Starting phenix.real_space_refine on Tue Aug 4 12:09:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pd7_71528/08_2026/9pd7_71528.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pd7_71528/08_2026/9pd7_71528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pd7_71528/08_2026/9pd7_71528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pd7_71528/08_2026/9pd7_71528.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pd7_71528/08_2026/9pd7_71528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pd7_71528/08_2026/9pd7_71528.map" } resolution = 3.4 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= 0.002 sd= 0.028 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: 3 Type Number sf(0) Gaussians C 1767 2.51 5 N 341 2.21 5 O 341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2449 Number of models: 1 Model: "" Number of chains: 62 Chain: "N" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.85, per 1000 atoms: 0.35 Number of scatterers: 2449 At special positions: 0 Unit cell: (54.78, 82.17, 66.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 341 8.00 N 341 7.00 C 1767 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=31, symmetry=0 Number of additional bonds: simple=31, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.15 Conformation dependent library (CDL) restraints added in 62.8 milliseconds 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 434 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'N' and resid 2 through 6 removed outlier: 3.591A pdb=" N GLY R 4 " --> pdb=" O PHE O 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY Y 4 " --> pdb=" O PHE S 3 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N LYS g 6 " --> pdb=" O PHE Z 3 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE Z 5 " --> pdb=" O LYS g 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 5 through 6 removed outlier: 7.752A pdb=" N PHE Q 5 " --> pdb=" O LYS T 6 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE T 5 " --> pdb=" O LYS U 6 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE U 5 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE a 5 " --> pdb=" O LYS b 6 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N PHE b 5 " --> pdb=" O LYS i 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 24 hydrogen bonds defined for protein. 72 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: 0.29 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 248 1.26 - 1.33: 102 1.33 - 1.40: 952 1.40 - 1.47: 279 1.47 - 1.54: 930 Bond restraints: 2511 Sorted by residual: bond pdb=" C ACE Q 0 " pdb=" N PHE Q 1 " ideal model delta sigma weight residual 1.329 1.464 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C ACE G 0 " pdb=" N PHE G 1 " ideal model delta sigma weight residual 1.329 1.464 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" C ACE j 0 " pdb=" N PHE j 1 " ideal model delta sigma weight residual 1.329 1.464 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C ACE U 0 " pdb=" N PHE U 1 " ideal model delta sigma weight residual 1.329 1.464 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C ACE b 0 " pdb=" N PHE b 1 " ideal model delta sigma weight residual 1.329 1.463 -0.134 2.00e-02 2.50e+03 4.52e+01 ... (remaining 2506 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 2901 1.58 - 3.17: 188 3.17 - 4.75: 65 4.75 - 6.33: 46 6.33 - 7.92: 24 Bond angle restraints: 3224 Sorted by residual: angle pdb=" CA PHE R 1 " pdb=" CB PHE R 1 " pdb=" CG PHE R 1 " ideal model delta sigma weight residual 113.80 108.66 5.14 1.00e+00 1.00e+00 2.64e+01 angle pdb=" CA PHE g 1 " pdb=" CB PHE g 1 " pdb=" CG PHE g 1 " ideal model delta sigma weight residual 113.80 108.87 4.93 1.00e+00 1.00e+00 2.43e+01 angle pdb=" CA PHE Y 1 " pdb=" CB PHE Y 1 " pdb=" CG PHE Y 1 " ideal model delta sigma weight residual 113.80 108.88 4.92 1.00e+00 1.00e+00 2.42e+01 angle pdb=" CA PHE V 1 " pdb=" CB PHE V 1 " pdb=" CG PHE V 1 " ideal model delta sigma weight residual 113.80 109.19 4.61 1.00e+00 1.00e+00 2.12e+01 angle pdb=" CA PHE S 1 " pdb=" CB PHE S 1 " pdb=" CG PHE S 1 " ideal model delta sigma weight residual 113.80 109.20 4.60 1.00e+00 1.00e+00 2.11e+01 ... (remaining 3219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 1207 36.00 - 72.00: 68 72.00 - 108.00: 3 108.00 - 144.00: 0 144.00 - 180.00: 24 Dihedral angle restraints: 1302 sinusoidal: 651 harmonic: 651 Sorted by residual: dihedral pdb=" CH3 ACE S 0 " pdb=" C ACE S 0 " pdb=" N PHE S 1 " pdb=" CA PHE S 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.00 -180.00 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE K 0 " pdb=" C ACE K 0 " pdb=" N PHE K 1 " pdb=" CA PHE K 1 " ideal model delta sinusoidal sigma weight residual 180.00 0.00 180.00 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE j 0 " pdb=" C ACE j 0 " pdb=" N PHE j 1 " pdb=" CA PHE j 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.01 -179.99 1 5.00e+00 4.00e-02 7.68e+02 ... (remaining 1299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 143 0.023 - 0.045: 68 0.045 - 0.067: 4 0.067 - 0.090: 1 0.090 - 0.112: 1 Chirality restraints: 217 Sorted by residual: chirality pdb=" CA LYS P 2 " pdb=" N LYS P 2 " pdb=" C LYS P 2 " pdb=" CB LYS P 2 " both_signs ideal model delta sigma weight residual False 2.51 2.62 -0.11 2.00e-01 2.50e+01 3.15e-01 chirality pdb=" CA LYS T 2 " pdb=" N LYS T 2 " pdb=" C LYS T 2 " pdb=" CB LYS T 2 " both_signs ideal model delta sigma weight residual False 2.51 2.60 -0.09 2.00e-01 2.50e+01 1.83e-01 chirality pdb=" CA LYS a 2 " pdb=" N LYS a 2 " pdb=" C LYS a 2 " pdb=" CB LYS a 2 " both_signs ideal model delta sigma weight residual False 2.51 2.58 -0.07 2.00e-01 2.50e+01 1.11e-01 ... (remaining 214 not shown) Planarity restraints: 