Starting phenix.real_space_refine on Mon May 19 07:30:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c0e_16364/05_2025/8c0e_16364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c0e_16364/05_2025/8c0e_16364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c0e_16364/05_2025/8c0e_16364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c0e_16364/05_2025/8c0e_16364.map" model { file = "/net/cci-nas-00/data/ceres_data/8c0e_16364/05_2025/8c0e_16364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c0e_16364/05_2025/8c0e_16364.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 11582 2.51 5 N 3210 2.21 5 O 3533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18385 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "B" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2203 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 10, 'TRANS': 264} Chain breaks: 1 Chain: "C" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "D" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2214 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 10, 'TRANS': 265} Chain breaks: 1 Chain: "E" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "F" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2218 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Chain: "G" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2383 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "H" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2218 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Time building chain proxies: 10.80, per 1000 atoms: 0.59 Number of scatterers: 18385 At special positions: 0 Unit cell: (119.78, 119.78, 144.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 3533 8.00 N 3210 7.00 C 11582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.83 Conformation dependent library (CDL) restraints added in 2.4 seconds 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 8 sheets defined 70.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 39 through 54 Processing helix chain 'A' and resid 69 through 72 Processing helix chain 'A' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.519A pdb=" N GLY A 337 " --> pdb=" O TRP A 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 54 Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 82 " --> pdb=" O GLN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 125 through 130 removed outlier: 3.527A pdb=" N LYS B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 278 Processing helix chain 'B' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY B 337 " --> pdb=" O TRP B 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 Processing helix chain 'C' and resid 69 through 72 Processing helix chain 'C' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 82 " --> pdb=" O GLN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 99 through 113 Processing helix chain 'C' and resid 114 through 125 Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS C 129 " --> pdb=" O THR C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY C 337 " --> pdb=" O TRP C 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 54 Processing helix chain 'D' and resid 69 through 72 Processing helix chain 'D' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 114 through 125 Processing helix chain 'D' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS D 129 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 241 removed outlier: 3.642A pdb=" N LEU D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 283 through 298 removed outlier: 3.730A pdb=" N ASP D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY D 337 " --> pdb=" O TRP D 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 54 Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 73 through 84 removed outlier: 4.306A pdb=" N SER E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU E 82 " --> pdb=" O GLN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 99 through 113 Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 125 through 130 removed outlier: 3.525A pdb=" N LYS E 129 " --> pdb=" O THR E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 241 removed outlier: 3.640A pdb=" N LEU E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 263 removed outlier: 3.759A pdb=" N LEU E 263 " --> pdb=" O MET E 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 260 through 263' Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY E 337 " --> pdb=" O TRP E 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 54 Processing helix chain 'F' and resid 69 through 72 Processing helix chain 'F' and resid 73 through 84 removed outlier: 4.306A pdb=" N SER F 77 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU F 82 " --> pdb=" O GLN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 99 through 113 Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS F 129 " --> pdb=" O THR F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE F 150 " --> pdb=" O LEU F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU F 179 " --> pdb=" O SER F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 278 Processing helix chain 'F' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY F 337 " --> pdb=" O TRP F 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 54 Processing helix chain 'G' and resid 69 through 72 Processing helix chain 'G' and resid 73 through 84 removed outlier: 4.306A pdb=" N SER G 77 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU G 82 " --> pdb=" O GLN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 92 Processing helix chain 'G' and resid 99 through 113 Processing helix chain 'G' and resid 114 through 125 Processing helix chain 'G' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS G 129 " --> pdb=" O THR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 150 removed outlier: 3.792A pdb=" N ILE G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU G 179 " --> pdb=" O SER G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 278 Processing helix chain 'G' and resid 283 through 298 removed outlier: 3.731A pdb=" N ASP G 287 " --> pdb=" O GLU G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY G 337 " --> pdb=" O TRP G 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 54 Processing helix chain 'H' and resid 69 through 72 Processing helix chain 'H' and resid 73 through 84 removed outlier: 4.307A pdb=" N SER H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU H 82 " --> pdb=" O GLN H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 92 Processing helix chain 'H' and resid 99 through 113 Processing helix chain 'H' and resid 114 through 125 Processing helix chain 'H' and resid 125 through 130 removed outlier: 3.526A pdb=" N LYS H 129 " --> pdb=" O THR H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 150 removed outlier: 3.791A pdb=" N ILE H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 241 removed outlier: 3.641A