Starting phenix.real_space_refine on Thu Sep 18 05:13:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ktm_62305/09_2025/9ktm_62305_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ktm_62305/09_2025/9ktm_62305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ktm_62305/09_2025/9ktm_62305_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ktm_62305/09_2025/9ktm_62305_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ktm_62305/09_2025/9ktm_62305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ktm_62305/09_2025/9ktm_62305.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 42 5.16 5 C 8890 2.51 5 N 2394 2.21 5 O 2751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14084 Number of models: 1 Model: "" Number of chains: 2 Chain: "G" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1979 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 232} Chain breaks: 3 Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Restraints were copied for chains: A, B, C, D, E, F Time building chain proxies: 2.01, per 1000 atoms: 0.14 Number of scatterers: 14084 At special positions: 0 Unit cell: (110.4, 111.32, 83.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 7 15.00 O 2751 8.00 N 2394 7.00 C 8890 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 616.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 42 sheets defined 7.0% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 205 through 209 Processing helix chain 'G' and resid 217 through 223 removed outlier: 3.563A pdb=" N SER G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 217 through 223 removed outlier: 3.563A pdb=" N SER A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 217 through 223 removed outlier: 3.563A pdb=" N SER B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 217 through 223 removed outlier: 3.563A pdb=" N SER C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 217 through 223 removed outlier: 3.562A pdb=" N SER D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 217 through 223 removed outlier: 3.562A pdb=" N SER E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 217 through 223 removed outlier: 3.562A pdb=" N SER F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'G' and resid 53 through 56 removed outlier: 4.744A pdb=" N LEU G 53 " --> pdb=" O ILE G 232 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE G 232 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL G 231 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 66 through 69 removed outlier: 3.835A pdb=" N ARG G 66 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR G 68 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY G 77 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE G 84 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY G 166 " --> pdb=" O GLU G 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 66 through 69 removed outlier: 3.835A pdb=" N ARG G 66 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR G 68 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY G 77 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP G 254 " --> pdb=" O PRO G 81 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA G 83 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 256 through 257 Processing sheet with id=AA6, first strand: chain 'G' and resid 284 through 285 Processing sheet with id=AA7, first strand: chain 'A' and resid 27 through 28 Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 56 removed outlier: 4.744A pdb=" N LEU A 53 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE A 232 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 231 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 66 through 69 removed outlier: 3.835A pdb=" N ARG A 66 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 68 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY A 77 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 84 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY A 166 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 66 through 69 removed outlier: 3.835A pdb=" N ARG A 66 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 68 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY A 77 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP A 254 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 83 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 256 through 257 Processing sheet with id=AB3, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AB4, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 56 removed outlier: 4.744A pdb=" N LEU B 53 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE B 232 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 231 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 66 through 69 removed outlier: 3.835A pdb=" N ARG B 66 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 68 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLY B 77 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 84 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY B 166 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 66 through 69 removed outlier: 3.835A pdb=" N ARG B 66 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 68 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLY B 77 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP B 254 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 83 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 256 through 257 Processing sheet with id=AB9, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AC1, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 56 removed outlier: 4.744A pdb=" N LEU C 53 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE C 232 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL C 231 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 66 through 69 removed outlier: 3.835A pdb=" N ARG C 66 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 68 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 84 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY