Starting phenix.real_space_refine on Tue Aug 4 13:06:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pdt_71543/08_2026/9pdt_71543.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pdt_71543/08_2026/9pdt_71543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pdt_71543/08_2026/9pdt_71543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pdt_71543/08_2026/9pdt_71543.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pdt_71543/08_2026/9pdt_71543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pdt_71543/08_2026/9pdt_71543.map" } resolution = 2.8 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= 0.003 sd= 0.039 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 2337 2.51 5 N 451 2.21 5 O 451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 3239 Number of models: 1 Model: "" Number of chains: 82 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: "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: "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: "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: "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: "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: "d" 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: "d" 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "1" 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: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "2" 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: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "3" 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: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "4" 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: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "5" 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: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "6" 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: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "7" 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: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "9" 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: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AB" 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: "AB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AC" 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: "AC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AD" 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: "AD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AE" 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: "AE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AF" 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: "AF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AG" 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: "AG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AH" 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: "AH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AI" 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: "AI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AL" 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: "AL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AM" 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: "AM" 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: 0.80, per 1000 atoms: 0.25 Number of scatterers: 3239 At special positions: 0 Unit cell: (87.15, 85.49, 52.29, 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 451 8.00 N 451 7.00 C 2337 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=41, symmetry=0 Number of additional bonds: simple=41, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 77.5 milliseconds 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 574 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'T' and resid 2 through 4 removed outlier: 6.655A pdb=" N PHE V 3 " --> pdb=" O GLY X 4 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE Z 3 " --> pdb=" O GLY a 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'i' and resid 2 through 4 removed outlier: 6.723A pdb=" N PHE l 3 " --> pdb=" O GLY m 4 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE o 3 " --> pdb=" O GLY p 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'w' and resid 2 through 4 removed outlier: 6.723A pdb=" N PHE 1 3 " --> pdb=" O GLY 2 4 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE 5 3 " --> pdb=" O GLY 6 4 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '9' and resid 2 through 4 removed outlier: 6.655A pdb=" N PHEAC 3 " --> pdb=" O GLYAD 4 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHEAG 3 " --> pdb=" O GLYAH 4 " (cutoff:3.500A) 20 hydrogen bonds defined for protein. 