Starting phenix.real_space_refine on Thu Oct 22 17:36:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pd7_71528/10_2026/9pd7_71528.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pd7_71528/10_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9pd7_71528/10_2026/9pd7_71528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pd7_71528/10_2026/9pd7_71528.map" model { file = "/net/cci-nas-00/data/ceres_data/9pd7_71528/10_2026/9pd7_71528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pd7_71528/10_2026/9pd7_71528.cif" } 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-2.3rc1-6221/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: 0.55, per 1000 atoms: 0.22 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: 0.12 Conformation dependent library (CDL) restraints added in 31.6 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: 0.03 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: 0.14 Time building geometry restraints manager: 0.14 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 2.430 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.900 ------------------------------------------------------------------------------- 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 : 0.048 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: 0.0467 time to fit residues: 1.8996 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 : 0.048 ------------------------------------------------------------------------------- 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: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.156276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.133482 restraints weight = 3208.988| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 3.54 r_work: 0.3927 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2542 Z= 0.134 Angle : 1.026 11.235 3224 Z= 0.386 Chirality : 0.027 0.070 217 Planarity : 0.002 0.009 403 Dihedral : 52.991 179.923 282 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 1.84 % Allowed : 23.96 % Favored : 74.19 % 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: -3.93 (0.50), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE T 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 2511) covalent geometry : angle 1.02614 / 0.39 ( 3224) hydrogen bonds : bond 0.01463 / 0.85 ( 24) hydrogen bonds : angle 6.38929 / 4.21 ( 72) Misc. bond : bond 0.00028 / 0.02 ( 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 30 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.048 Fit side-chains REVERT: P 2 LYS cc_start: 0.7449 (tptp) cc_final: 0.7187 (tptp) REVERT: F 7 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.6347 (t80) REVERT: T 2 LYS cc_start: 0.7245 (tptp) cc_final: 0.7034 (tptp) REVERT: j 1 PHE cc_start: 0.7443 (m-80) cc_final: 0.7209 (m-80) outliers start: 4 outliers final: 1 residues processed: 29 average time/residue: 0.0409 time to fit residues: 1.4261 Evaluate side-chains 22 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain f residue 3 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.127778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.105214 restraints weight = 3717.988| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.61 r_work: 0.3483 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.039 2542 Z= 0.535 Angle : 1.271 13.968 3224 Z= 0.536 Chirality : 0.048 0.134 217 Planarity : 0.006 0.037 403 Dihedral : 52.690 179.981 279 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 5.53 % Allowed : 23.04 % Favored : 71.43 % 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: -4.55 (0.46), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.35), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.041 0.004 PHE I 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01326 / 0.54 ( 2511) covalent geometry : angle 1.27051 / 0.54 ( 3224) hydrogen bonds : bond 0.03559 / 1.80 ( 24) hydrogen bonds : angle 5.77974 / 3.74 ( 72) Misc. bond : bond 0.00120 / 0.07 ( 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 38 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.050 Fit side-chains revert: symmetry clash REVERT: O 8 GLU cc_start: 0.7859 (mp0) cc_final: 0.7605 (mp0) REVERT: P 6 LYS cc_start: 0.7795 (tptp) cc_final: 0.7507 (tptp) REVERT: T 2 LYS cc_start: 0.7901 (tptp) cc_final: 0.7534 (tptp) REVERT: a 2 LYS cc_start: 0.8116 (tptp) cc_final: 0.7789 (tptp) REVERT: W 3 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.6947 (p90) outliers start: 12 outliers final: 6 residues processed: 37 average time/residue: 0.0526 time to fit residues: 2.2432 Evaluate side-chains 31 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain J residue 7 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 7 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.144058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.122201 restraints weight = 3539.449| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.68 r_work: 0.3685 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2542 Z= 0.128 Angle : 1.062 11.954 3224 Z= 0.403 Chirality : 0.030 0.088 217 Planarity : 0.002 0.009 403 Dihedral : 53.161 179.810 279 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.15 % Allowed : 27.19 % Favored : 68.66 % 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: -4.40 (0.47), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.36), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE J 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 2511) covalent geometry : angle 1.06196 / 0.40 ( 3224) hydrogen bonds : bond 0.01116 / 0.61 ( 24) hydrogen bonds : angle 5.25921 / 3.43 ( 72) Misc. bond : bond 0.00029 / 0.02 ( 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 29 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.051 Fit side-chains REVERT: O 8 GLU cc_start: 0.7676 (mp0) cc_final: 0.7379 (mp0) REVERT: H 3 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: T 2 LYS cc_start: 0.7564 (tptp) cc_final: 0.7284 (tptp) REVERT: K 8 GLU cc_start: 0.7854 (pt0) cc_final: 0.7618 (pt0) REVERT: a 2 LYS cc_start: 0.7884 (tptp) cc_final: 0.7607 (tptp) REVERT: V 2 LYS cc_start: 0.7138 (tttt) cc_final: 0.6920 (mmmt) REVERT: W 3 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.7181 (p90) outliers start: 9 outliers final: 4 residues processed: 28 average time/residue: 0.0625 time to fit residues: 2.0194 Evaluate side-chains 25 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain K residue 3 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 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: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.126096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.103451 restraints weight = 4432.389| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.84 r_work: 0.3361 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.6130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.038 2542 Z= 0.517 Angle : 1.266 13.082 3224 Z= 0.528 Chirality : 0.048 0.143 217 Planarity : 0.005 0.022 403 Dihedral : 52.814 179.881 279 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.28 % Favored : 81.72 % Rotamer: Outliers : 6.91 % Allowed : 24.42 % Favored : 68.66 % 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: -4.91 (0.44), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.34), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.047 0.004 PHE I 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01284 / 0.52 ( 2511) covalent geometry : angle 1.26647 / 0.53 ( 3224) hydrogen bonds : bond 0.03340 / 1.62 ( 24) hydrogen bonds : angle 5.49481 / 3.53 ( 72) Misc. bond : bond 0.00114 / 0.07 ( 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 41 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 8 GLU cc_start: 0.7780 (mp0) cc_final: 0.7554 (mp0) REVERT: P 6 LYS cc_start: 0.7970 (tptp) cc_final: 0.7675 (tptp) REVERT: T 2 LYS cc_start: 0.7827 (tptp) cc_final: 0.7388 (tptp) REVERT: J 2 LYS cc_start: 0.7537 (tttt) cc_final: 0.7302 (mmmt) REVERT: a 2 LYS cc_start: 0.8143 (tptp) cc_final: 0.7694 (tptp) REVERT: W 3 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7125 (p90) REVERT: X 7 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7263 (t80) REVERT: c 1 PHE cc_start: 0.6272 (OUTLIER) cc_final: 0.5544 (m-80) REVERT: f 2 LYS cc_start: 0.7511 (mptt) cc_final: 0.7068 (mmtm) outliers start: 15 outliers final: 8 residues processed: 40 average time/residue: 0.0672 time to fit residues: 3.0444 Evaluate side-chains 36 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain T residue 8 GLU Chi-restraints excluded: chain J residue 7 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain W residue 3 PHE 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 e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.138071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.116122 restraints weight = 3812.509| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 3.73 r_work: 0.3616 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2542 Z= 0.129 Angle : 1.069 11.869 3224 Z= 0.407 Chirality : 0.031 0.096 217 Planarity : 0.002 0.011 403 Dihedral : 53.188 179.962 279 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 4.61 % Allowed : 26.27 % Favored : 69.12 % 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: -4.71 (0.46), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.35), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE J 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 2511) covalent geometry : angle 1.06923 / 0.41 ( 3224) hydrogen bonds : bond 0.01144 / 0.61 ( 24) hydrogen bonds : angle 4.93419 / 3.13 ( 72) Misc. bond : bond 0.00020 / 0.01 ( 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 33 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.106 Fit side-chains REVERT: O 8 GLU cc_start: 0.7742 (mp0) cc_final: 0.7426 (mp0) REVERT: H 2 LYS cc_start: 0.7648 (mmtm) cc_final: 0.7301 (mmtm) REVERT: H 3 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: T 2 LYS cc_start: 0.7755 (tptp) cc_final: 0.7408 (tptp) REVERT: J 2 LYS cc_start: 0.7615 (tttt) cc_final: 0.7402 (mmmt) REVERT: a 2 LYS cc_start: 0.8026 (tptp) cc_final: 0.7626 (tptp) REVERT: W 3 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.7416 (p90) REVERT: c 1 PHE cc_start: 0.5953 (OUTLIER) cc_final: 0.5352 (m-80) outliers start: 10 outliers final: 6 residues processed: 33 average time/residue: 0.0917 time