pdb=" N LEU H 179 " --> pdb=" O SER H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 278 Processing helix chain 'H' and resid 283 through 298 removed outlier: 3.730A pdb=" N ASP H 287 " --> pdb=" O GLU H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 337 removed outlier: 3.520A pdb=" N GLY H 337 " --> pdb=" O TRP H 333 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP A 163 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP A 65 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR A 311 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.842A pdb=" N ASP B 163 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP B 65 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N TYR B 311 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP C 163 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP C 65 " --> pdb=" O TYR C 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR C 311 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP D 163 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP D 65 " --> pdb=" O TYR D 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR D 311 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP E 163 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP E 65 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR E 311 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 151 through 153 removed outlier: 3.842A pdb=" N ASP F 163 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP F 65 " --> pdb=" O TYR F 311 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR F 311 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP G 163 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP G 65 " --> pdb=" O TYR G 311 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR G 311 " --> pdb=" O ASP G 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 151 through 153 removed outlier: 3.843A pdb=" N ASP H 163 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP H 65 " --> pdb=" O TYR H 311 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR H 311 " --> pdb=" O ASP H 65 " (cutoff:3.500A) 1290 hydrogen bonds defined for protein. 3798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.23 Time building geometry restraints manager: 5.47 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 40.510 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18737 Z= 0.156 Angle : 0.720 12.661 25359 Z= 0.368 Chirality : 0.039 0.203 2771 Planarity : 0.008 0.121 3323 Dihedral : 18.449 89.765 7028 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.12 % Favored : 96.53 % Rotamer: Outliers : 0.77 % Allowed : 28.16 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.18), residues: 2277 helix: 2.34 (0.14), residues: 1479 sheet: 0.25 (0.34), residues: 216 loop : -1.24 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 202 HIS 0.004 0.001 HIS F 193 PHE 0.014 0.001 PHE A 261 TYR 0.035 0.002 TYR H 115 ARG 0.007 0.001 ARG D 313 Details of bonding type rmsd hydrogen bonds : bond 0.12034 ( 1290) hydrogen bonds : angle 5.69927 ( 3798) covalent geometry : bond 0.00366 (18737) covalent geometry : angle 0.71951 (25359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 GLU cc_start: 0.7670 (tt0) cc_final: 0.7402 (tt0) REVERT: A 227 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6928 (mt-10) REVERT: A 267 MET cc_start: 0.6654 (mmm) cc_final: 0.6050 (tpp) REVERT: A 320 LYS cc_start: 0.8098 (pttp) cc_final: 0.7872 (mttt) REVERT: B 66 LYS cc_start: 0.8717 (ptpp) cc_final: 0.8343 (ptmm) REVERT: C 170 GLU cc_start: 0.7719 (tt0) cc_final: 0.7503 (tt0) REVERT: C 267 MET cc_start: 0.6856 (mmm) cc_final: 0.6283 (tpp) REVERT: C 320 LYS cc_start: 0.8208 (pttp) cc_final: 0.7925 (mttt) REVERT: D 66 LYS cc_start: 0.8719 (ptpp) cc_final: 0.8321 (ptmm) REVERT: E 106 ASP cc_start: 0.6900 (t0) cc_final: 0.6544 (m-30) REVERT: E 170 GLU cc_start: 0.7756 (tt0) cc_final: 0.7532 (tt0) REVERT: E 267 MET cc_start: 0.6439 (mmm) cc_final: 0.5822 (tpp) REVERT: E 292 MET cc_start: 0.8249 (mmm) cc_final: 0.8034 (tpp) REVERT: E 320 LYS cc_start: 0.8196 (pttp) cc_final: 0.7954 (mttt) REVERT: F 66 LYS cc_start: 0.8699 (ptpp) cc_final: 0.8320 (ptmm) REVERT: G 267 MET cc_start: 0.6595 (mmm) cc_final: 0.6139 (tpp) REVERT: G 320 LYS cc_start: 0.8150 (pttp) cc_final: 0.7926 (mttt) REVERT: H 66 LYS cc_start: 0.8716 (ptpp) cc_final: 0.8330 (ptmm) outliers start: 15 outliers final: 0 residues processed: 268 average time/residue: 0.3506 time to fit residues: 134.2054 Evaluate side-chains 145 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 307 GLN B 193 HIS B 307 GLN C 307 GLN D 193 HIS D 307 GLN E 240 GLN E 307 GLN F 193 HIS F 307 GLN G 307 GLN H 193 HIS H 307 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.194022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3653 r_free = 0.3653 target = 0.152587 restraints weight = 18624.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.152501 restraints weight = 20485.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.152381 restraints weight = 19153.293| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 18737 Z= 0.251 Angle : 0.709 8.308 25359 Z= 0.367 Chirality : 0.043 0.221 2771 Planarity : 0.009 0.127 3323 Dihedral : 4.755 34.244 2564 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.81 % Favored : 96.84 % Rotamer: Outliers : 5.05 % Allowed : 23.52 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.49 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.18), residues: 2277 helix: 2.11 (0.13), residues: 1479 sheet: 0.00 (0.34), residues: 200 loop : -1.22 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP A 333 HIS 0.004 0.001 HIS A 193 PHE 0.021 0.002 PHE E 328 TYR 0.021 0.002 TYR E 282 ARG 0.009 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.05055 ( 1290) hydrogen bonds : angle 4.45513 ( 3798) covalent geometry : bond 0.00560 (18737) covalent geometry : angle 0.70875 (25359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 207 time to evaluate : 2.123 Fit side-chains REVERT: A 137 LYS cc_start: 0.7859 (tppt) cc_final: 0.7472 (mtmt) REVERT: A 227 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7075 (mt-10) REVERT: A 236 LYS cc_start: 0.8583 (tttm) cc_final: 0.8313 (tttt) REVERT: A 241 GLN cc_start: 0.6603 (OUTLIER) cc_final: 0.6370 (mp-120) REVERT: A 267 MET cc_start: 0.7129 (mmm) cc_final: 0.6402 (tpp) REVERT: B 43 PHE cc_start: 0.2795 (OUTLIER) cc_final: 0.2053 (m-10) REVERT: B 57 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6864 (mm-30) REVERT: B 157 ASP cc_start: 0.7407 (m-30) cc_final: 0.7025 (m-30) REVERT: B 311 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: C 267 MET cc_start: 0.7061 (mmm) cc_final: 0.6381 (tpp) REVERT: D 43 PHE cc_start: 0.2660 (OUTLIER) cc_final: 0.1942 (m-10) REVERT: D 57 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6857 (mm-30) REVERT: D 157 ASP cc_start: 0.7381 (m-30) cc_final: 0.7022 (m-30) REVERT: D 311 