60 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: 0.36 Time building geometry restraints manager: 0.31 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: 328 1.26 - 1.33: 205 1.33 - 1.40: 1189 1.40 - 1.47: 369 1.47 - 1.55: 1230 Bond restraints: 3321 Sorted by residual: bond pdb=" C ACE 2 0 " pdb=" N PHE 2 1 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C ACEAH 0 " pdb=" N PHEAH 1 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C ACE a 0 " pdb=" N PHE a 1 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C ACE m 0 " pdb=" N PHE m 1 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C ACE e 0 " pdb=" N PHE e 1 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 3316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 3862 1.93 - 3.86: 327 3.86 - 5.79: 65 5.79 - 7.73: 0 7.73 - 9.66: 10 Bond angle restraints: 4264 Sorted by residual: angle pdb=" N GLU n 8 " pdb=" CA GLU n 8 " pdb=" CB GLU n 8 " ideal model delta sigma weight residual 110.50 120.16 -9.66 1.70e+00 3.46e-01 3.23e+01 angle pdb=" N GLUAI 8 " pdb=" CA GLUAI 8 " pdb=" CB GLUAI 8 " ideal model delta sigma weight residual 110.50 120.16 -9.66 1.70e+00 3.46e-01 3.23e+01 angle pdb=" N GLU 3 8 " pdb=" CA GLU 3 8 " pdb=" CB GLU 3 8 " ideal model delta sigma weight residual 110.50 120.16 -9.66 1.70e+00 3.46e-01 3.23e+01 angle pdb=" N GLU b 8 " pdb=" CA GLU b 8 " pdb=" CB GLU b 8 " ideal model delta sigma weight residual 110.50 120.16 -9.66 1.70e+00 3.46e-01 3.23e+01 angle pdb=" N GLU 7 8 " pdb=" CA GLU 7 8 " pdb=" CB GLU 7 8 " ideal model delta sigma weight residual 110.50 120.14 -9.64 1.70e+00 3.46e-01 3.22e+01 ... (remaining 4259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 1568 36.00 - 72.00: 122 72.00 - 108.00: 0 108.00 - 144.00: 0 144.00 - 180.00: 32 Dihedral angle restraints: 1722 sinusoidal: 861 harmonic: 861 Sorted by residual: dihedral pdb=" CH3 ACE b 0 " pdb=" C ACE b 0 " pdb=" N PHE b 1 " pdb=" CA PHE b 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 ACEAI 0 " pdb=" C ACEAI 0 " pdb=" N PHEAI 1 " pdb=" CA PHEAI 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 Y 0 " pdb=" C ACE Y 0 " pdb=" N PHE Y 1 " pdb=" CA PHE Y 1 " ideal model delta sinusoidal sigma weight residual 180.00 0.03 179.97 1 5.00e+00 4.00e-02 7.68e+02 ... (remaining 1719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 250 0.051 - 0.102: 18 0.102 - 0.153: 9 0.153 - 0.204: 0 0.204 - 0.255: 10 Chirality restraints: 287 Sorted by residual: chirality pdb=" CA GLU 7 8 " pdb=" N GLU 7 8 " pdb=" C GLU 7 8 " pdb=" CB GLU 7 8 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA GLUAM 8 " pdb=" N GLUAM 8 " pdb=" C GLUAM 8 " pdb=" CB GLUAM 8 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLUAI 8 " pdb=" N GLUAI 8 " pdb=" C GLUAI 8 " pdb=" CB GLUAI 8 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 284 not shown) Planarity restraints: 533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE Y 5 " 0.009 2.00e-02 2.50e+03 6.65e-03 7.74e-01 pdb=" CG PHE Y 5 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE Y 5 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE Y 5 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE Y 5 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE Y 5 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE Y 5 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 3 5 " -0.009 2.00e-02 2.50e+03 6.56e-03 7.54e-01 pdb=" CG PHE 3 5 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE 3 5 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE 3 5 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE 3 5 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 3 5 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE 3 5 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE n 5 " -0.009 2.00e-02 2.50e+03 6.56e-03 7.53e-01 pdb=" CG PHE n 5 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE n 5 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE n 5 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE n 5 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE n 5 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE n 5 " -0.006 2.00e-02 2.50e+03 ... (remaining 530 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 1145 2.85 - 3.36: 2153 3.36 - 3.87: 5522 3.87 - 4.39: 6069 4.39 - 4.90: 11001 Nonbonded interactions: 25890 Sorted by model distance: nonbonded pdb=" OE2 GLU i 8 " pdb=" NZ LYS 5 2 " model vdw 