C 166 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 66 through 69 removed outlier: 3.835A pdb=" N ARG C 66 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 68 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP C 254 " --> pdb=" O PRO C 81 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 83 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AC6, first strand: chain 'C' and resid 284 through 285 Processing sheet with id=AC7, first strand: chain 'D' and resid 27 through 28 Processing sheet with id=AC8, first strand: chain 'D' and resid 53 through 56 removed outlier: 4.743A pdb=" N LEU D 53 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE D 232 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL D 231 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 66 through 69 removed outlier: 3.834A pdb=" N ARG D 66 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR D 68 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY D 77 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE D 84 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY D 166 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 66 through 69 removed outlier: 3.834A pdb=" N ARG D 66 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR D 68 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY D 77 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP D 254 " --> pdb=" O PRO D 81 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA D 83 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 256 through 257 Processing sheet with id=AD3, first strand: chain 'D' and resid 284 through 285 Processing sheet with id=AD4, first strand: chain 'E' and resid 27 through 28 Processing sheet with id=AD5, first strand: chain 'E' and resid 53 through 56 removed outlier: 4.744A pdb=" N LEU E 53 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE E 232 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL E 231 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 66 through 69 removed outlier: 3.835A pdb=" N ARG E 66 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR E 68 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE E 84 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY E 166 " --> pdb=" O GLU E 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 66 through 69 removed outlier: 3.835A pdb=" N ARG E 66 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR E 68 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP E 254 " --> pdb=" O PRO E 81 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA E 83 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 256 through 257 Processing sheet with id=AD9, first strand: chain 'E' and resid 284 through 285 Processing sheet with id=AE1, first strand: chain 'F' and resid 27 through 28 Processing sheet with id=AE2, first strand: chain 'F' and resid 53 through 56 removed outlier: 4.744A pdb=" N LEU F 53 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE F 232 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL F 231 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 66 through 69 removed outlier: 3.835A pdb=" N ARG F 66 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR F 68 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY F 77 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE F 84 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY F 166 " --> pdb=" O GLU F 158 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 66 through 69 removed outlier: 3.835A pdb=" N ARG F 66 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR F 68 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY F 77 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP F 254 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA F 83 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 256 through 257 Processing sheet with id=AE6, first strand: chain 'F' and resid 284 through 285 203 hydrogen bonds defined for protein. 420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2428 1.32 - 1.44: 3897 1.44 - 1.56: 7962 1.56 - 1.69: 14 1.69 - 1.81: 84 Bond restraints: 14385 Sorted by residual: bond pdb=" C1 P1O C 301 " pdb=" O3 P1O C 301 " ideal model delta sigma weight residual 1.407 1.453 -0.046 2.00e-02 2.50e+03 5.18e+00 bond pdb=" C1 P1O F 301 " pdb=" O3 P1O F 301 " ideal model delta sigma weight residual 1.407 1.453 -0.046 2.00e-02 2.50e+03 5.18e+00 bond pdb=" C1 P1O G 301 " pdb=" O3 P1O G 301 " ideal model delta sigma weight residual 1.407 1.452 -0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" C1 P1O D 301 " pdb=" O3 P1O D 301 " ideal model delta sigma weight residual 1.407 1.452 -0.045 2.00e-02 2.50e+03 5.14e+00 bond pdb=" C1 P1O A 301 " pdb=" O3 P1O A 301 " ideal model delta sigma weight residual 1.407 1.452 -0.045 2.00e-02 2.50e+03 5.13e+00 ... (remaining 14380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 18777 1.94 - 3.87: 550 3.87 - 5.81: 70 5.81 - 7.74: 0 7.74 - 9.68: 7 Bond angle restraints: 19404 Sorted by residual: angle pdb=" N ILE A 5 " pdb=" CA ILE A 5 " pdb=" C ILE A 5 " ideal model delta sigma weight residual 112.83 108.63 4.20 9.90e-01 1.02e+00 1.80e+01 angle pdb=" N ILE F 5 " pdb=" CA ILE F 5 " pdb=" C ILE F 5 " ideal model delta sigma weight residual 112.83 108.68 4.15 9.90e-01 1.02e+00 1.76e+01 angle pdb=" N ILE G 5 " pdb=" CA ILE G 5 " pdb=" C ILE G 5 " ideal model delta sigma weight residual 112.83 108.69 4.14 9.90e-01 1.02e+00 1.75e+01 angle pdb=" N ILE D 5 " pdb=" CA ILE D 5 " pdb=" C ILE D 5 " ideal model delta sigma weight residual 112.83 108.70 4.13 9.90e-01 1.02e+00 1.74e+01 angle pdb=" N ILE C 5 " pdb=" CA ILE C 5 " pdb=" C ILE C 5 " ideal model delta sigma weight residual 112.83 108.71 4.12 9.90e-01 1.02e+00 1.73e+01 ... (remaining 19399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 8360 35.71 - 71.43: 299 71.43 - 107.14: 21 107.14 - 142.85: 0 142.85 - 178.57: 7 Dihedral angle restraints: 8687 sinusoidal: 3724 harmonic: 4963 Sorted by residual: dihedral pdb=" O5 P1O A 301 " pdb=" C7 P1O