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7414 (m-80) REVERT: E 106 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: E 267 MET cc_start: 0.6766 (mmm) cc_final: 0.6105 (tpp) REVERT: F 43 PHE cc_start: 0.2775 (OUTLIER) cc_final: 0.2035 (m-10) REVERT: F 57 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6895 (mm-30) REVERT: F 267 MET cc_start: 0.6105 (ptp) cc_final: 0.5822 (ptp) REVERT: G 236 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8186 (tttt) REVERT: G 267 MET cc_start: 0.7008 (mmm) cc_final: 0.6458 (tpp) REVERT: H 43 PHE cc_start: 0.2709 (OUTLIER) cc_final: 0.1963 (m-10) REVERT: H 57 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6852 (mm-30) REVERT: H 157 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7096 (m-30) REVERT: H 311 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7425 (m-80) outliers start: 98 outliers final: 29 residues processed: 290 average time/residue: 0.2703 time to fit residues: 122.3448 Evaluate side-chains 196 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 236 LYS Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 48 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 217 optimal weight: 0.0870 chunk 166 optimal weight: 2.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN C 276 GLN E 240 GLN E 241 GLN E 276 GLN G 276 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.189047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3595 r_free = 0.3595 target = 0.148221 restraints weight = 18778.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.148221 restraints weight = 16398.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.148221 restraints weight = 16397.377| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 18737 Z= 0.183 Angle : 0.603 7.538 25359 Z= 0.311 Chirality : 0.039 0.225 2771 Planarity : 0.007 0.128 3323 Dihedral : 4.587 34.255 2564 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.81 % Favored : 96.84 % Rotamer: Outliers : 3.66 % Allowed : 23.78 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.49 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.18), residues: 2277 helix: 2.35 (0.13), residues: 1483 sheet: -0.02 (0.36), residues: 200 loop : -1.27 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 202 HIS 0.004 0.001 HIS B 193 PHE 0.011 0.001 PHE B 306 TYR 0.013 0.002 TYR G 282 ARG 0.004 0.001 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 1290) hydrogen bonds : angle 4.24499 ( 3798) covalent geometry : bond 0.00429 (18737) covalent geometry : angle 0.60284 (25359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 168 time to evaluate : 1.930 Fit side-chains REVERT: A 85 LEU cc_start: 0.4985 (OUTLIER) cc_final: 0.4768 (mt) REVERT: A 137 LYS cc_start: 0.7853 (tppt) cc_final: 0.7517 (mtmt) REVERT: A 197 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6794 (mt-10) REVERT: A 227 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7049 (mt-10) REVERT: A 236 LYS cc_start: 0.8650 (tttm) cc_final: 0.8375 (tttt) REVERT: A 267 MET cc_start: 0.7313 (mmm) cc_final: 0.6992 (tpp) REVERT: A 332 MET cc_start: 0.5882 (mmp) cc_final: 0.3905 (tmm) REVERT: B 43 PHE cc_start: 0.2553 (OUTLIER) cc_final: 0.1909 (m-10) REVERT: B 57 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6916 (mm-30) REVERT: B 157 ASP cc_start: 0.7507 (m-30) cc_final: 0.7067 (m-30) REVERT: C 85 LEU cc_start: 0.4888 (OUTLIER) cc_final: 0.4676 (mt) REVERT: C 267 MET cc_start: 0.7280 (mmm) cc_final: 0.7070 (tpp) REVERT: C 276 GLN cc_start: 0.7379 (mt0) cc_final: 0.7161 (mm-40) REVERT: C 332 MET cc_start: 0.5916 (mmp) cc_final: 0.3940 (tmm) REVERT: D 43 PHE cc_start: 0.2488 (OUTLIER) cc_final: 0.1830 (m-10) REVERT: D 57 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6860 (mm-30) REVERT: E 110 MET cc_start: 0.7816 (ttm) cc_final: 0.7501 (ttm) REVERT: E 137 LYS cc_start: 0.7557 (tppt) cc_final: 0.7330 (mtmt) REVERT: E 236 LYS cc_start: 0.8561 (tttm) cc_final: 0.8285 (tttt) REVERT: E 332 MET cc_start: 0.5721 (mmp) cc_final: 0.3778 (tmm) REVERT: F 43 PHE cc_start: 0.2677 (OUTLIER) cc_final: 0.1996 (m-10) REVERT: F 57 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6868 (mm-30) REVERT: F 267 MET cc_start: 0.5841 (ptp) cc_final: 0.5400 (ptt) REVERT: F 311 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: G 85 LEU cc_start: 0.4866 (OUTLIER) cc_final: 0.4655 (mt) REVERT: G 276 GLN cc_start: 0.7409 (mt0) cc_final: 0.7181 (mm-40) REVERT: G 332 MET cc_start: 0.5878 (mmp) cc_final: 0.3946 (tmm) REVERT: H 43 PHE cc_start: 0.2622 (OUTLIER) cc_final: 0.1964 (m-10) REVERT: H 57 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6860 (mm-30) REVERT: H 157 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7154 (m-30) outliers start: 71 outliers final: 32 residues processed: 224 average time/residue: 0.3065 time to fit residues: 103.5325 Evaluate side-chains 190 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 228 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 F residue 314 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 157 ASP Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 197 optimal weight: 40.0000 chunk 203 optimal weight: 4.9990 chunk 56 optimal weight: 30.0000 chunk 23 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN C 193 HIS D 84 ASN E 276 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.193181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3648 r_free = 0.3648 target = 0.151593 restraints weight = 18645.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.151593 restraints weight = 16007.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.151593 restraints weight = 16001.476| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18737 Z= 0.220 Angle : 0.636 6.815 25359 Z= 0.327 Chirality : 0.040 0.214 2771 Planarity : 0.008 0.132 3323 Dihedral : 4.638 35.540 2564 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.94 % Favored : 96.71 % Rotamer: Outliers : 5.72 % Allowed : 21.87 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.18), residues: 2277 helix: 2.21 (0.13), residues: 1490 sheet: 0.04 (0.36), residues: 192 loop : -1.35 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 202 HIS 0.003 0.001 HIS D 193 PHE 0.013 0.002 PHE D 81 TYR 0.014 0.002 TYR C 115 ARG 0.006 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04965 ( 1290) hydrogen bonds : angle 4.17844 ( 3798) covalent geometry : bond 0.00536 (18737) covalent geometry : angle 0.63564 (25359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 189 time to evaluate : 1.901 Fit side-chains REVERT: A 85 LEU cc_start: 0.5291 (OUTLIER) cc_final: 0.5048 (mt) REVERT: A 227 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7019 (mt-10) REVERT: A 236 LYS cc_start: 0.8684 (tttm) cc_final: 0.8406 (tttt) REVERT: A 332 MET cc_start: 0.5731 (mmp) cc_final: 0.3604 (tmm) REVERT: B 43 PHE cc_start: 0.2491 (OUTLIER) cc_final: 0.1843 (m-10) REVERT: B 57 GLU cc_start: 0.7265 (mt-10) cc_final: 