2.335 3.120 nonbonded pdb=" OE2 GLU V 8 " pdb=" NZ LYS o 2 " model vdw 2.335 3.120 nonbonded pdb=" NZ LYS Z 2 " pdb=" OE2 GLU 9 8 " model vdw 2.358 3.120 nonbonded pdb=" OE2 GLU T 8 " pdb=" NZ LYS l 2 " model vdw 2.358 3.120 nonbonded pdb=" N PHE n 1 " pdb=" O PHE n 1 " model vdw 2.629 2.496 ... (remaining 25885 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '9' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' selection = chain 'AE' selection = chain 'AF' selection = chain 'AG' selection = chain 'AH' selection = chain 'AI' selection = chain 'AL' selection = chain 'AM' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'i' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'w' selection = chain 'z' } 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: 1.120 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.520 Find NCS groups from input model: 0.100 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:7.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 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 0.125 3362 Z= 0.969 Angle : 1.201 9.657 4264 Z= 0.630 Chirality : 0.061 0.255 287 Planarity : 0.002 0.007 533 Dihedral : 37.478 179.995 1148 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 23.17 % Favored : 76.42 % Rotamer: Outliers : 6.62 % Allowed : 25.78 % Favored : 67.60 % Cbeta Deviations : 3.48 % 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: -5.34 (0.46), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.001 PHE Y 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01581 / 0.78 ( 3321) covalent geometry : angle 1.20130 / 0.63 ( 4264) hydrogen bonds : bond 0.12171 / 6.63 ( 20) hydrogen bonds : angle 6.21895 / 4.26 ( 60) Misc. bond : bond 0.05250 / 3.20 ( 41) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.127 Fit side-chains REVERT: b 8 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7288 (pm20) REVERT: n 8 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7271 (pm20) REVERT: AI 8 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7260 (pm20) outliers start: 19 outliers final: 0 residues processed: 59 average time/residue: 1.1129 time to fit residues: 66.6740 Evaluate side-chains 47 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 GLU Chi-restraints excluded: chain n residue 8 GLU Chi-restraints excluded: chain AI 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 = 0.3212 r_free = 0.3212 target = 0.098177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.076829 restraints weight = 7371.854| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.31 r_work: 0.2719 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9246 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.265 3362 Z= 3.120 Angle : 3.340 34.301 4264 Z= 1.480 Chirality : 0.185 0.564 287 Planarity : 0.014 0.112 533 Dihedral : 37.377 179.956 378 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 2.44 % Allowed : 33.74 % Favored : 63.82 % Rotamer: Outliers : 24.39 % Allowed : 15.68 % Favored : 59.93 % Cbeta Deviations : 3.48 % 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: -6.69 (0.32), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.09 (0.24), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.101 0.009 PHE Y 7 Details of bonding type rmsd/Z covalent geometry : bond 0.07818 / 3.14 ( 3321) covalent geometry : angle 3.34015 / 1.48 ( 4264) hydrogen bonds : bond 0.07105 / 4.20 ( 20) hydrogen bonds : angle 5.28900 / 3.67 ( 60) Misc. bond : bond 0.00960 / 0.60 ( 41) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 44 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 6 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8764 (tptm) REVERT: Z 8 GLU cc_start: 0.9381 (tt0) cc_final: 0.9057 (tt0) REVERT: a 2 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8875 (mttt) REVERT: l 6 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8958 (tttm) REVERT: l 8 GLU cc_start: 0.9386 (tt0) cc_final: 0.9116 (tt0) REVERT: m 2 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8817 (mttt) REVERT: 1 6 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.9002 (tttm) REVERT: 1 8 GLU cc_start: 0.9374 (tt0) cc_final: 0.9098 (tt0) REVERT: 2 2 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8934 (mttt) REVERT: AG 6 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8980 (tttm) REVERT: AG 8 GLU cc_start: 0.9338 (tt0) cc_final: 0.9057 (tt0) REVERT: AH 2 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8975 (mttt) outliers start: 70 outliers final: 29 residues processed: 98 average time/residue: 0.7576 time to fit residues: 