403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE T 3 " -0.005 2.00e-02 2.50e+03 4.87e-03 4.15e-01 pdb=" CG PHE T 3 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE T 3 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE T 3 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE T 3 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE T 3 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE T 3 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 7 " -0.000 2.00e-02 2.50e+03 4.50e-03 3.54e-01 pdb=" CG PHE R 7 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE R 7 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 7 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE R 7 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE R 7 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 7 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Z 7 " -0.003 2.00e-02 2.50e+03 4.07e-03 2.89e-01 pdb=" CG PHE Z 7 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE Z 7 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE Z 7 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE Z 7 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE Z 7 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE Z 7 " -0.000 2.00e-02 2.50e+03 ... (remaining 400 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 975 2.87 - 3.38: 1591 3.38 - 3.89: 3804 3.89 - 4.39: 4373 4.39 - 4.90: 7812 Nonbonded interactions: 18555 Sorted by model distance: nonbonded pdb=" O LYS P 2 " pdb=" NZ LYS P 2 " model vdw 2.366 3.120 nonbonded pdb=" O LYS T 6 " pdb=" N GLU T 8 " model vdw 2.451 3.120 nonbonded pdb=" O LYS a 6 " pdb=" N GLU a 8 " model vdw 2.461 3.120 nonbonded pdb=" O PHE g 7 " pdb=" N NH2 h 9 " model vdw 2.472 3.120 nonbonded pdb=" O LYS i 6 " pdb=" N GLU i 8 " model vdw 2.481 3.120 ... (remaining 18550 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.050 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 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 : 0.017 0.135 2542 Z= 0.983 Angle : 1.311 7.917 3224 Z= 0.672 Chirality : 0.024 0.112 217 Planarity : 0.001 0.005 403 Dihedral : 35.623 179.999 868 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 2.69 % Allowed : 14.52 % Favored : 82.80 % Rotamer: Outliers : 4.15 % Allowed : 25.35 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -4.15 (0.50), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE T 3 Details of bonding type rmsd/Z covalent geometry : bond 0.01629 / 0.81 ( 2511) covalent geometry : angle 1.31112 / 0.67 ( 3224) hydrogen bonds : bond 0.14106 / 7.85 ( 24) hydrogen bonds : angle 9.36218 / 5.95 ( 72) Misc. bond : bond 0.05147 / 2.93 ( 31) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.094 Fit side-chains REVERT: K 8 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6868 (pm20) outliers start: 9 outliers final: 0 residues processed: 34 average time/residue: 0.0641 time to fit residues: 2.6260 Evaluate side-chains 23 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 8 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.070875 restraints weight = 5276.189| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.28 r_work: 0.2943 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.9942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.104 0.291 2542 Z= 4.254 Angle : 3.863 30.591 3224 Z= 1.965 Chirality : 0.221 0.589 217 Planarity : 0.024 0.069 403 Dihedral : 30.572 175.051 282 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 85.21 Ramachandran Plot: Outliers : 9.14 % Allowed : 48.92 % Favored : 41.94 % Rotamer: Outliers : 15.67 % Allowed : 27.19 % Favored : 57.14 % Cbeta Deviations : 4.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.14 (0.37), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.20 (0.28), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.140 0.018 PHE c 5 Details of bonding type rmsd/Z covalent geometry : bond 0.10416 / 4.28 ( 2511) covalent geometry : angle 3.86311 / 1.96 ( 3224) hydrogen bonds : bond 0.29401 / 15.68 ( 24) hydrogen bonds : angle 10.43610 / 6.55 ( 72) Misc. bond : bond 0.01103 / 0.66 ( 31) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 53 time to evaluate : 0.100 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 8 GLU cc_start: 0.7984 (mp0) cc_final: 0.7668 (mp0) REVERT: P 2 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7170 (tptp) REVERT: Q 2 LYS cc_start: 0.8355 (ttmt) cc_final: 0.6780 (tmtt) REVERT: G 2 LYS cc_start: 0.8871 (mttt) cc_final: 0.8180 (mmtt) REVERT: G 3 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8630 (p90) REVERT: H 2 LYS cc_start: 0.8169 (mptt) cc_final: 0.7775 (mmtm) REVERT: H 3 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8726 (t80) REVERT: S 8 GLU cc_start: 0.7849 (mp0) cc_final: 0.7349 (mp0) REVERT: U 2 LYS cc_start: 0.8213 (ttmt) cc_final: 0.6972 (tmtt) REVERT: I 2 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7331 (mttp) REVERT: K 2 LYS cc_start: 0.8652 (mttt) cc_final: 0.8224 (mttm) REVERT: L 3 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8787 (t80) REVERT: L 7 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8407 (t80) REVERT: Z 8 GLU cc_start: 0.8469 (tt0) cc_final: 0.8145 (mt-10) REVERT: a 2 LYS cc_start: 0.8390 (tptp) cc_final: 0.7932 (tptp) REVERT: b 2 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7843 (ttmt) REVERT: M 2 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7270 (mttp) REVERT: W 2 LYS cc_start: 0.8692 (mttt) cc_final: 0.8215 (mttm) REVERT: X 3 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8661 (t80) REVERT: X 6 LYS cc_start: 0.8065 (mttt) cc_final: 0.7663 (tptp) REVERT: h 8 GLU cc_start: 0.8398 (tt0) cc_final: 0.7816 (tm-30) REVERT: j 2 LYS cc_start: 0.7162 (tmtt) cc_final: 