0.7050 (mm-30) REVERT: B 84 ASN cc_start: 0.7072 (OUTLIER) cc_final: 0.6868 (m-40) REVERT: B 199 LYS cc_start: 0.8168 (mptt) cc_final: 0.7932 (mptt) REVERT: B 311 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: B 320 LYS cc_start: 0.7391 (tttm) cc_final: 0.7141 (mmmt) REVERT: C 48 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5690 (tt) REVERT: C 85 LEU cc_start: 0.4991 (OUTLIER) cc_final: 0.4722 (mt) REVERT: C 332 MET cc_start: 0.5827 (mmp) cc_final: 0.3722 (tmm) REVERT: D 43 PHE cc_start: 0.2482 (OUTLIER) cc_final: 0.1848 (m-10) REVERT: D 57 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6995 (mm-30) REVERT: D 311 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8239 (m-80) REVERT: D 320 LYS cc_start: 0.7338 (tttm) cc_final: 0.7038 (mmmt) REVERT: E 85 LEU cc_start: 0.5047 (OUTLIER) cc_final: 0.4753 (mt) REVERT: E 110 MET cc_start: 0.7820 (ttm) cc_final: 0.7575 (ttm) REVERT: E 236 LYS cc_start: 0.8530 (tttm) cc_final: 0.8314 (tttt) REVERT: E 267 MET cc_start: 0.6887 (tpp) cc_final: 0.6383 (tpp) REVERT: E 311 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.8602 (m-10) REVERT: E 332 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.3787 (tmm) REVERT: F 43 PHE cc_start: 0.2474 (OUTLIER) cc_final: 0.1817 (m-10) REVERT: F 57 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7043 (mm-30) REVERT: F 199 LYS cc_start: 0.8171 (mptt) cc_final: 0.7925 (mptt) REVERT: F 267 MET cc_start: 0.5843 (ptp) cc_final: 0.5384 (ptt) REVERT: F 311 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.8242 (m-80) REVERT: F 320 LYS cc_start: 0.7355 (tttm) cc_final: 0.7060 (mmmt) REVERT: G 48 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.5665 (tt) REVERT: G 85 LEU cc_start: 0.4988 (OUTLIER) cc_final: 0.4709 (mt) REVERT: G 267 MET cc_start: 0.6641 (tpp) cc_final: 0.6208 (tpp) REVERT: G 311 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8624 (m-10) REVERT: G 332 MET cc_start: 0.5819 (mmp) cc_final: 0.3751 (tmm) REVERT: H 43 PHE cc_start: 0.2547 (OUTLIER) cc_final: 0.1889 (m-10) REVERT: H 311 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.8259 (m-80) REVERT: H 320 LYS cc_start: 0.7326 (tttm) cc_final: 0.7037 (mmmt) outliers start: 111 outliers final: 50 residues processed: 286 average time/residue: 0.3458 time to fit residues: 142.8364 Evaluate side-chains 226 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 158 time to evaluate : 2.013 ------------------------------------------------------------------------------- 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 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 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain 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 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 0 optimal weight: 30.0000 chunk 97 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 202 optimal weight: 0.0060 chunk 217 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 112 optimal weight: 30.0000 chunk 48 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN C 240 GLN C 276 GLN G 240 GLN G 241 GLN G 276 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.202615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.158451 restraints weight = 19189.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.158845 restraints weight = 17051.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.158845 restraints weight = 14544.321| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4258 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= 0.127 Angle : 0.546 7.438 25359 Z= 0.283 Chirality : 0.036 0.220 2771 Planarity : 0.007 0.133 3323 Dihedral : 4.427 34.067 2564 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.94 % Favored : 96.71 % Rotamer: Outliers : 3.04 % Allowed : 24.60 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.18), residues: 2277 helix: 2.43 (0.14), residues: 1513 sheet: -0.00 (0.37), residues: 200 loop : -1.30 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 202 HIS 0.004 0.001 HIS D 193 PHE 0.011 0.001 PHE B 81 TYR 0.009 0.001 TYR B 286 ARG 0.004 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 1290) hydrogen bonds : angle 4.01779 ( 3798) covalent geometry : bond 0.00313 (18737) covalent geometry : angle 0.54638 (25359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 172 time to evaluate : 1.896 Fit side-chains REVERT: A 85 LEU cc_start: 0.4959 (OUTLIER) cc_final: 0.4733 (mt) REVERT: A 137 LYS cc_start: 0.7632 (tptt) cc_final: 0.6953 (mtmt) REVERT: A 227 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6870 (mt-10) REVERT: A 236 LYS cc_start: 0.8536 (tttm) cc_final: 0.8281 (tttt) REVERT: A 332 MET cc_start: 0.5495 (mmp) cc_final: 0.3509 (tmm) REVERT: B 43 PHE cc_start: 0.2539 (OUTLIER) cc_final: 0.1934 (m-10) REVERT: B 57 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6921 (mm-30) REVERT: B 311 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: B 320 LYS cc_start: 0.7395 (tttm) cc_final: 0.6996 (mmmt) REVERT: C 48 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5684 (tt) REVERT: C 85 LEU cc_start: 0.4776 (OUTLIER) cc_final: 0.4551 (mt) REVERT: C 137 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.6944 (mtmt) REVERT: C 241 GLN cc_start: 0.6687 (OUTLIER) cc_final: 0.6375 (mp10) REVERT: C 311 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.8397 (m-80) REVERT: C 332 MET cc_start: 0.5561 (mmp) cc_final: 0.3562 (tmm) REVERT: D 43 PHE cc_start: 0.2305 (OUTLIER) cc_final: 0.1704 (m-10) REVERT: D 57 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6936 (mm-30) REVERT: D 199 LYS cc_start: 0.8150 (mptt) cc_final: 0.7941 (mptt) REVERT: D 311 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: D 320 LYS cc_start: 0.7280 (tttm) cc_final: 0.6930 (mmmt) REVERT: E 48 LEU cc_start: 0.6150 (tt) cc_final: 0.5459 (tt) REVERT: E 85 LEU cc_start: 0.4908 (OUTLIER) cc_final: 0.4653 (mt) REVERT: E 137 LYS cc_start: 0.7614 (tptt) cc_final: 0.6937 (mtmt) REVERT: E 236 LYS cc_start: 0.8443 (tttm) cc_final: 0.8209 (tttt) REVERT: E 267 MET cc_start: 0.6815 (tpp) cc_final: 0.6350 (tpp) REVERT: E 311 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.8372 (m-80) REVERT: E 332 MET cc_start: 0.5621 (OUTLIER) cc_final: 0.3621 (tmm) REVERT: F 43 PHE cc_start: 0.2586 (OUTLIER) cc_final: 0.1949 (m-10) REVERT: F 57 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6894 (mm-30) REVERT: F 199 LYS cc_start: 0.8179 (mptt) cc_final: 0.7963 (mptt) REVERT: F 311 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: F 320 LYS cc_start: 0.7291 (tttm) cc_final: 0.6942 (mmmt) REVERT: G 48 LEU cc_start: 0.6251 (tt) cc_final: 0.5768 (tt) REVERT: G 85 LEU cc_start: 0.4793 (OUTLIER) cc_final: 0.4566 (mt) REVERT: G 137 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.6931 (mtmt) REVERT: G 267 MET cc_start: 0.6650 (tpp) cc_final: 0.6292 (tpp) REVERT: G 311 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.8385 (m-80) REVERT: G 332 MET cc_start: 0.5525 (mmp) cc_final: 0.3555 (tmm) REVERT: H 43 PHE cc_start: 0.2177 (OUTLIER) cc_final: 0.1562 (m-10) REVERT: H 311 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: H 320 LYS cc_start: 0.7264 (tttm) cc_final: 0.6938 (mmmt) outliers start: 59 outliers final: 32 residues processed: 221 average time/residue: 0.3496 time to fit residues: 111.1819 Evaluate side-chains 215 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 1.988 ------------------------------------------------------------------------------- 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 142 LEU 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 235 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 168 VAL 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 84 ASN Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 43 PHE 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 137 LYS Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 276 GLN B 84 ASN C 240 GLN C 276 GLN G 193 HIS G 240 GLN G 276 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.195133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.164398 restraints weight = 18896.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.150406 restraints weight = 35726.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.152335 restraints weight = 21534.342| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 18737 Z= 0.177 Angle : 0.581 7.193 25359 Z= 0.299 Chirality : 0.037 0.215 2771 Planarity : 0.007 0.135 3323 Dihedral : 4.411 34.222 2564 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.90 % Favored : 96.75 % Rotamer: Outliers : 4.44 % Allowed : 22.85 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.18), residues: 2277 helix: 2.41 (0.14), residues: 1513 sheet: 0.26 (0.39), residues: 184 loop : -1.39 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 202 HIS 0.004 0.001 HIS C 193 PHE 0.016 0.001 PHE B 81 TYR 0.012 0.002 TYR G 115 ARG 0.008 0.000 ARG H 88 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 1290) hydrogen bonds : angle 4.02025 ( 3798) covalent geometry : bond 0.00439 (18737) covalent geometry : angle 0.58148 (25359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 170 time to evaluate : 1.811 Fit side-chains REVERT: A 48 LEU cc_start: 0.5942 (tt) cc_final: 0.5266 (tt) REVERT: A 52 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.6406 (t80) REVERT: A 85 LEU cc_start: 0.5119 (OUTLIER) cc_final: 0.4872 (mt) REVERT: A 137 LYS cc_start: 0.7669 (tptt) cc_final: 0.6911 (mtmt) REVERT: A 227 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6820 (mt-10) REVERT: A 236 LYS cc_start: 0.8317 (tttm) cc_final: 0.8110 (tttt) REVERT: A 332 MET cc_start: 0.5322 (mmp) cc_final: 0.3363 (tmm) REVERT: B 43 PHE cc_start: 0.2427 (OUTLIER) cc_final: 0.1828 (m-10) REVERT: B 57 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6976 (mm-30) REVERT: B 311 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: B 320 LYS cc_start: 0.7401 (tttm) cc_final: 0.6993 (mmmt) REVERT: C 85 LEU cc_start: 0.4926 (OUTLIER) cc_final: 0.4648 (mt) REVERT: C 137 LYS cc_start: 0.7666 (tptt) cc_final: 0.6901 (mtmt) REVERT: C 241 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6363 (mp10) REVERT: C 311 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8536 (m-10) REVERT: C 332 MET cc_start: 0.5375 (mmp) cc_final: 0.3472 (tmm) REVERT: D 43 PHE cc_start: 0.2117 (OUTLIER) cc_final: 0.1507 (m-10) REVERT: D 57 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6973 (mm-30) REVERT: D 311 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.8187 (m-80) REVERT: D 320 LYS cc_start: 0.7312 (tttm) cc_final: 0.6945 (mmmt) REVERT: E 52 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.6563 (t80) REVERT: E 85 LEU cc_start: 0.5078 (OUTLIER) cc_final: 0.4800 (mt) REVERT: E 137 LYS cc_start: 0.7633 (tptt) cc_final: 0.6874 (mtmt) REVERT: E 236 LYS cc_start: 0.8334 (tttm) cc_final: 0.8094 (tttt) REVERT: E 240 GLN cc_start: 0.6914 (tt0) cc_final: 0.6665 (tt0) REVERT: E 267 MET cc_start: 0.6838 (tpp) cc_final: 0.6447 (tpp) REVERT: E 332 MET cc_start: 0.5419 (OUTLIER) cc_final: 0.3479 (tmm) REVERT: F 43 PHE cc_start: 0.2402 (OUTLIER) cc_final: 0.1790 (m-10) REVERT: F 57 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6985 (mm-30) REVERT: F 311 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: F 320 LYS cc_start: 0.7313 (tttm) cc_final: 0.6954 (mmmt) REVERT: G 85 LEU cc_start: 0.4934 (OUTLIER) cc_final: 0.4670 (mt) REVERT: G 137 LYS cc_start: 0.7676 (tptt) cc_final: 0.6904 (mtmt) REVERT: G 267 MET cc_start: 0.6804 (tpp) cc_final: 0.6501 (tpp) REVERT: G 332 MET cc_start: 0.5299 (mmp) cc_final: 0.3379 (tmm) REVERT: H 43 PHE cc_start: 0.2062 (OUTLIER) cc_final: 0.1465 (m-10) REVERT: H 311 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: H 320 LYS cc_start: 0.7284 (tttm) cc_final: 0.6942 (mmmt) outliers start: 86 outliers final: 56 residues processed: 246 average time/residue: 0.3312 time to fit residues: 118.9102 Evaluate side-chains 234 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 161 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 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 295 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 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 198 ILE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 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 198 ILE Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 15 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 198 optimal weight: 5.9990 chunk 209 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN D 148 ASN F 148 ASN G 240 GLN H 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.197036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.170081 restraints weight = 18636.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.151832 restraints weight = 29711.