A 301 " pdb=" C8 P1O A 301 " pdb=" O7 P1O A 301 " ideal model delta sinusoidal sigma weight residual 56.91 -124.52 -178.57 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 P1O B 301 " pdb=" C7 P1O B 301 " pdb=" C8 P1O B 301 " pdb=" O7 P1O B 301 " ideal model delta sinusoidal sigma weight residual 56.91 -124.53 -178.56 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 P1O F 301 " pdb=" C7 P1O F 301 " pdb=" C8 P1O F 301 " pdb=" O7 P1O F 301 " ideal model delta sinusoidal sigma weight residual 56.91 -124.53 -178.56 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 963 0.027 - 0.055: 702 0.055 - 0.082: 152 0.082 - 0.109: 154 0.109 - 0.136: 52 Chirality restraints: 2023 Sorted by residual: chirality pdb=" CA ILE F 284 " pdb=" N ILE F 284 " pdb=" C ILE F 284 " pdb=" CB ILE F 284 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE D 43 " pdb=" N ILE D 43 " pdb=" C ILE D 43 " pdb=" CB ILE D 43 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE G 284 " pdb=" N ILE G 284 " pdb=" C ILE G 284 " pdb=" CB ILE G 284 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 2020 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 159 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO D 160 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO D 160 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 160 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 159 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO B 160 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 159 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 160 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 160 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 160 " 0.017 5.00e-02 4.00e+02 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 182 2.42 - 3.04: 10430 3.04 - 3.66: 21746 3.66 - 4.28: 33274 4.28 - 4.90: 52206 Nonbonded interactions: 117838 Sorted by model distance: nonbonded pdb=" OG1 THR E 22 " pdb=" ND1 HIS F 48 " model vdw 1.801 3.120 nonbonded pdb=" OG1 THR C 22 " pdb=" ND1 HIS D 48 " model vdw 1.804 3.120 nonbonded pdb=" OG1 THR G 22 " pdb=" ND1 HIS A 48 " model vdw 1.805 3.120 nonbonded pdb=" OG1 THR D 22 " pdb=" ND1 HIS E 48 " model vdw 1.824 3.120 nonbonded pdb=" OG1 THR A 22 " pdb=" ND1 HIS B 48 " model vdw 1.835 3.120 ... (remaining 117833 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: 0.05 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.330 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4085 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 : 0.005 0.046 14385 Z= 0.259 Angle : 0.813 9.679 19404 Z= 0.454 Chirality : 0.045 0.136 2023 Planarity : 0.004 0.030 2464 Dihedral : 17.394 178.567 5467 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 39.07 Ramachandran Plot: Outliers : 0.43 % Allowed : 15.02 % Favored : 84.55 % Rotamer: Outliers : 2.73 % Allowed : 11.36 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.34 (0.18), residues: 1638 helix: -3.24 (0.38), residues: 77 sheet: -2.75 (0.21), residues: 469 loop : -3.09 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 253 TYR 0.008 0.002 TYR G 28 PHE 0.011 0.002 PHE A 39 TRP 0.010 0.001 TRP G 80 HIS 0.006 0.002 HIS G 259 Details of bonding type rmsd covalent geometry : bond 0.00505 (14385) covalent geometry : angle 0.81271 (19404) hydrogen bonds : bond 0.33399 ( 196) hydrogen bonds : angle 16.73221 ( 420) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 390 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 176 ASN cc_start: 0.5449 (t0) cc_final: 0.4945 (t0) REVERT: G 271 LYS cc_start: 0.5158 (mtmm) cc_final: 0.4747 (mmtt) REVERT: A 176 ASN cc_start: 0.4759 (t0) cc_final: 0.4439 (t0) REVERT: A 271 LYS cc_start: 0.5035 (mtmm) cc_final: 0.4576 (tptt) REVERT: B 271 LYS cc_start: 0.5006 (mtmm) cc_final: 0.4543 (tptt) REVERT: C 271 LYS cc_start: 0.5270 (mtmm) cc_final: 0.4942 (ttmt) REVERT: D 30 LYS cc_start: 0.5546 (mppt) cc_final: 0.5332 (mptt) REVERT: D 176 ASN cc_start: 0.5134 (t0) cc_final: 0.4549 (t0) REVERT: D 271 LYS cc_start: 0.5017 (mtmm) cc_final: 0.4653 (mmtt) REVERT: E 176 ASN cc_start: 0.4943 (t0) cc_final: 0.4700 (t0) REVERT: E 271 LYS cc_start: 0.5113 (mtmm) cc_final: 0.4739 (mmtt) REVERT: F 176 ASN cc_start: 0.4758 (t0) cc_final: 0.4367 (t0) REVERT: F 271 LYS cc_start: 0.5289 (mtmm) cc_final: 0.4880 (mmtt) outliers start: 42 outliers final: 13 residues processed: 418 average time/residue: 0.5983 time to fit residues: 275.0562 Evaluate side-chains 257 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 244 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 268 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 32 ASN G 35 HIS G 97 GLN G 173 ASN ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN B 173 ASN ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN C 173 ASN C 209 ASN C 259 HIS D 35 HIS D 97 GLN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS E 97 GLN E 173 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5139 r_free = 0.5139 target = 0.300683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5043 r_free = 0.5043 target = 0.288062 restraints weight = 19321.921| |-----------------------------------------------------------------------------| r_work (start): 0.5053 rms_B_bonded: 1.65 r_work: 0.4981 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work (final): 0.4981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4429 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14385 Z= 0.185 Angle : 0.786 10.318 19404 Z= 0.422 Chirality : 0.049 0.173 2023 Planarity : 0.005 0.060 2464 Dihedral : 15.597 169.214 2030 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.83 % Favored : 89.38 % Rotamer: Outliers : 7.34 % Allowed : 16.62 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.97 (0.18), residues: 1638 helix: -4.04 (0.18), residues: 77 sheet: -2.18 (0.23), residues: 434 loop : -2.90 (0.16), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 253 TYR 0.026 0.002 TYR E 65 PHE 0.016 0.002 PHE E 84 TRP 0.031 0.002 TRP F 80 HIS 0.003 