0.6944 (tmtt) REVERT: c 2 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7449 (mmtp) REVERT: c 3 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8625 (m-10) REVERT: e 5 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8440 (p90) REVERT: f 2 LYS cc_start: 0.8045 (mptt) cc_final: 0.7843 (mmtm) outliers start: 34 outliers final: 22 residues processed: 84 average time/residue: 0.1089 time to fit residues: 10.0107 Evaluate side-chains 86 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 53 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 3 PHE Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain Z residue 7 PHE Chi-restraints excluded: chain M residue 2 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain W residue 1 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 5 PHE Chi-restraints excluded: chain X residue 2 LYS Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 7 PHE Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 7 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.085370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.068481 restraints weight = 5675.354| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.16 r_work: 0.2837 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 1.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.104 0.285 2542 Z= 4.243 Angle : 3.818 29.558 3224 Z= 1.963 Chirality : 0.228 0.706 217 Planarity : 0.022 0.060 403 Dihedral : 30.924 175.986 282 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 90.33 Ramachandran Plot: Outliers : 8.60 % Allowed : 57.53 % Favored : 33.87 % Rotamer: Outliers : 23.04 % Allowed : 30.41 % Favored : 46.54 % Cbeta Deviations : 6.91 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.99 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.83 (0.34), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.72 (0.26), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.136 0.016 PHE E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.10414 / 4.27 ( 2511) covalent geometry : angle 3.81790 / 1.96 ( 3224) hydrogen bonds : bond 0.31189 / 16.59 ( 24) hydrogen bonds : angle 10.10253 / 6.46 ( 72) Misc. bond : bond 0.01053 / 0.64 ( 31) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 55 time to evaluate : 0.095 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 2 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.6970 (tptp) REVERT: F 2 LYS cc_start: 0.7724 (tttt) cc_final: 0.7154 (mmtt) REVERT: G 2 LYS cc_start: 0.8799 (mttt) cc_final: 0.8144 (mmtt) REVERT: H 2 LYS cc_start: 0.8228 (mptt) cc_final: 0.7892 (mptt) REVERT: H 3 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8715 (t80) REVERT: S 8 GLU cc_start: 0.7835 (mp0) cc_final: 0.7406 (mp0) REVERT: J 2 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7644 (tttp) REVERT: K 2 LYS cc_start: 0.8848 (mttt) cc_final: 0.8425 (mttt) REVERT: L 2 LYS cc_start: 0.8214 (mptt) cc_final: 0.7968 (mptt) REVERT: L 6 LYS cc_start: 0.8407 (tttt) cc_final: 0.8068 (tptm) REVERT: L 8 GLU cc_start: 0.7623 (mp0) cc_final: 0.7418 (mp0) REVERT: Z 8 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7808 (tm-30) REVERT: M 2 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7473 (mtmm) REVERT: W 2 LYS cc_start: 0.8771 (mttt) cc_final: 0.8317 (mtpm) REVERT: c 2 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7391 (mmtp) REVERT: c 3 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8400 (m-10) REVERT: f 6 LYS cc_start: 0.4655 (tppt) cc_final: 0.3173 (mmtt) REVERT: f 8 GLU cc_start: 0.7782 (mp0) cc_final: 0.7526 (mp0) outliers start: 50 outliers final: 27 residues processed: 98 average time/residue: 0.1072 time to fit residues: 11.4788 Evaluate side-chains 89 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 3 PHE Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain I residue 1 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain Z residue 7 PHE Chi-restraints excluded: chain M residue 2 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain W residue 1 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 5 PHE Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.084097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.068081 restraints weight = 5530.666| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.08 r_work: 0.2838 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 1.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.104 0.285 2542 Z= 4.249 Angle : 3.770 29.405 3224 Z= 1.939 Chirality : 0.227 0.653 217 Planarity : 0.021 0.062 403 Dihedral : 31.271 176.187 282 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 89.89 Ramachandran Plot: Outliers : 6.45 % Allowed : 61.83 % Favored : 31.72 % Rotamer: Outliers : 22.12 % Allowed : 32.26 % Favored : 45.62 % Cbeta Deviations : 6.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.99 (0.32), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.85 (0.25), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.132 0.015 PHE E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.10429 / 4.27 ( 2511) covalent geometry : angle 3.76982 / 1.94 ( 3224) hydrogen bonds : bond 0.31890 / 16.96 ( 24) hydrogen bonds : angle 10.33793 / 6.62 ( 72) Misc. bond : bond 0.01063 / 0.64 ( 31) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 57 time to evaluate : 0.060 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 2 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.6985 (tptp) REVERT: Q 2 LYS cc_start: 0.8308 (ttmt) cc_final: 0.6998 (tmtt) REVERT: F 2 LYS cc_start: 0.7735 (tttt) cc_final: 0.7020 (mmtt) REVERT: G 2 LYS cc_start: 0.8846 (mttt) cc_final: 0.8175 (mmtt) REVERT: H 2 LYS cc_start: 0.8194 (mptt) cc_final: 0.7815 (mptt) REVERT: H 3 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8667 (t80) REVERT: S 8 GLU cc_start: 0.7828 (mp0) cc_final: 0.7431 (mp0) REVERT: J 2 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.6866 (mttt) REVERT: K 2 LYS cc_start: 0.8836 (mttt) cc_final: 0.8264 (mttm) REVERT: L 2 LYS cc_start: 0.8350 (mptt) cc_final: 0.8135 (mptt) REVERT: L 6 LYS cc_start: 0.8378 (tttt) cc_final: 0.8012 (tptm) REVERT: L 8 GLU cc_start: 0.7665 (mp0) cc_final: 0.7351 (mp0) REVERT: Z 8 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7623 (tm-30) REVERT: b 2 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7097 (tmtt) REVERT: V 2 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.6783 (mttt) REVERT: W 2 LYS cc_start: 0.8689 (mttt) cc_final: 0.8293 (mttm) REVERT: W 6 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8498 (tttm) REVERT: h 7 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: c 2 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7386 (mmtp) REVERT: c 3 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8382 (m-10) REVERT: f 2 LYS cc_start: 0.8108 (mptt) cc_final: 0.7782 (mmtm) REVERT: f 8 GLU cc_start: 0.7928 (mp0) cc_final: 0.7577 (mp0) outliers start: 48 outliers final: 30 residues processed: 97 average time/residue: 0.1014 time to fit residues: 10.7014 Evaluate side-chains 95 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 57 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 3 PHE Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain I residue 3 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain Z residue 7 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain W residue 1 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 5 PHE Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain W residue 8 GLU Chi-restraints excluded: chain h residue 7 PHE Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.084855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.068457 restraints weight = 6085.152| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.29 r_work: 0.2822 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 1.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.104 0.286 2542 Z= 4.248 Angle : 3.831 44.276 3224 Z= 1.954 Chirality : 0.230 0.646 217 Planarity : 0.021 0.059 403 Dihedral : 30.136 177.064 282 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 87.63 Ramachandran Plot: Outliers : 5.91 % Allowed : 62.37 % Favored : 31.72 % Rotamer: Outliers : 25.35 % Allowed : 30.41 % Favored : 44.24 % Cbeta Deviations : 6.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -9.00 (0.32), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.86 (0.24), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.131 0.015 PHE E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.10432 / 4.27 ( 2511) covalent geometry : angle 3.83121 / 1.95 ( 3224) hydrogen bonds : bond 0.32063 / 17.02 ( 24) hydrogen bonds : angle 10.44118 / 6.70 ( 72) Misc. bond : bond 0.01052 / 0.63 ( 31) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 57 time to evaluate : 0.059 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 8 GLU cc_start: 0.7807 (mp0) cc_final: 0.7581 (mp0) REVERT: P 2 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.6921 (tptp) REVERT: Q 2 LYS cc_start: 0.8295 (ttmt) cc_final: 0.6979 (tmtt) REVERT: F 2 LYS cc_start: 0.7759 (tttt) cc_final: 0.7017 (mmtt) REVERT: G 2 LYS cc_start: 0.8859 (mttt) cc_final: 0.8232 (mmtt) REVERT: H 2 LYS cc_start: 0.8196 (mptt) cc_final: 0.7787 (mptt) REVERT: H 3 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8663 (t80) REVERT: S 8 GLU cc_start: 0.7821 (mp0) cc_final: 0.7447 (mp0) REVERT: I 6 LYS cc_start: 0.8489 (ttpp) cc_final: 0.8148 (ttpp) REVERT: J 2 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.6908 (mttt) REVERT: K 2 LYS cc_start: 0.8834 (mttt) cc_final: 0.8486 (mttt) REVERT: L 2 LYS cc_start: 0.8362 (mptt) cc_final: 0.8125 (mptt) REVERT: L 6 LYS cc_start: 0.8413 (tttt) cc_final: 0.8020 (tptm) REVERT: L 8 GLU cc_start: 0.7651 (mp0) cc_final: 0.7435 (mp0) REVERT: Z 8 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7555 (tm-30) REVERT: b 2 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7041 (tmtt) REVERT: V 2 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.6781 (mttt) REVERT: W 2 LYS cc_start: 0.8697 (mttt) cc_final: 0.8276 (mttm) REVERT: h 7 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7736 (m-80) REVERT: j 2 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7124 (tmtt) REVERT: c 2 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7184 (mmtp) REVERT: c 3 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8392 (m-10) REVERT: e 5 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8528 (p90) REVERT: f 2 LYS cc_start: 0.8148 (mptt) cc_final: 0.7876 (mmtm) REVERT: f 6 LYS cc_start: 0.3643 (OUTLIER) cc_final: 0.3015 (tppt) REVERT: f 8 GLU cc_start: 0.8008 (mp0) cc_final: 0.7624 (mp0) outliers start: 55 outliers final: 38 residues processed: 101 average time/residue: 0.1086 time to fit residues: 11.9572 Evaluate side-chains 104 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 56 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 3 PHE Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain I residue 1 PHE Chi-restraints excluded: chain I residue 3 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain Z residue 7 PHE Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain V residue 8 GLU Chi-restraints excluded: chain W residue 1 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 8 GLU Chi-restraints excluded: chain h residue 7 PHE Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain j residue 2 LYS Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 6 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.085418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.069329 restraints weight = 5634.692| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.14 r_work: 0.2809 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 1.