E 110 MET cc_start: 0.7815 (ttm) cc_final: 0.7528 (ttm) REVERT: E 137 LYS cc_start: 0.7673 (tptt) cc_final: 0.6988 (mtmt) REVERT: E 236 LYS cc_start: 0.8408 (tttm) cc_final: 0.8155 (tttt) REVERT: E 267 MET cc_start: 0.6556 (tpp) cc_final: 0.6248 (tpp) REVERT: E 332 MET cc_start: 0.5664 (mmp) cc_final: 0.3741 (tmm) REVERT: F 43 PHE cc_start: 0.2366 (OUTLIER) cc_final: 0.1760 (m-10) REVERT: F 57 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6951 (mm-30) REVERT: F 311 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: G 48 LEU cc_start: 0.5917 (OUTLIER) cc_final: 0.5506 (tt) REVERT: G 52 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.6577 (t80) REVERT: G 85 LEU cc_start: 0.4734 (OUTLIER) cc_final: 0.4489 (mt) REVERT: G 137 LYS cc_start: 0.7597 (tptt) cc_final: 0.6942 (mtmt) REVERT: G 267 MET cc_start: 0.6588 (tpp) cc_final: 0.6347 (tpp) REVERT: G 332 MET cc_start: 0.5175 (mmm) cc_final: 0.3677 (tmm) REVERT: H 43 PHE cc_start: 0.2175 (OUTLIER) cc_final: 0.1547 (m-10) REVERT: H 157 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7268 (m-30) REVERT: H 311 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.7859 (m-80) outliers start: 77 outliers final: 52 residues processed: 222 average time/residue: 0.1523 time to fit residues: 49.7412 Evaluate side-chains 219 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 150 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 198 ILE 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 48 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 52 TYR 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 241 GLN 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 198 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 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 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 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 48 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 193 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN G 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.196957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.155770 restraints weight = 18576.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.156246 restraints weight = 14793.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.156250 restraints weight = 12964.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.156250 restraints weight = 12938.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.156250 restraints weight = 12938.763| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4606 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= 0.148 Angle : 0.547 7.197 25359 Z= 0.281 Chirality : 0.037 0.218 2771 Planarity : 0.007 0.135 3323 Dihedral : 4.274 33.368 2564 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.90 % Favored : 96.75 % Rotamer: Outliers : 4.23 % Allowed : 21.35 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.18), residues: 2277 helix: 2.66 (0.14), residues: 1501 sheet: 0.02 (0.38), residues: 200 loop : -1.42 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 88 TYR 0.009 0.001 TYR A 127 PHE 0.008 0.001 PHE H 81 TRP 0.011 0.001 TRP D 202 HIS 0.002 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00374 (18737) covalent geometry : angle 0.54698 (25359) hydrogen bonds : bond 0.04215 ( 1290) hydrogen bonds : angle 3.92526 ( 3798) *********************** 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 238 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 156 time to evaluate : 0.601 Fit side-chains REVERT: A 85 LEU cc_start: 0.4975 (OUTLIER) cc_final: 0.4716 (mt) REVERT: A 137 LYS cc_start: 0.7639 (tptt) cc_final: 0.6981 (mtmt) REVERT: A 227 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7132 (mt-10) REVERT: A 236 LYS cc_start: 0.8558 (tttm) cc_final: 0.8293 (tttt) REVERT: A 332 MET cc_start: 0.5816 (mmm) cc_final: 0.4104 (tmm) REVERT: B 43 PHE cc_start: 0.2289 (OUTLIER) cc_final: 0.1642 (m-10) REVERT: B 311 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7829 (m-80) REVERT: C 48 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5749 (tt) REVERT: C 52 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.6606 (t80) REVERT: C 85 LEU cc_start: 0.4825 (OUTLIER) cc_final: 0.4573 (mt) REVERT: C 137 LYS cc_start: 0.7562 (tptt) cc_final: 0.6935 (mtmt) REVERT: C 267 MET cc_start: 0.6654 (tpp) cc_final: 0.6427 (tpp) REVERT: C 332 MET cc_start: 0.5390 (mmm) cc_final: 0.3868 (tmm) REVERT: D 43 PHE cc_start: 0.2295 (OUTLIER) cc_final: 0.1601 (m-10) REVERT: D 267 MET cc_start: 0.5529 (ptp) cc_final: 0.5003 (ptt) REVERT: D 311 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: E 85 LEU cc_start: 0.4802 (OUTLIER) cc_final: 0.4560 (mt) REVERT: E 110 MET cc_start: 0.7743 (ttm) cc_final: 0.7505 (ttm) REVERT: E 137 LYS cc_start: 0.7551 (tptt) cc_final: 0.6929 (mtmt) REVERT: E 236 LYS cc_start: 0.8558 (tttm) cc_final: 0.8258 (tttt) REVERT: E 267 MET cc_start: 0.6593 (tpp) cc_final: 0.6253 (tpp) REVERT: E 332 MET cc_start: 0.5834 (mmp) cc_final: 0.3990 (tmm) REVERT: F 43 PHE cc_start: 0.2306 (OUTLIER) cc_final: 0.1648 (m-10) REVERT: F 311 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: G 48 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5608 (tt) REVERT: G 52 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.6374 (t80) REVERT: G 85 LEU cc_start: 0.4752 (OUTLIER) cc_final: 0.4513 (mt) REVERT: G 137 LYS cc_start: 0.7579 (tptt) cc_final: 0.6940 (mtmt) REVERT: G 267 MET cc_start: 0.6546 (tpp) cc_final: 0.6313 (tpp) REVERT: G 311 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8482 (m-80) REVERT: G 332 MET cc_start: 0.5329 (mmm) cc_final: 0.3879 (tmm) REVERT: H 43 PHE cc_start: 0.2145 (OUTLIER) cc_final: 0.1447 (m-10) REVERT: H 157 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7232 (m-30) REVERT: H 311 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.7846 (m-80) outliers start: 82 outliers final: 56 residues processed: 228 average time/residue: 0.1476 time to fit residues: 50.1284 Evaluate side-chains 228 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 154 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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 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 51 SER Chi-restraints excluded: chain C residue 52 TYR 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 298 VAL 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 228 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 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 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 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 48 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 61 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 150 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN D 148 ASN E 276 GLN F 148 ASN G 212 GLN G 240 GLN G 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.195367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.3642 r_free = 0.3642 target = 0.152068 restraints weight = 18567.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.155061 restraints weight = 14986.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.154571 restraints weight = 13202.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.154942 restraints weight = 13029.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.155098 restraints weight = 11966.694| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4926 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= 0.155 Angle : 0.560 6.920 25359 Z= 0.288 Chirality : 0.037 0.217 2771 Planarity : 0.007 0.136 3323 Dihedral : 4.286 33.455 2564 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.90 % Favored : 96.75 % Rotamer: Outliers : 4.38 % Allowed : 21.14 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.18), residues: 2277 helix: 2.66 (0.14), residues: 1501 sheet: -0.19 (0.38), residues: 208 loop : -1.44 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 271 TYR 0.010 0.001 TYR H 127 PHE 0.008 0.001 PHE B 81 TRP 0.011 0.001 TRP D 202 HIS 0.002 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00388 (18737) covalent geometry : angle 0.55954 (25359) hydrogen bonds : bond 0.04276 ( 1290) hydrogen bonds : angle 3.93027 ( 3798) *********************** 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 243 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 158 time to evaluate : 0.650 Fit side-chains REVERT: A 52 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6522 (t80) REVERT: A 85 LEU cc_start: 0.5010 (OUTLIER) cc_final: 0.4738 (mt) REVERT: A 137 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.6914 (mtmt) REVERT: A 227 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7011 (mt-10) REVERT: A 236 LYS cc_start: 0.8343 (tttm) cc_final: 0.8114 (tttt) REVERT: A 332 MET cc_start: 0.5549 (mmm) cc_final: 0.3820 (tmm) REVERT: B 43 PHE cc_start: 0.2211 (OUTLIER) cc_final: 0.1621 (m-10) REVERT: B 267 MET cc_start: 0.5430 (ptp) cc_final: 0.4662 (ppp) REVERT: B 311 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: B 320 LYS cc_start: 0.7329 (tttm) cc_final: 0.7030 (mmmt) REVERT: C 48 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5640 (tt) REVERT: C 52 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.6618 (t80) REVERT: C 85 LEU cc_start: 0.4985 (OUTLIER) cc_final: 0.4712 (mt) REVERT: C 137 LYS cc_start: 0.7594 (tptt) cc_final: 0.6947 (mtmt) REVERT: C 332 MET cc_start: 0.5051 (mmm) cc_final: 0.3589 (tmm) REVERT: D 43 PHE cc_start: 0.1873 (OUTLIER) cc_final: 0.1290 (m-10) REVERT: D 267 MET cc_start: 0.5062 (ptp) cc_final: 0.4734 (ptt) REVERT: D 311 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: E 85 LEU cc_start: 0.5011 (OUTLIER) cc_final: 0.4764 (mt) REVERT: E 110 MET cc_start: 0.7700 (ttm) cc_final: 0.7483 (ttm) REVERT: E 137 LYS cc_start: 0.7582 (tptt) cc_final: 0.6918 (mtmt) REVERT: E 236 LYS cc_start: 0.8388 (tttm) cc_final: 0.8097 (tttt) REVERT: E 311 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: E 332 MET cc_start: 0.5572 (mmp) cc_final: 0.3699 (tmm) REVERT: F 43 PHE cc_start: 0.2194 (OUTLIER) cc_final: 0.1594 (m-10) REVERT: F 311 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: F 320 LYS cc_start: 0.7314 (tttm) cc_final: 0.7025 (mmmt) REVERT: G 48 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5610 (tt) REVERT: G 52 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.6582 (t80) REVERT: G 85 LEU cc_start: 0.4931 (OUTLIER) cc_final: 0.4687 (mt) REVERT: G 137 LYS cc_start: 0.7484 (tptt) cc_final: 0.6873 (mtmt) REVERT: G 332 MET cc_start: 0.4947 (mmm) cc_final: 0.3630 (tmm) REVERT: H 43 PHE cc_start: 0.1943 (OUTLIER) cc_final: 0.1362 (m-10) REVERT: H 157 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: H 311 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7828 (m-80) outliers start: 85 outliers final: 57 residues processed: 232 average time/residue: 0.1433 time to fit residues: 48.9722 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 : 0.664 ------------------------------------------------------------------------------- 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 110 MET Chi-restraints excluded: chain A residue 137 LYS 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 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 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 51 SER Chi-restraints excluded: chain C residue 52 TYR 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 241 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER 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 228 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 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 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 TYR 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 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 48 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 61 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 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 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 235 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 275 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 60 optimal weight: 4.9990 chunk 150 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.196755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.163588 restraints weight = 18493.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.153828 restraints weight = 34489.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.153433 restraints weight = 20907.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.154466 restraints weight = 16550.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.155399 restraints weight = 14102.442| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 18737 Z= 0.134 Angle : 0.546 9.394 25359 Z= 0.280 Chirality : 0.036 0.217 2771 Planarity : 0.007 0.136 3323 Dihedral : 4.235 33.234 2564 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.90 % Favored : 96.75 % Rotamer: Outliers : 3.51 % Allowed : 22.18 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.18), residues: 2277 helix: 2.72 (0.14), residues: 1499 sheet: -0.04 (0.39), residues: 200 loop : -1.49 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 271 TYR 0.009 0.001 TYR H 127 PHE 0.009 0.001 PHE B 81 TRP 0.011 0.001 TRP B 202 HIS 0.002 0.000 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00341 (18737) covalent geometry : angle 0.54614 (25359) hydrogen bonds : bond 0.04089 ( 1290) hydrogen bonds : angle 3.89329 ( 3798) ********************** 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 221 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 153 time to evaluate : 0.674 Fit side-chains REVERT: A 52 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.6539 (t80) REVERT: A 85 LEU cc_start: 0.4961 (OUTLIER) cc_final: 0.4697 (mt) REVERT: A 137 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.6835 (mtmt) REVERT: A 227 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7028 (mt-10) REVERT: A 236 LYS cc_start: 0.8333 (tttm) cc_final: 0.8107 (tttt) REVERT: A 332 MET cc_start: 0.5584 (mmm) cc_final: 0.3921 (tmm) REVERT: B 43 PHE cc_start: 0.2124 (OUTLIER) cc_final: 0.1489 (m-10) REVERT: B 267 MET cc_start: 0.5545 (ptp) cc_final: 0.4751 (ppp) REVERT: B 311 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: B 320 LYS cc_start: 0.7309 (tttm) cc_final: 0.7000 (mmmt) REVERT: C 48 LEU cc_start: 0.5879 (OUTLIER) cc_final: 0.5643 (tt) REVERT: C 52 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.6570 (t80) REVERT: C 85 LEU cc_start: 0.4894 (OUTLIER) cc_final: 0.4660 (mt) REVERT: C 137 LYS cc_start: 0.7552 (tptt) cc_final: 0.6862 (mtmt) REVERT: C 259 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7036 (pm20) REVERT: C 332 MET cc_start: 0.5153 (mmm) cc_final: 0.3792 (tmm) REVERT: D 43 PHE cc_start: 0.1928 (OUTLIER) cc_final: 0.1340 (m-10) REVERT: D 267 MET cc_start: 0.5075 (ptp) cc_final: 0.4513 (ptt) REVERT: D 271 ARG cc_start: 0.7491 (ttp80) cc_final: 0.7061 (mtp-110) REVERT: D 311 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: D 320 LYS cc_start: 0.7289 (tttm) cc_final: 0.6996 (mmmt) REVERT: E 85 LEU cc_start: 0.4962 (OUTLIER) cc_final: 0.4723 (mt) REVERT: E 110 MET cc_start: 0.7673 (ttm) cc_final: 0.7462 (ttm) REVERT: E 137 LYS cc_start: 0.7532 (tptt) cc_final: 0.6826 (mtmt) REVERT: E 236 LYS cc_start: 0.8405 (tttm) cc_final: 0.8100 (tttt) REVERT: E 311 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8428 (m-80) REVERT: E 332 MET cc_start: 0.5663 (mmp) cc_final: 0.3792 (tmm) REVERT: F 43 PHE cc_start: 0.2251 (OUTLIER) cc_final: 0.1633 (m-10) REVERT: F 311 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: F 320 LYS cc_start: 0.7298 (tttm) cc_final: 0.6997 (mmmt) REVERT: G 48 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5795 (tt) REVERT: G 52 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.6578 (t80) REVERT: G 85 LEU cc_start: 0.4874 (OUTLIER) cc_final: 0.4646 (mt) REVERT: G 137 LYS cc_start: 0.7544 (tptt) cc_final: 0.6844 (mtmt) REVERT: G 332 MET cc_start: 0.5183 (mmm) cc_final: 0.3816 (tmm) REVERT: H 43 PHE cc_start: 0.1862 (OUTLIER) cc_final: 0.1224 (m-10) REVERT: H 157 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: H 311 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7683 (m-80) outliers start: 68 outliers final: 47 residues processed: 210 average time/residue: 0.1488 time to fit residues: 45.9983 Evaluate side-chains 217 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 150 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 110 MET Chi-restraints excluded: chain A residue 137 LYS 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 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 51 SER Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 85 LEU 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 241 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 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 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 TYR 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 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 48 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 61 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 228 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 104 optimal weight: 0.9990 chunk 133 optimal weight: 0.0670 chunk 40 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 141 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 193 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN C 241 GLN F 289 ASN ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.198916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.169632 restraints weight = 18633.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.156094 restraints weight = 29952.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.156758 restraints weight = 19398.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.158094 restraints weight = 14379.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.158691 restraints weight = 13017.843| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 18737 Z= 0.120 Angle : 0.532 9.075 25359 Z= 0.272 Chirality : 0.036 0.217 2771 Planarity : 0.007 0.136 3323 Dihedral : 4.123 32.881 2564 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.94 % Favored : 96.71 % Rotamer: Outliers : 3.15 % Allowed : 22.49 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.19), residues: 2277 helix: 2.82 (0.14), residues: 1499 sheet: -0.34 (0.38), residues: 216 loop : -1.43 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 271 TYR 0.009 0.001 TYR H 127 PHE 0.008 0.001 PHE D 81 TRP 0.011 0.001 TRP B 202 HIS 0.001 0.000 HIS B 193 Details of bonding type rmsd covalent geometry : bond 0.00309 (18737) covalent geometry : angle 0.53210 (25359) hydrogen bonds : bond 0.03817 ( 1290) hydrogen bonds : angle 3.84064 ( 3798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.76 seconds wall clock time: 48 minutes 22.98 seconds (2902.98 seconds total)