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00389 (14385) covalent geometry : angle 0.78625 (19404) hydrogen bonds : bond 0.03944 ( 196) hydrogen bonds : angle 10.67657 ( 420) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 284 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 237 LYS cc_start: 0.5062 (OUTLIER) cc_final: 0.3643 (tmmt) REVERT: B 291 MET cc_start: 0.2780 (OUTLIER) cc_final: 0.2308 (mtp) REVERT: D 28 TYR cc_start: 0.5436 (t80) cc_final: 0.3521 (p90) REVERT: E 28 TYR cc_start: 0.5125 (t80) cc_final: 0.3711 (p90) REVERT: F 171 PHE cc_start: 0.3448 (t80) cc_final: 0.3235 (t80) outliers start: 113 outliers final: 43 residues processed: 355 average time/residue: 0.4728 time to fit residues: 188.9673 Evaluate side-chains 256 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 272 ASP Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 291 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 130 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 97 GLN G 269 ASN ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 HIS ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN C 35 HIS C 97 GLN C 269 ASN D 97 GLN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 ASN ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 HIS F 97 GLN F 173 ASN F 176 ASN F 269 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.301938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.290164 restraints weight = 19667.641| |-----------------------------------------------------------------------------| r_work (start): 0.5031 rms_B_bonded: 1.52 r_work: 0.4965 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4854 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4631 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14385 Z= 0.176 Angle : 0.743 10.374 19404 Z= 0.397 Chirality : 0.048 0.167 2023 Planarity : 0.005 0.050 2464 Dihedral : 15.005 170.476 2027 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.81 % Favored : 88.71 % Rotamer: Outliers : 6.62 % Allowed : 21.43 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.74 (0.18), residues: 1638 helix: -3.89 (0.21), residues: 77 sheet: -2.29 (0.20), residues: 567 loop : -2.55 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 251 TYR 0.027 0.003 TYR C 65 PHE 0.013 0.002 PHE G 210 TRP 0.052 0.002 TRP F 80 HIS 0.004 0.002 HIS G 259 Details of bonding type rmsd covalent geometry : bond 0.00396 (14385) covalent geometry : angle 0.74339 (19404) hydrogen bonds : bond 0.03690 ( 196) hydrogen bonds : angle 9.71336 ( 420) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 226 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: G 282 TYR cc_start: 0.3486 (OUTLIER) cc_final: 0.2711 (m-80) REVERT: G 291 MET cc_start: 0.3104 (OUTLIER) cc_final: 0.2849 (ttt) REVERT: A 209 ASN cc_start: 0.2903 (t0) cc_final: 0.2665 (m-40) REVERT: A 234 MET cc_start: 0.2914 (OUTLIER) cc_final: 0.1758 (tpp) REVERT: A 291 MET cc_start: 0.3174 (mtp) cc_final: 0.2409 (mtp) REVERT: B 237 LYS cc_start: 0.4769 (OUTLIER) cc_final: 0.3641 (tmmt) REVERT: B 291 MET cc_start: 0.2794 (ttp) cc_final: 0.2522 (ttt) REVERT: C 234 MET cc_start: 0.2940 (OUTLIER) cc_final: 0.1667 (tpp) REVERT: E 30 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.5486 (mptt) REVERT: E 282 TYR cc_start: 0.3549 (OUTLIER) cc_final: 0.2904 (m-80) REVERT: E 291 MET cc_start: 0.2714 (OUTLIER) cc_final: 0.2242 (mtp) REVERT: F 169 VAL cc_start: 0.7546 (OUTLIER) cc_final: 0.7323 (p) REVERT: F 234 MET cc_start: 0.2837 (OUTLIER) cc_final: 0.1432 (mtm) outliers start: 102 outliers final: 51 residues processed: 288 average time/residue: 0.4194 time to fit residues: 138.4404 Evaluate side-chains 253 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 192 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 282 TYR Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 291 MET Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 237 LYS Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 284 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 73 optimal weight: 1.9990 chunk 153 optimal weight: 0.0770 chunk 106 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 chunk 125 optimal weight: 0.0010 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 HIS ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.301075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.289295 restraints weight = 19860.888| |-----------------------------------------------------------------------------| r_work (start): 0.5045 rms_B_bonded: 1.58 r_work: 0.4979 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4868 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4544 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14385 Z= 0.137 Angle : 0.670 10.139 19404 Z= 0.359 Chirality : 0.046 0.167 2023 Planarity : 0.004 0.044 2464 Dihedral : 14.572 171.589 2026 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.85 % Favored : 90.72 % Rotamer: Outliers : 5.32 % Allowed : 26.95 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (0.18), residues: 1638 helix: -3.69 (0.24), residues: 77 sheet: -1.92 (0.21), residues: 532 loop : -2.54 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.018 0.002 TYR F 40 PHE 0.010 0.002 PHE G 210 TRP 0.053 0.002 TRP E 80 HIS 0.004 0.001 HIS G 259 Details of bonding type rmsd covalent geometry : bond 0.00301 (14385) covalent geometry : angle 0.67005 (19404) hydrogen bonds : bond 0.03233 ( 196) hydrogen bonds : angle 8.75756 ( 420) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 210 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: G 171 PHE cc_start: 0.3658 (t80) cc_final: 0.3417 (t80) REVERT: G 266 LYS cc_start: 0.5404 (OUTLIER) cc_final: 0.4607 (tptp) REVERT: G 282 TYR cc_start: 0.3505 (OUTLIER) cc_final: 0.2708 (m-80) REVERT: A 234 MET cc_start: 0.3071 (mmp) cc_final: 0.1769 (tpp) REVERT: A 272 ASP cc_start: 0.3706 (m-30) cc_final: 0.3367 (m-30) REVERT: B 237 LYS cc_start: 0.4558 (OUTLIER) cc_final: 0.3490 (tmmt) REVERT: B 291 MET cc_start: 0.2548 (ttp) cc_final: 0.2319 (ttt) REVERT: C 50 LYS cc_start: 0.5502 (OUTLIER) cc_final: 0.5267 (mptt) REVERT: C 234 MET cc_start: 0.2967 (mmp) cc_final: 0.1599 (tpp) REVERT: D 30 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.5245 (mmpt) REVERT: D 266 LYS cc_start: 0.4679 (tptt) cc_final: 0.3907 (tptp) REVERT: D 291 MET cc_start: 0.2167 (ttt) cc_final: 0.1811 (mtp) REVERT: E 30 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.5555 (mptt) REVERT: E 291 MET cc_start: 0.2603 (OUTLIER) cc_final: 0.1844 (mpt) outliers start: 82 outliers final: 39 residues processed: 262 average time/residue: 0.4251 time to fit residues: 127.2624 Evaluate side-chains 232 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 266 LYS Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 282 TYR Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 177 GLN Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 284 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 120 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 93 optimal weight: 0.0870 chunk 130 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 141 optimal weight: 0.0030 chunk 151 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 176 ASN ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 HIS ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 HIS C 177 GLN C 193 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN F 97 GLN F 177 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.292709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.280809 restraints weight = 19992.704| |-----------------------------------------------------------------------------| r_work (start): 0.4989 rms_B_bonded: 1.58 r_work: 0.4921 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4808 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4863 moved from start: 0.6883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14385 Z= 0.193 Angle : 0.764 10.427 19404 Z= 0.408 Chirality : 0.048 0.162 2023 Planarity : 0.005 0.045 2464 Dihedral : 14.489 171.732 2023 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.84 % Favored : 87.73 % Rotamer: Outliers : 6.23 % Allowed : 29.61 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.62 (0.18), residues: 1638 helix: -3.12 (0.35), residues: 77 sheet: -2.34 (0.22), residues: 497 loop : -2.49 (0.16), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 251 TYR 0.015 0.002 TYR E 65 PHE 0.017 0.003 PHE F 42 TRP 0.075 0.003 TRP B 80 HIS 0.005 0.002 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00435 (14385) covalent geometry : angle 0.76433 (19404) hydrogen bonds : bond 0.03223 ( 196) hydrogen bonds : angle 9.29838 ( 420) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 225 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: G 197 MET cc_start: 0.4720 (pmm) cc_final: 0.4354 (pmm) REVERT: G 266 LYS cc_start: 0.5510 (OUTLIER) cc_final: 0.4633 (tptp) REVERT: G 282 TYR cc_start: 0.4122 (OUTLIER) cc_final: 0.3909 (m-10) REVERT: A 81 PRO cc_start: 0.7785 (Cg_endo) cc_final: 0.7460 (Cg_exo) REVERT: A 234 MET cc_start: 0.2971 (mmp) cc_final: 0.2055 (tpp) REVERT: A 266 LYS cc_start: 0.4693 (tptt) cc_final: 0.3882 (tptp) REVERT: B 110 LYS cc_start: 0.5513 (tptt) cc_final: 0.4649 (tptp) REVERT: B 237 LYS cc_start: 0.4676 (OUTLIER) cc_final: 0.3482 (tmmt) REVERT: B 266 LYS cc_start: 0.4764 (tptt) cc_final: 0.3855 (tptp) REVERT: B 282 TYR cc_start: 0.3957 (OUTLIER) cc_final: 0.3220 (m-80) REVERT: B 291 MET cc_start: 0.2707 (ttp) cc_final: 0.2417 (ttt) REVERT: C 50 LYS cc_start: 0.5501 (OUTLIER) cc_final: 0.5286 (mptt) REVERT: C 197 MET cc_start: 0.4472 (tmm) cc_final: 0.3314 (ttp) REVERT: C 234 MET cc_start: 0.2904 (mmp) cc_final: 0.1710 (tpp) REVERT: C 266 LYS cc_start: 0.5175 (tptm) cc_final: 0.4410 (tptp) REVERT: D 30 LYS cc_start: 0.6460 (OUTLIER) cc_final: 0.5468 (mmpt) REVERT: D 234 MET cc_start: 0.2592 (mmp) cc_final: 0.1594 (tpt) REVERT: D 266 LYS cc_start: 0.4620 (tptt) cc_final: 0.3794 (tptp) REVERT: D 274 TRP cc_start: 0.4248 (OUTLIER) cc_final: 0.2982 (m100) REVERT: E 30 LYS cc_start: 0.6950 (mmtm) cc_final: 0.5786 (mptt) REVERT: E 274 TRP cc_start: 0.4298 (OUTLIER) cc_final: 0.3283 (m100) REVERT: E 291 MET cc_start: 0.2803 (OUTLIER) cc_final: 0.2083 (mpt) REVERT: F 171 PHE cc_start: 0.5004 (t80) cc_final: 0.4432 (t80) REVERT: F 282 TYR cc_start: 0.3999 (OUTLIER) cc_final: 0.3209 (m-80) outliers start: 96 outliers final: 46 residues processed: 282 average time/residue: 0.4393 time to fit residues: 141.1157 Evaluate side-chains 259 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 203 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 266 LYS Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 282 TYR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 274 TRP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 274 TRP Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 282 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 63 optimal weight: 0.0060 chunk 152 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 154 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 ASN A 48 HIS ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 209 ASN C 177 GLN D 173 ASN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5092 r_free = 0.5092 target = 0.293930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4998 r_free = 0.4998 target = 0.282183 restraints weight = 19989.898| |-----------------------------------------------------------------------------| r_work (start): 0.5012 rms_B_bonded: 1.56 r_work: 0.4943 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4834 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4833 moved from start: 0.7379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14385 Z= 0.163 Angle : 0.727 10.151 19404 Z= 0.387 Chirality : 0.047 0.159 2023 Planarity : 0.004 0.057 2464 Dihedral : 14.210 170.410 2023 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.89 % Favored : 89.68 % Rotamer: Outliers : 5.91 % Allowed : 30.91 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.47 (0.18), residues: 1638 