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.104 0.286 2542 Z= 4.252 Angle : 3.837 40.075 3224 Z= 1.958 Chirality : 0.230 0.645 217 Planarity : 0.021 0.058 403 Dihedral : 30.370 177.529 282 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 87.61 Ramachandran Plot: Outliers : 6.45 % Allowed : 62.37 % Favored : 31.18 % Rotamer: Outliers : 25.81 % Allowed : 30.41 % Favored : 43.78 % Cbeta Deviations : 6.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -9.03 (0.31), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.88 (0.24), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.131 0.015 PHE E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.10442 / 4.28 ( 2511) covalent geometry : angle 3.83679 / 1.96 ( 3224) hydrogen bonds : bond 0.31990 / 16.97 ( 24) hydrogen bonds : angle 10.61707 / 6.83 ( 72) Misc. bond : bond 0.01037 / 0.62 ( 31) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 57 time to evaluate : 0.062 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 8 GLU cc_start: 0.7844 (mp0) cc_final: 0.7611 (mp0) REVERT: P 1 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.6055 (t80) REVERT: P 2 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.6889 (tptp) REVERT: Q 2 LYS cc_start: 0.8322 (ttmt) cc_final: 0.7019 (tmtt) REVERT: F 2 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7044 (mmtt) REVERT: G 2 LYS cc_start: 0.8855 (mttt) cc_final: 0.8234 (mmtt) REVERT: G 6 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8096 (ttmt) REVERT: H 3 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.8658 (t80) REVERT: S 8 GLU cc_start: 0.7830 (mp0) cc_final: 0.7412 (mp0) REVERT: J 2 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.6884 (mttt) REVERT: K 2 LYS cc_start: 0.8837 (mttt) cc_final: 0.8493 (mttt) REVERT: L 2 LYS cc_start: 0.8346 (mptt) cc_final: 0.8115 (mptt) REVERT: L 6 LYS cc_start: 0.8420 (tttt) cc_final: 0.8043 (tptm) REVERT: L 8 GLU cc_start: 0.7688 (mp0) cc_final: 0.7432 (mp0) REVERT: Z 8 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7900 (mp0) REVERT: b 2 LYS cc_start: 0.8177 (ttpt) cc_final: 0.7114 (tmtt) REVERT: V 2 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.6761 (mttt) REVERT: W 2 LYS cc_start: 0.8720 (mttt) cc_final: 0.8214 (mttm) REVERT: j 2 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7359 (tmtt) REVERT: c 2 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.6977 (mmtp) REVERT: c 3 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8292 (m-10) REVERT: e 5 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8517 (p90) REVERT: f 2 LYS cc_start: 0.8151 (mptt) cc_final: 0.7892 (mmtm) REVERT: f 6 LYS cc_start: 0.3597 (OUTLIER) cc_final: 0.3266 (tppt) REVERT: f 8 GLU cc_start: 0.8040 (mp0) cc_final: 0.7734 (mp0) outliers start: 56 outliers final: 40 residues processed: 102 average time/residue: 0.1088 time to fit residues: 12.0680 Evaluate side-chains 109 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 57 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 3 PHE Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain I residue 1 PHE Chi-restraints excluded: chain I residue 3 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain Z residue 7 PHE Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain V residue 8 GLU Chi-restraints excluded: chain W residue 1 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 5 PHE Chi-restraints excluded: chain h residue 7 PHE Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain j residue 2 LYS Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 6 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.071532 restraints weight = 5758.116| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.05 r_work: 0.2943 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 1.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.104 0.287 2542 Z= 4.250 Angle : 3.829 37.471 3224 Z= 1.957 Chirality : 0.231 0.640 217 Planarity : 0.021 0.058 403 Dihedral : 30.441 177.854 282 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 88.45 Ramachandran Plot: Outliers : 5.91 % Allowed : 63.44 % Favored : 30.65 % Rotamer: Outliers : 27.65 % Allowed : 29.03 % Favored : 43.32 % Cbeta Deviations : 6.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -9.12 (0.31), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.95 (0.23), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.132 0.014 PHE E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.10438 / 4.27 ( 2511) covalent geometry : angle 3.82918 / 1.96 ( 3224) hydrogen bonds : bond 0.32207 / 17.06 ( 24) hydrogen bonds : angle 10.72391 / 6.90 ( 72) Misc. bond : bond 0.01035 / 0.62 ( 31) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 56 time to evaluate : 0.104 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 8 GLU cc_start: 0.7924 (mp0) cc_final: 0.7723 (mp0) REVERT: P 1 PHE cc_start: 0.6661 (OUTLIER) cc_final: 0.6176 (t80) REVERT: P 2 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7006 (tptp) REVERT: Q 2 LYS cc_start: 0.8408 (ttmt) cc_final: 0.7200 (tmtt) REVERT: F 2 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7187 (mmtt) REVERT: G 2 LYS cc_start: 0.8887 (mttt) cc_final: 0.8290 (mmtt) REVERT: G 6 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8128 (ttmt) REVERT: H 2 LYS cc_start: 0.8253 (mptt) cc_final: 0.7891 (mptt) REVERT: H 3 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.8667 (t80) REVERT: S 8 GLU cc_start: 0.7883 (mp0) cc_final: 0.7477 (mp0) REVERT: T 6 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8777 (tmtt) REVERT: I 6 