75.5849 Evaluate side-chains 81 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 44 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Y residue 1 PHE Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain b residue 1 PHE Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain e residue 8 GLU Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain m residue 2 LYS Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain q residue 1 PHE Chi-restraints excluded: chain q residue 5 PHE Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 2 residue 2 LYS Chi-restraints excluded: chain 3 residue 1 PHE Chi-restraints excluded: chain 3 residue 3 PHE Chi-restraints excluded: chain 3 residue 5 PHE Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 7 residue 1 PHE Chi-restraints excluded: chain 7 residue 5 PHE Chi-restraints excluded: chain AB residue 6 LYS Chi-restraints excluded: chain AE residue 1 PHE Chi-restraints excluded: chain AE residue 5 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AH residue 2 LYS Chi-restraints excluded: chain AI residue 1 PHE Chi-restraints excluded: chain AI residue 3 PHE Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 5 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 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 = 0.3209 r_free = 0.3209 target = 0.097620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.075602 restraints weight = 6556.796| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.12 r_work: 0.2688 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9261 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.273 3362 Z= 3.132 Angle : 3.353 33.962 4264 Z= 1.463 Chirality : 0.198 0.580 287 Planarity : 0.012 0.038 533 Dihedral : 36.874 179.830 369 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 4.07 % Allowed : 30.08 % Favored : 65.85 % Rotamer: Outliers : 21.95 % Allowed : 18.47 % Favored : 59.58 % Cbeta Deviations : 3.48 % 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: -6.42 (0.32), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.89 (0.25), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.055 0.008 PHEAE 5 Details of bonding type rmsd/Z covalent geometry : bond 0.07859 / 3.15 ( 3321) covalent geometry : angle 3.35258 / 1.46 ( 4264) hydrogen bonds : bond 0.08918 / 5.31 ( 20) hydrogen bonds : angle 6.08521 / 4.22 ( 60) Misc. bond : bond 0.00995 / 0.62 ( 41) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 59 time to evaluate : 0.132 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: Z 6 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8756 (tptm) REVERT: Z 8 GLU cc_start: 0.9347 (tt0) cc_final: 0.9031 (tt0) REVERT: l 6 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8934 (tttm) REVERT: l 8 GLU cc_start: 0.9359 (tt0) cc_final: 0.9086 (tt0) REVERT: n 2 LYS cc_start: 0.8127 (tttt) cc_final: 0.7750 (tttp) REVERT: 1 6 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8969 (tttm) REVERT: 1 8 GLU cc_start: 0.9349 (tt0) cc_final: 0.9077 (tt0) REVERT: AE 6 LYS cc_start: 0.8858 (mttt) cc_final: 0.8398 (mtpm) REVERT: AG 6 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8974 (tttm) REVERT: AG 8 GLU cc_start: 0.9336 (tt0) cc_final: 0.9042 (tt0) outliers start: 63 outliers final: 43 residues processed: 109 average time/residue: 0.7592 time to fit residues: 84.1359 Evaluate side-chains 106 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 59 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Y residue 1 PHE Chi-restraints excluded: chain Y residue 3 PHE Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain b residue 1 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain e residue 8 GLU Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain m residue 6 LYS Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain p residue 2 LYS Chi-restraints excluded: chain q residue 1 PHE Chi-restraints excluded: chain q residue 5 PHE Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 3 residue 1 PHE Chi-restraints excluded: chain 3 residue 3 PHE Chi-restraints excluded: chain 3 residue 5 PHE Chi-restraints excluded: chain 3 residue 7 PHE Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 7 residue 1 PHE Chi-restraints excluded: chain 7 residue 5 PHE Chi-restraints excluded: chain 7 residue 8 GLU Chi-restraints excluded: chain AB residue 6 LYS Chi-restraints excluded: chain AE residue 1 PHE Chi-restraints excluded: chain AE residue 2 LYS Chi-restraints excluded: chain AE residue 5 PHE Chi-restraints excluded: chain AE residue 8 GLU Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AH