to fit residues: 3.5206 Evaluate side-chains 31 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.126979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.103946 restraints weight = 4842.804| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 4.10 r_work: 0.3404 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.6608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.039 2542 Z= 0.517 Angle : 1.257 12.967 3224 Z= 0.522 Chirality : 0.047 0.149 217 Planarity : 0.005 0.021 403 Dihedral : 52.807 179.968 279 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.20 % Favored : 82.80 % Rotamer: Outliers : 9.22 % Allowed : 23.04 % Favored : 67.74 % 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: -5.20 (0.42), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.32), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.046 0.003 PHE M 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01284 / 0.52 ( 2511) covalent geometry : angle 1.25705 / 0.52 ( 3224) hydrogen bonds : bond 0.03354 / 1.59 ( 24) hydrogen bonds : angle 5.17393 / 3.29 ( 72) Misc. bond : bond 0.00096 / 0.06 ( 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 48 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 28 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 8 GLU cc_start: 0.7767 (mp0) cc_final: 0.7503 (mp0) REVERT: P 6 LYS cc_start: 0.8067 (tptp) cc_final: 0.7787 (tptp) REVERT: H 2 LYS cc_start: 0.7942 (mmtm) cc_final: 0.7485 (mptt) REVERT: T 2 LYS cc_start: 0.7929 (tptp) cc_final: 0.7435 (tptp) REVERT: J 2 LYS cc_start: 0.7852 (tttt) cc_final: 0.7531 (mmmt) REVERT: L 2 LYS cc_start: 0.8009 (mptt) cc_final: 0.7569 (mptt) REVERT: L 5 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: a 1 PHE cc_start: 0.7128 (m-10) cc_final: 0.6912 (m-10) REVERT: a 2 LYS cc_start: 0.8157 (tptp) cc_final: 0.7712 (tptp) REVERT: W 3 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7254 (p90) REVERT: X 7 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7330 (t80) REVERT: c 1 PHE cc_start: 0.6092 (OUTLIER) cc_final: 0.5183 (m-80) REVERT: f 2 LYS cc_start: 0.7753 (mptt) cc_final: 0.7294 (mmtm) outliers start: 20 outliers final: 14 residues processed: 44 average time/residue: 0.0664 time to fit residues: 3.3083 Evaluate side-chains 45 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 27 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain T residue 8 GLU Chi-restraints excluded: chain U residue 8 GLU Chi-restraints excluded: chain J residue 7 PHE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain X residue 7 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain j residue 8 GLU Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 5 PHE Chi-restraints excluded: chain f residue 7 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.139462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.117919 restraints weight = 3585.042| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.64 r_work: 0.3626 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2542 Z= 0.131 Angle : 1.072 11.901 3224 Z= 0.411 Chirality : 0.030 0.096 217 Planarity : 0.002 0.011 403 Dihedral : 53.161 179.934 279 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 5.99 % Allowed : 25.81 % Favored : 68.20 % 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: -4.87 (0.45), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.34), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.001 PHE K 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 2511) covalent geometry : angle 1.07213 / 0.41 ( 3224) hydrogen bonds : bond 0.00980 / 0.54 ( 24) hydrogen bonds : angle 4.62080 / 2.93 ( 72) Misc. bond : bond 0.00015 / 0.01 ( 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 37 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: O 8 GLU cc_start: 0.7699 (mp0) cc_final: 0.7345 (mp0) REVERT: H 2 LYS cc_start: 0.7593 (mmtm) cc_final: 0.7105 (mptt) REVERT: H 3 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: T 2 LYS cc_start: 0.7697 (tptp) cc_final: 0.7311 (tptp) REVERT: J 2 LYS cc_start: 0.7763 (tttt) cc_final: 0.7479 (mmmt) REVERT: Y 8 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7781 (mp0) REVERT: a 2 LYS cc_start: 0.7918 (tptp) cc_final: 0.7515 (tptp) REVERT: W 3 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7388 (p90) REVERT: c 1 PHE cc_start: 0.5717 (OUTLIER) cc_final: 0.4984 (m-80) outliers start: 13 outliers final: 6 residues processed: 37 average time/residue: 0.0860 time to fit residues: 3.6299 Evaluate side-chains 32 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain J residue 7 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.123472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.099642 restraints weight = 5316.931| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 4.37 r_work: 0.3317 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.038 2542 Z= 0.510 Angle : 1.276 13.109 3224 Z= 0.533 Chirality : 0.048 0.155 217 Planarity : 0.005 0.021 403 Dihedral : 52.881 179.972 279 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.74 % Favored : 82.26 % Rotamer: Outliers : 6.91 % Allowed : 26.27 % Favored : 66.82 % 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: -5.56 (0.41), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.32), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.048 0.003 PHE M 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01260 / 0.51 ( 2511) covalent geometry : angle 1.27642 / 0.53 ( 3224) hydrogen bonds : bond 0.03366 / 1.64 ( 24) hydrogen bonds : angle 5.07605 / 3.21 ( 72) Misc. bond : bond 0.00091 / 0.05 ( 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 44 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: O 8 GLU cc_start: 0.7763 (mp0) cc_final: 0.7524 (mp0) REVERT: P 6 LYS cc_start: 0.8105 (tptp) cc_final: 0.7842 (tptp) REVERT: F 2 LYS cc_start: 0.7883 (tttt) cc_final: 0.7561 (mmmt) REVERT: H 2 LYS cc_start: 0.8039 (mmtm) cc_final: 0.7733 (mmtm) REVERT: H 3 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8064 (t80) REVERT: T 2 LYS cc_start: 0.7903 (tptp) cc_final: 0.7385 (tptp) REVERT: T 6 LYS cc_start: 0.8003 (tptp) cc_final: 0.7791 (tptm) REVERT: J 2 LYS cc_start: 0.7954 (tttt) cc_final: 0.7653 (mmmt) REVERT: L 2 LYS cc_start: 0.8028 (mptt) cc_final: 0.7536 (mptt) REVERT: L 3 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.7930 (t80) REVERT: a 1 PHE cc_start: 0.7255 (m-10) cc_final: 0.6866 (m-10) REVERT: a 2 LYS cc_start: 0.8041 (tptp) cc_final: 0.7607 (tptp) REVERT: W 3 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7297 (p90) REVERT: X 7 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7327 (t80) REVERT: c 1 PHE cc_start: 0.6027 (OUTLIER) cc_final: 0.4941 (m-80) REVERT: f 2 LYS cc_start: 0.7863 (mptt) cc_final: 0.7371 (mmtm) outliers start: 15 outliers final: 8 residues processed: 42 average time/residue: 0.1114 time to fit residues: 5.2266 Evaluate side-chains 41 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain J residue 7 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain X residue 7 PHE Chi-restraints excluded: chain j residue 8 GLU Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Chi-restraints excluded: chain f residue 5 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.140827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.118897 restraints weight = 3929.192| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.74 r_work: 0.3610 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2542 Z= 0.134 Angle : 1.090 12.100 3224 Z= 0.423 Chirality : 0.031 0.103 217 Planarity : 0.002 0.010 403 Dihedral : 53.151 179.988 279 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 3.69 % Allowed : 28.11 % Favored : 68.20 % 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: -5.17 (0.43), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.33), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE i 1 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 2511) covalent geometry : angle 1.09018 / 0.42 ( 3224) hydrogen bonds : bond 0.00990 / 0.53 ( 24) hydrogen bonds : angle 4.52295 / 2.85 ( 72) Misc. bond : bond 0.00016 / 0.01 ( 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 31 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: O 8 GLU cc_start: 0.7815 (mp0) cc_final: 0.7549 (mp0) REVERT: H 2 LYS cc_start: 0.7578 (mmtm) cc_final: 0.7101 (mptt) REVERT: H 3 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7607 (t80) REVERT: T 2 LYS cc_start: 0.7781 (tptp) cc_final: 0.7440 (tptp) REVERT: J 2 LYS cc_start: 0.7733 (tttt) cc_final: 0.7470 (mmmt) REVERT: Y 8 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7781 (mp0) REVERT: a 2 LYS cc_start: 0.7949 (tptp) cc_final: 0.7559 (tptp) REVERT: c 1 PHE cc_start: 0.5754 (OUTLIER) cc_final: 0.4917 (m-80) outliers start: 8 outliers final: 5 residues processed: 31 average time/residue: 0.1037 time to fit residues: 3.6411 Evaluate side-chains 30 residues out of total 217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain X residue 3 PHE Chi-restraints excluded: chain X residue 5 PHE Chi-restraints excluded: chain c residue 1 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain f residue 3 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.123256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.100532 restraints weight = 4637.647| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.93 r_work: 0.3412 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.7115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.038 2542 Z= 0.508 Angle : 1.271 13.128 3224 Z= 0.529 Chirality : 0.047 0.149 217 Planarity : 0.004 0.021 403 Dihedral : 52.882 179.993 279 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.28 % Favored : 81.72 % Rotamer: Outliers : 5.07 % Allowed : 26.27 % Favored : 68.66 % 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: -5.75 (0.41), residues: 186 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.31), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.047 0.003 PHE M 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01256 / 0.51 ( 2511) covalent geometry : angle 1.27052 / 0.53 ( 3224) hydrogen bonds : bond 0.03350 / 1.68 ( 24) hydrogen bonds : angle 4.90074 / 3.07 ( 72) Misc. bond : bond 0.00090 / 0.05 ( 31) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 368.39 seconds wall clock time: 7 minutes 6.51 seconds (426.51 seconds total)