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8234 (ttpp) REVERT: J 2 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.6955 (mttt) REVERT: K 2 LYS cc_start: 0.8883 (mttt) cc_final: 0.8523 (mttt) REVERT: L 2 LYS cc_start: 0.8370 (mptt) cc_final: 0.8155 (mptt) REVERT: L 6 LYS cc_start: 0.8486 (tttt) cc_final: 0.8186 (tptm) REVERT: Z 8 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7972 (mp0) REVERT: b 2 LYS cc_start: 0.8286 (ttpt) cc_final: 0.7250 (tmtt) REVERT: V 2 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.6889 (mttt) REVERT: W 2 LYS cc_start: 0.8752 (mttt) cc_final: 0.8280 (mttm) REVERT: h 7 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7835 (t80) REVERT: j 2 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7508 (tmtt) REVERT: c 2 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7178 (mmtp) REVERT: c 3 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8421 (m-10) REVERT: e 5 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8590 (p90) REVERT: f 2 LYS cc_start: 0.8225 (mptt) cc_final: 0.8014 (mmtm) REVERT: f 6 LYS cc_start: 0.3797 (OUTLIER) cc_final: 0.3427 (tppt) REVERT: f 8 GLU cc_start: 0.8076 (mp0) cc_final: 0.7797 (mp0) outliers start: 60 outliers final: 43 residues processed: 104 average time/residue: 0.1173 time to fit residues: 13.2673 Evaluate side-chains 113 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 56 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 3 PHE Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain T residue 6 LYS Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain I residue 1 PHE Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 3 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain Z residue 7 PHE Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain M residue 2 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain V residue 8 GLU Chi-restraints excluded: chain W residue 1 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 5 PHE Chi-restraints excluded: chain W residue 8 GLU Chi-restraints excluded: chain h residue 7 PHE Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain i residue 8 GLU Chi-restraints excluded: chain j residue 2 LYS Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 6 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.067735 restraints weight = 5660.033| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.16 r_work: 0.2810 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 1.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.104 0.287 2542 Z= 4.255 Angle : 3.822 37.340 3224 Z= 1.957 Chirality : 0.232 0.647 217 Planarity : 0.021 0.058 403 Dihedral : 30.498 177.775 282 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 90.31 Ramachandran Plot: Outliers : 6.99 % Allowed : 62.37 % Favored : 30.65 % Rotamer: Outliers : 26.73 % Allowed : 29.95 % Favored : 43.32 % Cbeta Deviations : 6.91 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -9.11 (0.31), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.94 (0.23), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.131 0.015 PHE E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.10450 / 4.28 ( 2511) covalent geometry : angle 3.82193 / 1.96 ( 3224) hydrogen bonds : bond 0.32344 / 17.07 ( 24) hydrogen bonds : angle 10.83619 / 6.98 ( 72) Misc. bond : bond 0.01049 / 0.63 ( 31) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 58 time to evaluate : 0.058 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 8 GLU cc_start: 0.7879 (mp0) cc_final: 0.7665 (mp0) REVERT: P 1 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.6055 (t80) REVERT: P 2 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.6909 (tptp) REVERT: Q 2 LYS cc_start: 0.8339 (ttmt) cc_final: 0.7051 (tmtt) REVERT: F 2 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7064 (mmtt) REVERT: G 2 LYS cc_start: 0.8860 (mttt) cc_final: 0.8236 (mmtt) REVERT: G 6 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8100 (ttmt) REVERT: H 2 LYS cc_start: 0.8227 (mptt) cc_final: 0.7845 (mptt) REVERT: H 3 PHE cc_start: 0.9347 (OUTLIER) cc_final: 0.8578 (t80) REVERT: S 8 GLU cc_start: 0.7840 (mp0) cc_final: 0.7440 (mp0) REVERT: T 6 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8739 (tmtt) REVERT: I 6 LYS cc_start: 0.8431 (ttpp) cc_final: 0.8141 (ttpp) REVERT: J 2 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.6901 (mttt) REVERT: K 2 LYS cc_start: 0.8816 (mttt) cc_final: 0.8537 (mttt) REVERT: L 2 LYS cc_start: 0.8346 (mptt) cc_final: 0.8119 (mptt) REVERT: L 6 LYS cc_start: 0.8598 (tttt) cc_final: 0.8058 (tptm) REVERT: L 8 GLU cc_start: 0.8006 (mp0) cc_final: 0.7586 (mp0) REVERT: Z 8 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7886 (mp0) REVERT: b 2 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7124 (tmtt) REVERT: V 2 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.6826 (mttt) REVERT: W 2 LYS cc_start: 0.8708 (mttt) cc_final: 0.8245 (mttm) REVERT: h 7 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7376 (t80) REVERT: j 2 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7382 (tmtt) REVERT: c 2 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7171 (mmtp) REVERT: c 3 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8403 (m-10) REVERT: e 5 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8539 (p90) REVERT: f 2 LYS cc_start: 0.8179 (mptt) cc_final: 0.7958 (mmtm) REVERT: f 6 LYS cc_start: 0.3620 (OUTLIER) cc_final: 0.3254 (tppt) REVERT: f 8 GLU cc_start: 0.8055 (mp0) cc_final: 0.7767 (mp0) outliers start: 58 outliers final: 43 residues processed: 104 average time/residue: 0.1101 time to fit residues: 12.4579 Evaluate side-chains 115 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 58 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 