residue 6 LYS Chi-restraints excluded: chain AI residue 1 PHE Chi-restraints excluded: chain AI residue 2 LYS Chi-restraints excluded: chain AI residue 3 PHE Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain AL residue 2 LYS Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 8 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 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 = 0.3188 r_free = 0.3188 target = 0.096408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.073851 restraints weight = 7629.922| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.28 r_work: 0.2657 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9291 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.284 3362 Z= 3.142 Angle : 3.336 32.814 4264 Z= 1.452 Chirality : 0.204 0.581 287 Planarity : 0.012 0.045 533 Dihedral : 36.622 179.909 369 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 4.47 % Allowed : 33.74 % Favored : 61.79 % Rotamer: Outliers : 23.00 % Allowed : 19.16 % Favored : 57.84 % Cbeta Deviations : 3.48 % 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: -6.11 (0.34), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.65 (0.26), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.056 0.008 PHEAE 5 Details of bonding type rmsd/Z covalent geometry : bond 0.07885 / 3.16 ( 3321) covalent geometry : angle 3.33626 / 1.45 ( 4264) hydrogen bonds : bond 0.10210 / 6.03 ( 20) hydrogen bonds : angle 6.50246 / 4.53 ( 60) Misc. bond : bond 0.00965 / 0.61 ( 41) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 64 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 6 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8812 (tptm) REVERT: Z 8 GLU cc_start: 0.9364 (tt0) cc_final: 0.9038 (tt0) REVERT: b 6 LYS cc_start: 0.8973 (mttt) cc_final: 0.8506 (ttmm) REVERT: d 2 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9059 (tttt) REVERT: l 6 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8966 (tttm) REVERT: l 8 GLU cc_start: 0.9379 (tt0) cc_final: 0.9106 (tt0) REVERT: n 1 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8849 (m-80) REVERT: n 2 LYS cc_start: 0.8238 (tttt) cc_final: 0.7596 (mtmm) REVERT: n 6 LYS cc_start: 0.8897 (mttt) cc_final: 0.8460 (ttmm) REVERT: S 6 LYS cc_start: 0.8383 (mttt) cc_final: 0.8158 (mttp) REVERT: 1 6 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.9001 (tttm) REVERT: 1 8 GLU cc_start: 0.9369 (tt0) cc_final: 0.9102 (tt0) REVERT: 3 6 LYS cc_start: 0.8857 (mttt) cc_final: 0.8340 (ttmm) REVERT: 4 6 LYS cc_start: 0.8366 (mttt) cc_final: 0.8160 (mttp) REVERT: AE 6 LYS cc_start: 0.8888 (mttt) cc_final: 0.8444 (ttmm) REVERT: AG 6 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8999 (tttm) REVERT: AG 8 GLU cc_start: 0.9342 (tt0) cc_final: 0.9047 (tt0) REVERT: AI 6 LYS cc_start: 0.8894 (mttt) cc_final: 0.8433 (ttmm) outliers start: 66 outliers final: 43 residues processed: 116 average time/residue: 0.7385 time to fit residues: 87.2058 Evaluate side-chains 113 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 64 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Y residue 1 PHE Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain b residue 1 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain e residue 1 PHE Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain p residue 2 LYS Chi-restraints excluded: chain q residue 1 PHE Chi-restraints excluded: chain q residue 5 PHE Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain z residue 1 PHE Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 3 residue 1 PHE Chi-restraints excluded: chain 3 residue 3 PHE Chi-restraints excluded: chain 3 residue 5 PHE Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 6 residue 8 GLU Chi-restraints excluded: chain 7 residue 1 PHE Chi-restraints excluded: chain 7 residue 2 LYS Chi-restraints excluded: chain 7 residue 5 PHE Chi-restraints excluded: chain 7 residue 8 GLU Chi-restraints excluded: chain AB residue 6 LYS Chi-restraints excluded: chain AE residue 1 PHE Chi-restraints excluded: chain AE residue 2 LYS Chi-restraints excluded: chain AE residue 5 PHE Chi-restraints excluded: chain AF residue 1 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AI residue 1 PHE Chi-restraints excluded: chain AI residue 2 LYS Chi-restraints excluded: chain AI residue 3 PHE Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain AL residue 2 LYS Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 2 LYS Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 8 