helix: -3.00 (0.37), residues: 77 sheet: -1.92 (0.21), residues: 595 loop : -2.56 (0.16), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 251 TYR 0.014 0.002 TYR C 65 PHE 0.019 0.002 PHE D 171 TRP 0.080 0.002 TRP D 80 HIS 0.006 0.002 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00363 (14385) covalent geometry : angle 0.72738 (19404) hydrogen bonds : bond 0.02840 ( 196) hydrogen bonds : angle 8.86859 ( 420) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 220 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 197 MET cc_start: 0.4551 (OUTLIER) cc_final: 0.4330 (pmm) REVERT: G 266 LYS cc_start: 0.5612 (OUTLIER) cc_final: 0.4533 (tptp) REVERT: G 272 ASP cc_start: 0.4141 (m-30) cc_final: 0.3688 (m-30) REVERT: G 282 TYR cc_start: 0.4264 (OUTLIER) cc_final: 0.4057 (m-10) REVERT: A 171 PHE cc_start: 0.4698 (t80) cc_final: 0.4420 (t80) REVERT: A 234 MET cc_start: 0.2643 (OUTLIER) cc_final: 0.2002 (tpp) REVERT: A 266 LYS cc_start: 0.4743 (tptt) cc_final: 0.3850 (tptp) REVERT: B 237 LYS cc_start: 0.4240 (OUTLIER) cc_final: 0.3173 (tmmt) REVERT: B 266 LYS cc_start: 0.4813 (tptt) cc_final: 0.4029 (tptp) REVERT: B 282 TYR cc_start: 0.3951 (OUTLIER) cc_final: 0.3740 (m-10) REVERT: C 234 MET cc_start: 0.3119 (OUTLIER) cc_final: 0.1997 (tpp) REVERT: C 266 LYS cc_start: 0.5127 (tptm) cc_final: 0.4389 (tptp) REVERT: D 30 LYS cc_start: 0.6560 (OUTLIER) cc_final: 0.5494 (mmpt) REVERT: D 266 LYS cc_start: 0.4750 (tptt) cc_final: 0.4003 (tptp) REVERT: E 30 LYS cc_start: 0.6900 (mmtm) cc_final: 0.5764 (mptt) REVERT: F 234 MET cc_start: 0.2302 (mmp) cc_final: 0.1598 (tpp) REVERT: F 266 LYS cc_start: 0.5329 (tptt) cc_final: 0.3943 (tptp) REVERT: F 272 ASP cc_start: 0.3959 (m-30) cc_final: 0.3691 (m-30) outliers start: 91 outliers final: 56 residues processed: 273 average time/residue: 0.3734 time to fit residues: 118.3590 Evaluate side-chains 257 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 193 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 266 LYS Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 282 TYR Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 193 ASN Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 270 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 149 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 HIS ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 HIS ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN C 193 ASN D 48 HIS ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 ASN F 176 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5081 r_free = 0.5081 target = 0.292117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.280802 restraints weight = 19785.259| |-----------------------------------------------------------------------------| r_work (start): 0.4991 rms_B_bonded: 1.50 r_work: 0.4925 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4820 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4872 moved from start: 0.7740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14385 Z= 0.167 Angle : 0.738 11.288 19404 Z= 0.393 Chirality : 0.047 0.178 2023 Planarity : 0.005 0.053 2464 Dihedral : 14.103 170.197 2023 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.84 % Favored : 87.67 % Rotamer: Outliers : 6.75 % Allowed : 32.01 % Favored : 61.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.43 (0.18), residues: 1638 helix: -2.93 (0.37), residues: 77 sheet: -1.82 (0.21), residues: 595 loop : -2.60 (0.16), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 200 TYR 0.014 0.002 TYR C 182 PHE 0.014 0.002 PHE C 42 TRP 0.095 0.003 TRP B 80 HIS 0.008 0.002 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00380 (14385) covalent geometry : angle 0.73787 (19404) hydrogen bonds : bond 0.02801 ( 196) hydrogen bonds : angle 8.89045 ( 420) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 204 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 48 HIS cc_start: 0.2558 (OUTLIER) cc_final: 0.2248 (t-170) REVERT: G 266 LYS cc_start: 0.5756 (OUTLIER) cc_final: 0.4665 (tptp) REVERT: G 272 ASP cc_start: 0.4211 (m-30) cc_final: 0.3814 (m-30) REVERT: G 282 TYR cc_start: 0.4653 (OUTLIER) cc_final: 0.4378 (m-10) REVERT: A 48 HIS cc_start: 0.2560 (OUTLIER) cc_final: 0.2287 (t-170) REVERT: A 234 MET cc_start: 0.2718 (OUTLIER) cc_final: 0.2128 (tpp) REVERT: A 266 LYS cc_start: 0.4954 (tptt) cc_final: 0.3924 (tptp) REVERT: B 266 LYS cc_start: 0.4885 (tptt) cc_final: 0.4073 (tptp) REVERT: B 272 ASP cc_start: 0.4142 (m-30) cc_final: 0.3755 (m-30) REVERT: B 282 TYR cc_start: 0.4059 (OUTLIER) cc_final: 0.3852 (m-10) REVERT: C 197 MET cc_start: 0.4115 (tmm) cc_final: 0.3759 (pmt) REVERT: C 234 MET cc_start: 0.3063 (OUTLIER) cc_final: 0.2223 (tpp) REVERT: C 266 LYS cc_start: 0.5187 (tptm) cc_final: 0.4516 (tptt) REVERT: D 30 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.5424 (mmpt) REVERT: D 48 HIS cc_start: 0.2710 (OUTLIER) cc_final: 0.2476 (t-170) REVERT: D 110 LYS cc_start: 0.5185 (tptp) cc_final: 0.4477 (tptt) REVERT: D 266 LYS cc_start: 0.4844 (tptt) cc_final: 0.4075 (tptp) REVERT: E 30 LYS cc_start: 0.7012 (mmtm) cc_final: 0.5834 (mptt) REVERT: E 266 LYS cc_start: 0.5366 (mtpt) cc_final: 0.4394 (tmtt) REVERT: F 95 VAL cc_start: 0.5991 (OUTLIER) cc_final: 0.5604 (t) REVERT: F 110 LYS cc_start: 0.5486 (tptt) cc_final: 0.5175 (tptp) REVERT: F 234 MET cc_start: 0.2394 (mmp) cc_final: 0.1989 (tpp) REVERT: F 266 LYS cc_start: 0.5390 (tptt) cc_final: 0.4234 (tptp) REVERT: F 272 ASP cc_start: 0.4195 (m-30) cc_final: 0.3875 (m-30) outliers start: 104 outliers final: 55 residues processed: 276 average time/residue: 0.3867 time to fit residues: 123.4517 Evaluate side-chains 252 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 266 LYS Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 282 TYR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 48 HIS Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 193 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 193 ASN Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 270 