3 PHE Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain T residue 6 LYS Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain I residue 1 PHE Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 3 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain Z residue 7 PHE Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain M residue 2 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain V residue 8 GLU Chi-restraints excluded: chain W residue 1 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 5 PHE Chi-restraints excluded: chain W residue 8 GLU Chi-restraints excluded: chain h residue 7 PHE Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain i residue 8 GLU Chi-restraints excluded: chain j residue 2 LYS Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 6 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.086873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.070327 restraints weight = 5734.523| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.21 r_work: 0.2811 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 1.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.104 0.287 2542 Z= 4.255 Angle : 3.819 37.523 3224 Z= 1.953 Chirality : 0.231 0.643 217 Planarity : 0.021 0.058 403 Dihedral : 30.501 177.707 282 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 89.51 Ramachandran Plot: Outliers : 6.99 % Allowed : 62.90 % Favored : 30.11 % Rotamer: Outliers : 27.19 % Allowed : 29.95 % Favored : 42.86 % Cbeta Deviations : 6.91 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.76 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -9.10 (0.31), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.93 (0.23), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.131 0.015 PHE E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.10450 / 4.28 ( 2511) covalent geometry : angle 3.81853 / 1.95 ( 3224) hydrogen bonds : bond 0.32296 / 17.02 ( 24) hydrogen bonds : angle 10.92128 / 7.02 ( 72) Misc. bond : bond 0.01047 / 0.63 ( 31) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 58 time to evaluate : 0.097 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 8 GLU cc_start: 0.7887 (mp0) cc_final: 0.7679 (mp0) REVERT: P 1 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.6054 (t80) REVERT: P 2 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.6905 (tptp) REVERT: Q 2 LYS cc_start: 0.8339 (ttmt) cc_final: 0.7047 (tmtt) REVERT: F 2 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7072 (mmtt) REVERT: G 2 LYS cc_start: 0.8858 (mttt) cc_final: 0.8234 (mmtt) REVERT: G 6 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8079 (ttmt) REVERT: H 3 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8580 (t80) REVERT: S 8 GLU cc_start: 0.7817 (mp0) cc_final: 0.7454 (mp0) REVERT: T 6 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8733 (tmtt) REVERT: I 6 LYS cc_start: 0.8429 (ttpp) cc_final: 0.8126 (ttpp) REVERT: J 2 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.6898 (mttt) REVERT: L 2 LYS cc_start: 0.8345 (mptt) cc_final: 0.8123 (mptt) REVERT: L 6 LYS cc_start: 0.8564 (tttt) cc_final: 0.8029 (tptm) REVERT: L 8 GLU cc_start: 0.7943 (mp0) cc_final: 0.7385 (mp0) REVERT: Z 8 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7882 (mp0) REVERT: b 2 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7129 (tmtt) REVERT: V 2 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.6810 (mttt) REVERT: W 2 LYS cc_start: 0.8712 (mttt) cc_final: 0.8244 (mttm) REVERT: j 2 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7376 (tmtt) REVERT: c 2 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7129 (mmtp) REVERT: c 3 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8410 (m-10) REVERT: c 6 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8030 (mtmm) REVERT: e 5 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8530 (p90) REVERT: f 2 LYS cc_start: 0.8174 (mptt) cc_final: 0.7950 (mmtm) REVERT: f 6 LYS cc_start: 0.3667 (OUTLIER) cc_final: 0.3297 (tppt) REVERT: f 8 GLU cc_start: 0.8061 (mp0) cc_final: 0.7775 (mp0) outliers start: 59 outliers final: 44 residues processed: 106 average time/residue: 0.0955 time to fit residues: 11.0582 Evaluate side-chains 115 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 58 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 3 PHE Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain T residue 6 LYS Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain I residue 1 PHE Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 3 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain Z residue 7 PHE Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain M residue 2 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain V residue 8 GLU Chi-restraints excluded: chain W residue 1 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 5 PHE Chi-restraints excluded: chain W residue 8 GLU Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain i residue 8 GLU Chi-restraints excluded: chain j residue 2 LYS Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 6 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.086642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.070506 restraints weight = 5416.647| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.09 r_work: 0.2819 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 1.