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.096149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.073282 restraints weight = 8275.983| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.38 r_work: 0.2645 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9296 moved from start: 0.6184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.289 3362 Z= 3.145 Angle : 3.323 32.827 4264 Z= 1.447 Chirality : 0.206 0.579 287 Planarity : 0.012 0.050 533 Dihedral : 36.512 179.970 369 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 25.26 Ramachandran Plot: Outliers : 5.69 % Allowed : 32.52 % Favored : 61.79 % Rotamer: Outliers : 26.13 % Allowed : 16.72 % Favored : 57.14 % Cbeta Deviations : 3.48 % 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 (0.37), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.28), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.056 0.008 PHEAE 5 Details of bonding type rmsd/Z covalent geometry : bond 0.07886 / 3.16 ( 3321) covalent geometry : angle 3.32333 / 1.45 ( 4264) hydrogen bonds : bond 0.10269 / 6.06 ( 20) hydrogen bonds : angle 6.68570 / 4.63 ( 60) Misc. bond : bond 0.00957 / 0.60 ( 41) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 64 time to evaluate : 0.127 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: M 1 PHE cc_start: 0.9507 (OUTLIER) cc_final: 0.8653 (t80) REVERT: Y 7 PHE cc_start: 0.9367 (OUTLIER) cc_final: 0.9152 (m-80) REVERT: Z 6 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8810 (tptm) REVERT: Z 8 GLU cc_start: 0.9361 (tt0) cc_final: 0.9015 (tt0) REVERT: b 6 LYS cc_start: 0.9008 (mttt) cc_final: 0.8558 (ttmm) REVERT: d 2 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.9033 (tttt) REVERT: Q 1 PHE cc_start: 0.9490 (OUTLIER) cc_final: 0.8678 (t80) REVERT: l 6 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8965 (tttm) REVERT: l 8 GLU cc_start: 0.9378 (tt0) cc_final: 0.9085 (tt0) REVERT: n 1 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8846 (m-80) REVERT: n 2 LYS cc_start: 0.8271 (tttt) cc_final: 0.7614 (mtmm) REVERT: n 6 LYS cc_start: 0.8921 (mttt) cc_final: 0.8504 (ttmm) REVERT: p 2 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8951 (tttt) REVERT: 1 6 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8990 (tttm) REVERT: 1 8 GLU cc_start: 0.9361 (tt0) cc_final: 0.9072 (tt0) REVERT: 3 6 LYS cc_start: 0.8893 (mttt) cc_final: 0.8437 (ttmm) REVERT: 6 2 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8988 (tttt) REVERT: AB 1 PHE cc_start: 0.9492 (OUTLIER) cc_final: 0.8680 (t80) REVERT: AE 6 LYS cc_start: 0.8906 (mttt) cc_final: 0.8479 (ttmm) REVERT: AG 6 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.9000 (tttm) REVERT: AG 8 GLU cc_start: 0.9345 (tt0) cc_final: 0.9043 (tt0) REVERT: AI 6 LYS cc_start: 0.8930 (mttt) cc_final: 0.8489 (ttmm) REVERT: AL 2 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9064 (tttt) outliers start: 75 outliers final: 47 residues processed: 120 average time/residue: 0.6793 time to fit residues: 83.0412 Evaluate side-chains 124 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 64 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Y residue 1 PHE Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain Y residue 7 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain b residue 1 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d 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 5 PHE Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain p residue 2 LYS Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain q residue 1 PHE Chi-restraints excluded: chain q residue 5 PHE Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain z residue 1 PHE Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 3 residue 1 PHE Chi-restraints excluded: chain 3 residue 3 PHE Chi-restraints excluded: chain 3 residue 5 PHE Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 6 residue 8 GLU Chi-restraints excluded: chain 7 residue 1 PHE Chi-restraints excluded: chain 7 residue 2 LYS Chi-restraints excluded: chain 7 residue 5 PHE Chi-restraints excluded: chain 7 residue 8 GLU Chi-restraints excluded: chain AB residue 1 PHE Chi-restraints excluded: chain AB residue 6 LYS Chi-restraints excluded: chain AE residue 1 PHE Chi-restraints excluded: chain AE residue 2 LYS Chi-restraints excluded: chain AE residue 5 PHE Chi-restraints excluded: chain AF residue 1 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AI residue 1 PHE Chi-restraints excluded: chain AI residue 2 LYS Chi-restraints excluded: chain AI residue 3 PHE Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain AI residue 7 PHE Chi-restraints excluded: chain AL residue 2 LYS Chi-restraints excluded: chain AL residue 8 GLU Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 2 LYS Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 8 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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 = 0.3178 r_free = 0.3178 target = 0.095804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.073439 restraints weight = 7086.116| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.21 r_work: 0.2655 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9294 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.289 3362 Z= 3.148 Angle : 3.336 32.813 4264 Z= 1.454 Chirality : 0.208 0.581 287 Planarity : 0.012 0.053 533 Dihedral : 36.428 179.914 369 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 5.69 % Allowed : 31.71 % Favored : 62.60 % Rotamer: Outliers : 23.00 % Allowed : 19.51 % Favored : 57.49 % Cbeta Deviations : 3.48 % 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: -5.45 (0.41), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.15 (0.31), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.057 0.008 PHE Y 5 Details of bonding type rmsd/Z covalent geometry : bond 0.07897 / 3.17 ( 3321) covalent geometry : angle 3.33600 / 1.45 ( 4264) hydrogen bonds : bond 0.10326 / 6.10 ( 20) hydrogen bonds : angle 6.76147 / 4.69 ( 60) Misc. bond : bond 0.00942 / 0.60 ( 41) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 69 time to evaluate : 0.132 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: M 1 PHE cc_start: 0.9503 (OUTLIER) cc_final: 0.8742 (t80) REVERT: Y 6 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8197 (mmmm) REVERT: Z 6 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8836 (tptm) REVERT: Z 8 GLU cc_start: 0.9344 (tt0) cc_final: 0.9039 (tt0) REVERT: b 6 LYS cc_start: 0.8968 (mttt) cc_final: 0.8540 (ttmm) REVERT: d 2 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9035 (tttt) REVERT: Q 1 PHE cc_start: 0.9507 (OUTLIER) cc_final: 0.8775 (t80) REVERT: l 6 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8975 (tttm) REVERT: l 8 GLU cc_start: 0.9365 (tt0) cc_final: 0.9100 (tt0) REVERT: n 1 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8835 (m-80) REVERT: n 2 LYS cc_start: 0.8309 (tttt) cc_final: 0.7630 (mtmm) REVERT: n 6 LYS cc_start: 0.8883 (mttt) cc_final: 0.8468 (ttmm) REVERT: p 2 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8952 (tttt) REVERT: 1 6 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8996 (tttm) REVERT: 1 8 GLU cc_start: 0.9354 (tt0) cc_final: 0.9100 (tt0) REVERT: 3 6 LYS cc_start: 0.8855 (mttt) cc_final: 0.8429 (ttmm) REVERT: 6 2 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8996 (tttt) REVERT: AB 1 PHE cc_start: 0.9482 (OUTLIER) cc_final: 0.8765 (t80) REVERT: AE 6 LYS cc_start: 0.8869 (mttt) cc_final: 0.8424 (ttmm) REVERT: AG 6 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8999 (tttm) REVERT: AG 8 GLU cc_start: 0.9335 (tt0) cc_final: 0.9058 (tt0) REVERT: AI 6 LYS cc_start: 0.8905 (mttt) cc_final: 0.8488 (ttmm) REVERT: AL 2 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9049 (tttt) outliers start: 66 outliers final: 48 residues processed: 117 average time/residue: 0.6626 time to fit residues: 78.9460 Evaluate side-chains 129 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 69 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Y residue 1 PHE Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain b residue 1 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d 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 5 PHE Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain p residue 2 LYS Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain q residue 1 PHE Chi-restraints excluded: chain q residue 5 PHE Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain z residue 1 PHE Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 3 residue 1 PHE Chi-restraints excluded: chain 3 residue 3 PHE Chi-restraints excluded: chain 3 residue 5 PHE Chi-restraints excluded: chain 3 residue 7 PHE Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 6 residue 8 GLU Chi-restraints excluded: chain 7 residue 1 PHE Chi-restraints excluded: chain 7 residue 2 LYS Chi-restraints excluded: chain 7 residue 5 PHE Chi-restraints excluded: chain 7 residue 8 GLU Chi-restraints excluded: chain AB residue 1 PHE Chi-restraints excluded: chain AB residue 6 LYS Chi-restraints excluded: chain AE residue 1 PHE Chi-restraints excluded: chain AE residue 2 LYS