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 158 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 HIS G 209 ASN G 269 ASN ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN A 259 HIS B 269 ASN C 177 GLN C 193 ASN C 269 ASN D 48 HIS D 269 ASN ** E 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN F 259 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.286678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.275811 restraints weight = 19724.195| |-----------------------------------------------------------------------------| r_work (start): 0.4948 rms_B_bonded: 1.50 r_work: 0.4885 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4781 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5098 moved from start: 0.8253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14385 Z= 0.247 Angle : 0.880 13.378 19404 Z= 0.469 Chirality : 0.051 0.208 2023 Planarity : 0.006 0.054 2464 Dihedral : 14.526 171.110 2023 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.61 % Allowed : 14.16 % Favored : 85.23 % Rotamer: Outliers : 6.62 % Allowed : 32.60 % Favored : 60.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.62 (0.18), residues: 1638 helix: -3.25 (0.32), residues: 77 sheet: -1.78 (0.21), residues: 623 loop : -2.86 (0.16), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 251 TYR 0.022 0.003 TYR C 191 PHE 0.020 0.004 PHE D 42 TRP 0.115 0.004 TRP D 80 HIS 0.013 0.003 HIS D 48 Details of bonding type rmsd covalent geometry : bond 0.00554 (14385) covalent geometry : angle 0.87985 (19404) hydrogen bonds : bond 0.03135 ( 196) hydrogen bonds : angle 9.58014 ( 420) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 242 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 30 LYS cc_start: 0.4664 (mptt) cc_final: 0.4404 (mppt) REVERT: G 194 GLN cc_start: 0.5052 (OUTLIER) cc_final: 0.4791 (mp10) REVERT: A 234 MET cc_start: 0.2825 (mmp) cc_final: 0.2307 (ptp) REVERT: A 266 LYS cc_start: 0.4804 (tptt) cc_final: 0.3945 (tptp) REVERT: B 110 LYS cc_start: 0.5285 (tptt) cc_final: 0.4667 (tptp) REVERT: B 266 LYS cc_start: 0.4862 (tptt) cc_final: 0.4088 (tptp) REVERT: B 282 TYR cc_start: 0.4628 (OUTLIER) cc_final: 0.4394 (m-10) REVERT: C 110 LYS cc_start: 0.4949 (tptt) cc_final: 0.4659 (tptp) REVERT: C 197 MET cc_start: 0.3945 (tmm) cc_final: 0.3360 (mtm) REVERT: C 234 MET cc_start: 0.3075 (mmp) cc_final: 0.2170 (tpp) REVERT: C 266 LYS cc_start: 0.5041 (tptm) cc_final: 0.4333 (tptp) REVERT: C 272 ASP cc_start: 0.4666 (m-30) cc_final: 0.4421 (m-30) REVERT: D 30 LYS cc_start: 0.6556 (OUTLIER) cc_final: 0.5686 (mptt) REVERT: D 40 TYR cc_start: 0.4721 (OUTLIER) cc_final: 0.4214 (p90) REVERT: D 266 LYS cc_start: 0.5133 (tptt) cc_final: 0.4393 (tptp) REVERT: E 30 LYS cc_start: 0.7083 (mmtm) cc_final: 0.5497 (mmpt) REVERT: E 110 LYS cc_start: 0.5369 (tmtt) cc_final: 0.4717 (tptp) REVERT: E 266 LYS cc_start: 0.5519 (mtpt) cc_final: 0.4303 (tmtt) REVERT: F 110 LYS cc_start: 0.5618 (tptt) cc_final: 0.5326 (tptp) REVERT: F 154 LYS cc_start: 0.7426 (pmtt) cc_final: 0.6981 (tttt) REVERT: F 234 MET cc_start: 0.2438 (mmp) cc_final: 0.1479 (mmp) REVERT: F 266 LYS cc_start: 0.5425 (tptt) cc_final: 0.4282 (tptp) outliers start: 102 outliers final: 62 residues processed: 310 average time/residue: 0.4316 time to fit residues: 152.4698 Evaluate side-chains 283 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 217 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 193 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 272 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 31 optimal weight: 0.0030 chunk 12 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 ASN A 48 HIS ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 269 ASN E 193 ASN F 193 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5075 r_free = 0.5075 target = 0.290866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.280126 restraints weight = 19690.251| |-----------------------------------------------------------------------------| r_work (start): 0.4991 rms_B_bonded: 1.52 r_work: 0.4926 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4821 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.4821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4871 moved from start: 0.8650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14385 Z= 0.145 Angle : 0.746 13.776 19404 Z= 0.388 Chirality : 0.046 0.217 2023 Planarity : 0.004 0.043 2464 Dihedral : 14.097 169.860 2023 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.42 % Favored : 90.84 % Rotamer: Outliers : 5.52 % Allowed : 35.32 % Favored : 59.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.48 (0.18), residues: 1638 helix: -3.20 (0.32), residues: 77 sheet: -1.87 (0.20), residues: 595 loop : -2.60 (0.16), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 251 TYR 0.018 0.002 TYR C 182 PHE 0.023 0.002 PHE G 42 TRP 0.098 0.003 TRP D 80 HIS 0.005 0.001 HIS C 48 Details of bonding type rmsd covalent geometry : bond 0.00323 (14385) covalent geometry : angle 0.74583 (19404) hydrogen bonds : bond 0.02767 ( 196) hydrogen bonds : angle 8.56827 ( 420) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 223 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 48 HIS cc_start: 0.2793 (OUTLIER) cc_final: 0.2155 (t70) REVERT: G 266 LYS cc_start: 0.5293 (OUTLIER) cc_final: 0.4691 (tptp) REVERT: A 234 MET cc_start: 0.2598 (OUTLIER) cc_final: 0.2352 (tpp) REVERT: A 266 LYS cc_start: 0.4597 (tptt) cc_final: 0.3624 (tptp) REVERT: B 40 TYR cc_start: 0.4110 (p90) cc_final: 0.3878 (p90) REVERT: B 266 LYS cc_start: 0.4716 (tptt) cc_final: 0.3765 (tptt) REVERT: B 272 ASP cc_start: 0.4855 (m-30) cc_final: 0.4405 (m-30) REVERT: C 110 LYS cc_start: 0.4722 (tptt) cc_final: 0.4284 (tptp) REVERT: C 234 MET cc_start: 0.2707 (OUTLIER) cc_final: 0.2189 (tpp) REVERT: C 266 LYS cc_start: 0.5046 (tptm) cc_final: 0.4274 (tptp) REVERT: D 30 LYS cc_start: 0.6390 (OUTLIER) cc_final: 0.5355 (mmpt) REVERT: D 110 LYS cc_start: 0.5850 (tptp) cc_final: 0.5427 (tptp) REVERT: D 204 MET cc_start: 0.3823 (pmm) cc_final: 