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.154250 restraints weight = 21176.657| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4696 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= 0.139 Angle : 0.542 7.140 25359 Z= 0.279 Chirality : 0.036 0.219 2771 Planarity : 0.007 0.135 3323 Dihedral : 4.329 33.756 2564 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.94 % Favored : 96.71 % Rotamer: Outliers : 4.38 % Allowed : 22.38 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.18), residues: 2277 helix: 2.53 (0.14), residues: 1513 sheet: 0.32 (0.39), residues: 184 loop : -1.38 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 202 HIS 0.003 0.001 HIS C 193 PHE 0.010 0.001 PHE H 90 TYR 0.010 0.001 TYR H 127 ARG 0.007 0.000 ARG H 271 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 1290) hydrogen bonds : angle 3.98177 ( 3798) covalent geometry : bond 0.00348 (18737) covalent geometry : angle 0.54210 (25359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 165 time to evaluate : 1.846 Fit side-chains REVERT: A 52 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6470 (t80) REVERT: A 85 LEU cc_start: 0.5093 (OUTLIER) cc_final: 0.4857 (mt) REVERT: A 137 LYS cc_start: 0.7482 (tptt) cc_final: 0.6791 (mtmt) REVERT: A 227 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6999 (mt-10) REVERT: A 236 LYS cc_start: 0.8444 (tttm) cc_final: 0.8217 (tttt) REVERT: A 332 MET cc_start: 0.5662 (mmp) cc_final: 0.3581 (tmm) REVERT: B 43 PHE cc_start: 0.2363 (OUTLIER) cc_final: 0.1713 (m-10) REVERT: B 57 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7028 (mm-30) REVERT: B 63 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8497 (mt) REVERT: B 311 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: B 320 LYS cc_start: 0.7401 (tttm) cc_final: 0.7015 (mmmt) REVERT: C 85 LEU cc_start: 0.4967 (OUTLIER) cc_final: 0.4725 (mt) REVERT: C 137 LYS cc_start: 0.7601 (tptt) cc_final: 0.6875 (mtmt) REVERT: C 241 GLN cc_start: 0.6891 (OUTLIER) cc_final: 0.6522 (mp10) REVERT: C 311 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.8503 (m-10) REVERT: C 332 MET cc_start: 0.5563 (mmp) cc_final: 0.3598 (tmm) REVERT: D 43 PHE cc_start: 0.2239 (OUTLIER) cc_final: 0.1582 (m-10) REVERT: D 57 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6964 (mm-30) REVERT: D 63 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8474 (mt) REVERT: D 311 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: D 320 LYS cc_start: 0.7293 (tttm) cc_final: 0.6955 (mmmt) REVERT: E 85 LEU cc_start: 0.5078 (OUTLIER) cc_final: 0.4815 (mt) REVERT: E 137 LYS cc_start: 0.7476 (tptt) cc_final: 0.6788 (mtmt) REVERT: E 236 LYS cc_start: 0.8456 (tttm) cc_final: 0.8211 (tttt) REVERT: E 240 GLN cc_start: 0.6974 (tt0) cc_final: 0.6742 (tt0) REVERT: E 267 MET cc_start: 0.6572 (tpp) cc_final: 0.6323 (tpp) REVERT: E 332 MET cc_start: 0.5653 (OUTLIER) cc_final: 0.3696 (tmm) REVERT: F 43 PHE cc_start: 0.2477 (OUTLIER) cc_final: 0.1837 (m-10) REVERT: F 57 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6975 (mm-30) REVERT: F 63 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8470 (mt) REVERT: F 302 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7364 (mt) REVERT: F 311 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: F 320 LYS cc_start: 0.7295 (tttm) cc_final: 0.6958 (mmmt) REVERT: G 85 LEU cc_start: 0.4940 (OUTLIER) cc_final: 0.4675 (mt) REVERT: G 137 LYS cc_start: 0.7599 (tptt) cc_final: 0.6863 (mtmt) REVERT: G 267 MET cc_start: 0.6684 (tpp) cc_final: 0.6454 (tpp) REVERT: G 311 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8519 (m-10) REVERT: G 332 MET cc_start: 0.5541 (mmp) cc_final: 0.3598 (tmm) REVERT: H 43 PHE cc_start: 0.2038 (OUTLIER) cc_final: 0.1388 (m-10) REVERT: H 63 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8510 (mt) REVERT: H 311 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.8010 (m-80) REVERT: H 320 LYS cc_start: 0.7273 (tttm) cc_final: 0.6942 (mmmt) outliers start: 85 outliers final: 50 residues processed: 240 average time/residue: 0.3266 time to fit residues: 114.6176 Evaluate side-chains 234 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 162 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 168 VAL 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 63 ILE Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 SER 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 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 332 MET 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 198 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 237 ILE Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 70 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 223 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN B 148 ASN D 148 ASN F 148 ASN G 240 GLN H 148 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.195814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.169338 restraints weight = 18664.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.151573 restraints weight = 34408.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.152804 restraints weight = 23395.747| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 18737 Z= 0.151 Angle : 0.548 7.132 25359 Z= 0.282 Chirality : 0.037 0.218 2771 Planarity : 0.007 0.136 3323 Dihedral : 4.305 33.465 2564 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.90 % Favored : 96.75 % Rotamer: Outliers : 4.33 % Allowed : 22.07 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.18), residues: 2277 helix: 2.56 (0.14), residues: 1513 sheet: 0.30 (0.39), residues: 184 loop : -1.38 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 202 HIS 0.003 0.001 HIS A 193 PHE 0.010 0.001 PHE H 90 TYR 0.010 0.001 TYR H 127 ARG 0.009 0.000 ARG F 271 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 1290) hydrogen bonds : angle 3.95707 ( 3798) covalent geometry : bond 0.00380 (18737) covalent geometry : angle 0.54826 (25359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 165 time to evaluate : 1.898 Fit side-chains REVERT: A 52 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6519 (t80) REVERT: A 85 LEU cc_start: 0.4924 (OUTLIER) cc_final: 0.4718 (mt) REVERT: A 137 LYS cc_start: 0.7480 (tptt) cc_final: 0.6752 (mtmt) REVERT: A 227 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6985 (mt-10) REVERT: A 236 LYS cc_start: 0.8409 (tttm) cc_final: 0.8178 (tttt) REVERT: A 332 MET cc_start: 0.5613 (mmp) cc_final: 0.3559 (tmm) REVERT: B 57 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6959 (mm-30) REVERT: B 63 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8494 (mt) REVERT: B 311 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: B 320 LYS cc_start: 0.7410 (tttm) cc_final: 0.6993 (mmmt) REVERT: C 85 LEU cc_start: 0.5031 (OUTLIER) cc_final: 0.4796 (mt) REVERT: C 137 LYS cc_start: 0.7481 (tptt) cc_final: 0.6744 (mtmt) REVERT: C 241 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.6278 (mp10) REVERT: C 311 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8543 (m-10) REVERT: C 332 MET cc_start: 0.5526 (mmp) cc_final: 0.3617 (tmm) REVERT: D 57 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6911 (mm-30) REVERT: D 63 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8466 (mt) REVERT: D 267 MET cc_start: 0.5276 (ptp) cc_final: 0.4723 (ptt) REVERT: D 311 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: D 320 LYS cc_start: 0.7307 (tttm) cc_final: 0.6943 (mmmt) REVERT: E 48 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5723 (tt) REVERT: E 52 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.6684 (t80) REVERT: E 85 LEU cc_start: 0.5141 (OUTLIER) cc_final: 0.4884 (mt) REVERT: E 137 LYS cc_start: 0.7466 (tptt) cc_final: 0.6724 (mtmt) REVERT: E 236 LYS cc_start: 0.8430 (tttm) cc_final: 0.8170 (tttt) REVERT: E 240 GLN cc_start: 0.6890 (tt0) cc_final: 0.6659 (tt0) REVERT: E 267 MET cc_start: 0.6716 (tpp) cc_final: 0.6482 (tpp) REVERT: E 311 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.8555 (m-10) REVERT: E 332 MET cc_start: 0.5623 (OUTLIER) cc_final: 0.3716 (tmm) REVERT: F 43 PHE cc_start: 0.2291 (OUTLIER) cc_final: 0.1656 (m-10) REVERT: F 57 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6952 (mm-30) REVERT: F 63 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8478 (mt) REVERT: F 311 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.8128 (m-80) REVERT: F 320 LYS cc_start: 0.7314 (tttm) cc_final: 0.6941 (mmmt) REVERT: G 85 LEU cc_start: 0.5053 (OUTLIER) cc_final: 0.4790 (mt) REVERT: G 137 LYS cc_start: 0.7490 (tptt) cc_final: 0.6746 (mtmt) REVERT: G 259 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6635 (pm20) REVERT: G 332 MET cc_start: 0.5505 (mmp) cc_final: 0.3568 (tmm) REVERT: H 63 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8480 (mt) REVERT: H 199 LYS cc_start: 0.8377 (mttt) cc_final: 0.8173 (mttp) REVERT: H 311 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: H 320 LYS cc_start: 0.7286 (tttm) cc_final: 0.6932 (mmmt) outliers start: 84 outliers final: 56 residues processed: 241 average time/residue: 0.3258 time to fit residues: 116.1833 Evaluate side-chains 233 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 157 time to evaluate : 1.954 ------------------------------------------------------------------------------- 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 168 VAL 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 B residue 63 ILE Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 175 SER 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 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 84 ASN 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 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 188 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 214 optimal weight: 0.8980 chunk 152 optimal weight: 0.3980 chunk 198 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 193 HIS ** G 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.195912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.164051 restraints weight = 18681.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.151782 restraints weight = 33751.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.152742 restraints weight = 21905.687| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5019 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= 0.159 Angle : 0.552 6.963 25359 Z= 0.283 Chirality : 0.037 0.281 2771 Planarity : 0.007 0.136 3323 Dihedral : 4.312 33.503 2564 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.81 % Favored : 96.84 % Rotamer: Outliers : 4.49 % Allowed : 22.33 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.18), residues: 2277 helix: 2.58 (0.14), residues: 1513 sheet: 0.10 (0.39), residues: 188 loop : -1.35 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 202 HIS 0.003 0.001 HIS G 193 PHE 0.013 0.001 PHE D 90 TYR 0.010 0.001 TYR B 127 ARG 0.013 0.000 ARG F 271 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 1290) hydrogen bonds : angle 3.97313 ( 3798) covalent geometry : bond 0.00399 (18737) covalent geometry : angle 0.55205 (25359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 161 time to evaluate : 1.936 Fit side-chains revert: symmetry clash REVERT: A 52 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6539 (t80) REVERT: A 85 LEU cc_start: 0.4981 (OUTLIER) cc_final: 0.4767 (mt) REVERT: A 137 LYS cc_start: 0.7515 (tptt) cc_final: 0.6745 (mtmt) REVERT: A 227 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7007 (mt-10) REVERT: A 236 LYS cc_start: 0.8425 (tttm) cc_final: 0.8200 (tttt) REVERT: A 332 MET cc_start: 0.5716 (mmp) cc_final: 0.3704 (tmm) REVERT: B 43 PHE cc_start: 0.2405 (OUTLIER) cc_final: 0.1725 (m-10) REVERT: B 57 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7039 (mm-30) REVERT: B 63 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8442 (mt) REVERT: B 214 LYS cc_start: 0.7899 (mmmm) cc_final: 0.7653 (mptt) REVERT: B 267 MET cc_start: 0.5486 (ptp) cc_final: 0.4695 (ppp) REVERT: B 311 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: B 320 LYS cc_start: 0.7338 (tttm) cc_final: 0.6924 (mmmt) REVERT: C 85 LEU cc_start: 0.5104 (OUTLIER) cc_final: 0.4857 (mt) REVERT: C 137 LYS cc_start: 0.7502 (tptt) cc_final: 0.6775 (mtmt) REVERT: C 241 GLN cc_start: 0.6541 (OUTLIER) cc_final: 0.6088 (mp10) REVERT: C 259 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6588 (pm20) REVERT: C 311 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8551 (m-10) REVERT: C 332 MET cc_start: 0.5597 (mmp) cc_final: 0.3663 (tmm) REVERT: D 43 PHE cc_start: 0.2234 (OUTLIER) cc_final: 0.1597 (m-10) REVERT: D 57 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6925 (mm-30) REVERT: D 63 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8450 (mt) REVERT: D 267 MET cc_start: 0.5075 (ptp) cc_final: 0.4741 (ptt) REVERT: D 311 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: D 320 LYS cc_start: 0.7302 (tttm) cc_final: 0.6944 (mmmt) REVERT: E 48 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5838 (tt) REVERT: E 52 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.6623 (t80) REVERT: E 85 LEU cc_start: 0.5148 (OUTLIER) cc_final: 0.4888 (mt) REVERT: E 137 LYS cc_start: 0.7507 (tptt) cc_final: 0.6745 (mtmt) REVERT: E 236 LYS cc_start: 0.8469 (tttm) cc_final: 0.8183 (tttt) REVERT: E 240 GLN cc_start: 0.6947 (tt0) cc_final: 0.6698 (tt0) REVERT: E 267 MET cc_start: 0.6705 (tpp) cc_final: 0.6434 (tpp) REVERT: E 311 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.8553 (m-10) REVERT: E 332 MET cc_start: 0.5722 (OUTLIER) cc_final: 0.3871 (tmm) REVERT: F 57 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6962 (mm-30) REVERT: F 63 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8429 (mt) REVERT: F 214 LYS cc_start: 0.7897 (mmmm) cc_final: 0.7640 (mptt) REVERT: F 311 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: F 320 LYS cc_start: 0.7298 (tttm) cc_final: 0.6907 (mmmt) REVERT: G 85 LEU cc_start: 0.5088 (OUTLIER) cc_final: 0.4823 (mt) REVERT: G 137 LYS cc_start: 0.7470 (tptt) cc_final: 0.6750 (mtmt) REVERT: G 311 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8546 (m-10) REVERT: G 332 MET cc_start: 0.5562 (mmp) cc_final: 0.3623 (tmm) REVERT: H 63 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8454 (mt) REVERT: H 199 LYS cc_start: 0.8286 (mttt) cc_final: 0.8030 (mttm) REVERT: H 311 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8159 (m-80) REVERT: H 320 LYS cc_start: 0.7279 (tttm) cc_final: 0.6919 (mmmt) outliers start: 87 outliers final: 61 residues processed: 237 average time/residue: 0.3304 time to fit residues: 114.9219 Evaluate side-chains 240 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 157 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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 168 VAL 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 A residue 314 THR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 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 295 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 84 ASN 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 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 201 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 289 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 = 0.4132 r_free = 0.4132 target = 0.196183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.154404 restraints weight = 18693.