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.104 0.286 2542 Z= 4.253 Angle : 3.820 37.509 3224 Z= 1.953 Chirality : 0.231 0.642 217 Planarity : 0.021 0.058 403 Dihedral : 30.513 177.578 282 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 88.87 Ramachandran Plot: Outliers : 6.99 % Allowed : 62.90 % Favored : 30.11 % Rotamer: Outliers : 26.27 % Allowed : 30.41 % Favored : 43.32 % Cbeta Deviations : 6.91 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.76 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -9.11 (0.31), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.94 (0.23), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.131 0.015 PHE E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.10447 / 4.28 ( 2511) covalent geometry : angle 3.81968 / 1.95 ( 3224) hydrogen bonds : bond 0.32444 / 17.06 ( 24) hydrogen bonds : angle 11.08946 / 7.13 ( 72) Misc. bond : bond 0.01044 / 0.62 ( 31) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 372 Ramachandran restraints generated. 186 Oldfield, 0 Emsley, 186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 58 time to evaluate : 0.058 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 8 GLU cc_start: 0.7881 (mp0) cc_final: 0.7674 (mp0) REVERT: P 1 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.6057 (t80) REVERT: P 2 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.6903 (tptp) REVERT: Q 2 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7047 (tmtt) REVERT: F 2 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7121 (mmtt) REVERT: G 2 LYS cc_start: 0.8859 (mttt) cc_final: 0.8239 (mmtt) REVERT: G 6 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8075 (ttmt) REVERT: H 3 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8576 (t80) REVERT: S 8 GLU cc_start: 0.7828 (mp0) cc_final: 0.7479 (mp0) REVERT: T 6 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8738 (tmtt) REVERT: I 6 LYS cc_start: 0.8436 (ttpp) cc_final: 0.8131 (ttpp) REVERT: J 2 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.6890 (mttt) REVERT: L 2 LYS cc_start: 0.8341 (mptt) cc_final: 0.8118 (mptt) REVERT: L 6 LYS cc_start: 0.8559 (tttt) cc_final: 0.8033 (tptm) REVERT: L 8 GLU cc_start: 0.7963 (mp0) cc_final: 0.7552 (mp0) REVERT: Z 8 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7877 (mp0) REVERT: b 2 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7136 (tmtt) REVERT: V 2 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.6769 (mttt) REVERT: W 2 LYS cc_start: 0.8709 (mttt) cc_final: 0.8235 (mttm) REVERT: j 2 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7386 (tmtt) REVERT: c 2 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7179 (mmtp) REVERT: c 3 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8411 (m-10) REVERT: c 6 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8099 (mtmm) REVERT: e 5 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8532 (p90) REVERT: f 2 LYS cc_start: 0.8173 (mptt) cc_final: 0.7948 (mmtm) REVERT: f 6 LYS cc_start: 0.3654 (OUTLIER) cc_final: 0.3310 (tppt) REVERT: f 8 GLU cc_start: 0.8075 (mp0) cc_final: 0.7785 (mp0) outliers start: 57 outliers final: 44 residues processed: 104 average time/residue: 0.0984 time to fit residues: 11.1194 Evaluate side-chains 115 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 58 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain P residue 1 PHE Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 3 PHE Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain Q residue 8 GLU Chi-restraints excluded: chain E residue 1 PHE Chi-restraints excluded: chain E residue 2 LYS Chi-restraints excluded: chain E residue 3 PHE Chi-restraints excluded: chain E residue 5 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain T residue 6 LYS Chi-restraints excluded: chain U residue 1 PHE Chi-restraints excluded: chain I residue 1 PHE Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 3 PHE Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain K residue 1 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain K residue 5 PHE Chi-restraints excluded: chain K residue 6 LYS Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain Z residue 7 PHE Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain M residue 2 LYS Chi-restraints excluded: chain M residue 3 PHE Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain V residue 6 LYS Chi-restraints excluded: chain V residue 8 GLU Chi-restraints excluded: chain W residue 1 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 5 PHE Chi-restraints excluded: chain W residue 8 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain i residue 8 GLU Chi-restraints excluded: chain j residue 2 LYS Chi-restraints excluded: chain j residue 7 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 6 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.084734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.067780 restraints weight = 6009.368| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.36 r_work: 0.2799 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 1.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.104 0.286 2542 Z= 4.252 Angle : 3.823 37.575 3224 Z= 1.954 Chirality : 0.231 0.643 217 Planarity : 0.021 0.058 403 Dihedral : 30.520 177.553 282 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 89.09 Ramachandran Plot: Outliers : 6.99 % Allowed : 63.44 % Favored : 29.57 % Rotamer: Outliers : 27.19 % Allowed : 29.95 % Favored : 42.86 % Cbeta Deviations : 6.91 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.76 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -9.11 (0.31), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.94 (0.23), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.131 0.015 PHE E 5 Details of bonding type rmsd/Z covalent geometry : bond 0.10444 / 4.28 ( 2511) covalent geometry : angle 3.82260 / 1.95 ( 3224) hydrogen bonds : bond 0.32414 / 17.05 ( 24) hydrogen bonds : angle 11.02302 / 7.08 ( 72) Misc. bond : bond 0.01046 / 0.63 ( 31) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 494.47 seconds wall clock time: 9 minutes 13.87 seconds (553.87 seconds total)