0.3471 (pmm) REVERT: D 266 LYS cc_start: 0.5140 (tptt) cc_final: 0.3869 (tptp) REVERT: D 272 ASP cc_start: 0.4417 (m-30) cc_final: 0.4190 (m-30) REVERT: E 30 LYS cc_start: 0.6972 (mmtm) cc_final: 0.5394 (mmpt) REVERT: E 110 LYS cc_start: 0.5293 (tmtt) cc_final: 0.4946 (tptp) REVERT: E 266 LYS cc_start: 0.5170 (mtpt) cc_final: 0.4171 (tmtt) REVERT: E 272 ASP cc_start: 0.4853 (m-30) cc_final: 0.4528 (m-30) REVERT: F 110 LYS cc_start: 0.5220 (tptt) cc_final: 0.4955 (tptp) REVERT: F 266 LYS cc_start: 0.5299 (tptt) cc_final: 0.4189 (tptp) outliers start: 85 outliers final: 64 residues processed: 282 average time/residue: 0.3950 time to fit residues: 128.6205 Evaluate side-chains 271 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 202 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 266 LYS Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 193 ASN Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 272 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 102 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS C 193 ASN C 269 ASN F 193 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5070 r_free = 0.5070 target = 0.290301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.279736 restraints weight = 19764.855| |-----------------------------------------------------------------------------| r_work (start): 0.4986 rms_B_bonded: 1.50 r_work: 0.4924 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4821 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.4821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4911 moved from start: 0.8867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14385 Z= 0.155 Angle : 0.759 14.720 19404 Z= 0.393 Chirality : 0.046 0.243 2023 Planarity : 0.005 0.050 2464 Dihedral : 13.966 169.479 2023 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.79 % Allowed : 10.01 % Favored : 89.19 % Rotamer: Outliers : 4.94 % Allowed : 36.30 % Favored : 58.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.42 (0.18), residues: 1638 helix: -3.07 (0.35), residues: 77 sheet: -1.80 (0.20), residues: 623 loop : -2.60 (0.17), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 251 TYR 0.017 0.002 TYR F 68 PHE 0.020 0.002 PHE C 228 TRP 0.105 0.003 TRP E 80 HIS 0.006 0.002 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00350 (14385) covalent geometry : angle 0.75869 (19404) hydrogen bonds : bond 0.02656 ( 196) hydrogen bonds : angle 8.54781 ( 420) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 212 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 48 HIS cc_start: 0.2844 (OUTLIER) cc_final: 0.2173 (t70) REVERT: G 266 LYS cc_start: 0.5382 (OUTLIER) cc_final: 0.4730 (tptp) REVERT: A 234 MET cc_start: 0.2567 (OUTLIER) cc_final: 0.2211 (tpp) REVERT: A 266 LYS cc_start: 0.4631 (tptt) cc_final: 0.3684 (tptt) REVERT: B 40 TYR cc_start: 0.3890 (p90) cc_final: 0.3676 (p90) REVERT: B 266 LYS cc_start: 0.4793 (tptt) cc_final: 0.3838 (tptt) REVERT: C 110 LYS cc_start: 0.5151 (tptt) cc_final: 0.4473 (tptp) REVERT: C 169 VAL cc_start: 0.7311 (OUTLIER) cc_final: 0.7086 (p) REVERT: C 234 MET cc_start: 0.2764 (OUTLIER) cc_final: 0.2179 (tpp) REVERT: C 266 LYS cc_start: 0.5018 (tptm) cc_final: 0.4176 (tptp) REVERT: D 30 LYS cc_start: 0.6334 (OUTLIER) cc_final: 0.5428 (mptt) REVERT: D 204 MET cc_start: 0.4072 (pmm) cc_final: 0.3710 (pmm) REVERT: D 266 LYS cc_start: 0.4992 (tptt) cc_final: 0.3708 (tptp) REVERT: E 30 LYS cc_start: 0.6942 (mmtm) cc_final: 0.5418 (mmpt) REVERT: E 110 LYS cc_start: 0.5247 (tmtt) cc_final: 0.4980 (tptp) REVERT: E 266 LYS cc_start: 0.5252 (mtpt) cc_final: 0.4372 (tmtt) REVERT: E 272 ASP cc_start: 0.4692 (m-30) cc_final: 0.4424 (m-30) REVERT: F 110 LYS cc_start: 0.5438 (tptt) cc_final: 0.5084 (tptp) REVERT: F 266 LYS cc_start: 0.5328 (tptt) cc_final: 0.3737 (tptt) outliers start: 76 outliers final: 60 residues processed: 265 average time/residue: 0.3849 time to fit residues: 118.2016 Evaluate side-chains 266 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 200 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 9 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 101 TYR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 266 LYS Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 48 HIS Chi-restraints excluded: chain F residue 101 TYR Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 270 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 21 optimal weight: 0.0370 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 117 optimal weight: 0.0770 chunk 81 optimal weight: 0.3980 chunk 165 optimal weight: 3.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS F 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.292970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.282500 restraints weight = 19729.183| |-----------------------------------------------------------------------------| r_work (start): 0.5007 rms_B_bonded: 1.49 r_work: 0.4944 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4840 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4809 moved from start: 0.9050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14385 Z= 0.133 Angle : 0.728 12.517 19404 Z= 0.377 Chirality : 0.046 0.240 2023 Planarity : 0.004 0.044 2464 Dihedral : 13.812 169.025 2023 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.57 % Favored : 91.58 % Rotamer: Outliers : 4.94 % Allowed : 36.69 % Favored : 58.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.45 (0.18), residues: 1638 helix: -3.04 (0.36), residues: 77 sheet: -1.96 (0.20), residues: 595 loop : -2.50 (0.17), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 251 TYR 0.017 0.002 TYR E 65 PHE 0.023 0.002 PHE C 228 TRP 0.098 0.003 TRP E 80 HIS 0.008 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00299 (14385) covalent geometry : angle 0.72847 (19404) hydrogen bonds : bond 0.02601 ( 196) hydrogen bonds : angle 8.23275 ( 420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5402.92 seconds wall clock time: 93 minutes 24.81 seconds (5604.81 seconds total)