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.155489 restraints weight = 14996.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.155484 restraints weight = 13021.597| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 18737 Z= 0.148 Angle : 0.543 8.894 25359 Z= 0.278 Chirality : 0.037 0.218 2771 Planarity : 0.007 0.136 3323 Dihedral : 4.259 33.282 2564 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.81 % Favored : 96.84 % Rotamer: Outliers : 4.13 % Allowed : 22.80 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.18), residues: 2277 helix: 2.65 (0.14), residues: 1511 sheet: -0.23 (0.38), residues: 204 loop : -1.40 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 202 HIS 0.003 0.001 HIS G 193 PHE 0.011 0.001 PHE D 90 TYR 0.010 0.001 TYR H 127 ARG 0.006 0.000 ARG H 88 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 1290) hydrogen bonds : angle 3.93705 ( 3798) covalent geometry : bond 0.00374 (18737) covalent geometry : angle 0.54304 (25359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 162 time to evaluate : 1.967 Fit side-chains revert: symmetry clash REVERT: A 52 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.6367 (t80) REVERT: A 85 LEU cc_start: 0.4944 (OUTLIER) cc_final: 0.4694 (mt) REVERT: A 137 LYS cc_start: 0.7543 (tptt) cc_final: 0.6925 (mtmt) REVERT: A 236 LYS cc_start: 0.8530 (tttm) cc_final: 0.8298 (tttt) REVERT: A 311 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8542 (m-10) REVERT: A 332 MET cc_start: 0.5808 (mmp) cc_final: 0.3854 (tmm) REVERT: B 43 PHE cc_start: 0.2226 (OUTLIER) cc_final: 0.1532 (m-10) REVERT: B 267 MET cc_start: 0.5632 (ptp) cc_final: 0.5020 (ppp) REVERT: B 311 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: B 320 LYS cc_start: 0.7337 (tttm) cc_final: 0.7035 (mmmt) REVERT: C 85 LEU cc_start: 0.4960 (OUTLIER) cc_final: 0.4709 (mt) REVERT: C 137 LYS cc_start: 0.7508 (tptt) cc_final: 0.6895 (mtmt) REVERT: C 311 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8551 (m-10) REVERT: C 332 MET cc_start: 0.5938 (mmp) cc_final: 0.3960 (tmm) REVERT: D 267 MET cc_start: 0.5381 (ptp) cc_final: 0.4911 (ptt) REVERT: D 311 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: D 320 LYS cc_start: 0.7285 (tttm) cc_final: 0.7016 (mmmt) REVERT: E 48 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5905 (tt) REVERT: E 52 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.6495 (t80) REVERT: E 85 LEU cc_start: 0.4910 (OUTLIER) cc_final: 0.4669 (mt) REVERT: E 137 LYS cc_start: 0.7517 (tptt) cc_final: 0.6880 (mtmt) REVERT: E 240 GLN cc_start: 0.7083 (tt0) cc_final: 0.6875 (tt0) REVERT: E 311 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.8555 (m-10) REVERT: E 332 MET cc_start: 0.5750 (OUTLIER) cc_final: 0.3940 (tmm) REVERT: F 43 PHE cc_start: 0.2343 (OUTLIER) cc_final: 0.1642 (m-10) REVERT: F 271 ARG cc_start: 0.7674 (ttp80) cc_final: 0.7034 (mtp-110) REVERT: F 311 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: F 320 LYS cc_start: 0.7236 (tttm) cc_final: 0.6995 (mmmt) REVERT: G 85 LEU cc_start: 0.4982 (OUTLIER) cc_final: 0.4719 (mt) REVERT: G 137 LYS cc_start: 0.7516 (tptt) cc_final: 0.6897 (mtmt) REVERT: G 259 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6795 (pm20) REVERT: G 311 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8548 (m-10) REVERT: G 332 MET cc_start: 0.5763 (mmp) cc_final: 0.3904 (tmm) REVERT: H 43 PHE cc_start: 0.2042 (OUTLIER) cc_final: 0.1362 (m-10) REVERT: H 311 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: H 320 LYS cc_start: 0.7258 (tttm) cc_final: 0.7001 (mmmt) outliers start: 80 outliers final: 56 residues processed: 231 average time/residue: 0.3321 time to fit residues: 112.1086 Evaluate side-chains 232 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 157 time to evaluate : 1.923 ------------------------------------------------------------------------------- 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 168 VAL 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 A residue 311 TYR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 311 TYR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain D residue 71 MET 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 298 VAL Chi-restraints excluded: chain D residue 311 TYR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 110 MET Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 TYR Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 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 298 VAL Chi-restraints excluded: chain F residue 311 TYR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 TYR Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 311 TYR Chi-restraints excluded: chain H residue 314 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 125 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 194 optimal weight: 0.1980 chunk 77 optimal weight: 0.0770 chunk 119 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 240 GLN C 241 GLN ** G 241 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 = 0.4157 r_free = 0.4157 target = 0.200278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.173197 restraints weight = 19107.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.152566 restraints weight = 35915.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.155129 restraints weight = 23523.421| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 18737 Z= 0.135 Angle : 0.540 8.210 25359 Z= 0.276 Chirality : 0.036 0.226 2771 Planarity : 0.007 0.136 3323 Dihedral : 4.215 33.115 2564 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.72 % Favored : 96.93 % Rotamer: Outliers : 3.82 % Allowed : 23.26 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.20 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.18), residues: 2277 helix: 2.72 (0.13), residues: 1511 sheet: -0.28 (0.38), residues: 208 loop : -1.36 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 202 HIS 0.003 0.001 HIS G 193 PHE 0.012 0.001 PHE D 90 TYR 0.010 0.001 TYR H 127 ARG 0.011 0.000 ARG F 88 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 1290) hydrogen bonds : angle 3.92323 ( 3798) covalent geometry : bond 0.00344 (18737) covalent geometry : angle 0.53987 (25359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5238.23 seconds wall clock time: 92 minutes 32.12 seconds (5552.12 seconds total)