Chi-restraints excluded: chain AE residue 5 PHE Chi-restraints excluded: chain AF residue 1 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AI residue 1 PHE Chi-restraints excluded: chain AI residue 2 LYS Chi-restraints excluded: chain AI residue 3 PHE Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain AI residue 7 PHE Chi-restraints excluded: chain AL residue 2 LYS Chi-restraints excluded: chain AL residue 8 GLU Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 2 LYS Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 8 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 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 = 0.3179 r_free = 0.3179 target = 0.095886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.073015 restraints weight = 8284.184| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.40 r_work: 0.2641 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9297 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.288 3362 Z= 3.145 Angle : 3.332 32.840 4264 Z= 1.455 Chirality : 0.209 0.579 287 Planarity : 0.012 0.054 533 Dihedral : 36.428 179.991 369 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 6.50 % Allowed : 31.30 % Favored : 62.20 % Rotamer: Outliers : 23.00 % Allowed : 21.25 % Favored : 55.75 % Cbeta Deviations : 3.48 % 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: -5.61 (0.39), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.30), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.057 0.008 PHEAE 5 Details of bonding type rmsd/Z covalent geometry : bond 0.07890 / 3.16 ( 3321) covalent geometry : angle 3.33206 / 1.45 ( 4264) hydrogen bonds : bond 0.10397 / 6.13 ( 20) hydrogen bonds : angle 6.76081 / 4.68 ( 60) Misc. bond : bond 0.00939 / 0.59 ( 41) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 68 time to evaluate : 0.131 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: M 1 PHE cc_start: 0.9506 (OUTLIER) cc_final: 0.8750 (t80) REVERT: Y 6 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8207 (mmmm) REVERT: Z 6 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8852 (tptm) REVERT: Z 8 GLU cc_start: 0.9330 (tt0) cc_final: 0.9035 (tt0) REVERT: b 6 LYS cc_start: 0.8955 (mttt) cc_final: 0.8497 (ttmm) REVERT: d 2 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9035 (tttt) REVERT: Q 1 PHE cc_start: 0.9511 (OUTLIER) cc_final: 0.8783 (t80) REVERT: l 6 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8964 (tttm) REVERT: l 8 GLU cc_start: 0.9352 (tt0) cc_final: 0.9076 (tt0) REVERT: n 1 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8837 (m-80) REVERT: n 2 LYS cc_start: 0.8314 (tttt) cc_final: 0.7616 (mtmm) REVERT: n 6 LYS cc_start: 0.8896 (mttt) cc_final: 0.8446 (ttmm) REVERT: p 2 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8948 (tttt) REVERT: 1 6 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8981 (tttm) REVERT: 1 8 GLU cc_start: 0.9340 (tt0) cc_final: 0.9087 (tt0) REVERT: 3 6 LYS cc_start: 0.8889 (mttt) cc_final: 0.8435 (ttmm) REVERT: 6 2 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8988 (tttt) REVERT: AB 1 PHE cc_start: 0.9508 (OUTLIER) cc_final: 0.8792 (t80) REVERT: AE 6 LYS cc_start: 0.8860 (mttt) cc_final: 0.8437 (ttmm) REVERT: AG 6 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8993 (tttm) REVERT: AG 8 GLU cc_start: 0.9318 (tt0) cc_final: 0.9034 (tt0) REVERT: AI 6 LYS cc_start: 0.8892 (mttt) cc_final: 0.8441 (ttmm) REVERT: AL 2 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.9034 (tttt) outliers start: 66 outliers final: 49 residues processed: 116 average time/residue: 0.7793 time to fit residues: 91.9838 Evaluate side-chains 129 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 68 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Y residue 1 PHE Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain b residue 1 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d 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 5 PHE Chi-restraints excluded: chain e residue 8 GLU Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain p residue 2 LYS Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain q residue 1 PHE Chi-restraints excluded: chain q residue 5 PHE Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain z residue 1 PHE Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 3 residue 1 PHE Chi-restraints excluded: chain 3 residue 3 PHE Chi-restraints excluded: chain 3 residue 5 PHE Chi-restraints excluded: chain 3 residue 7 PHE Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 6 residue 8 GLU Chi-restraints excluded: chain 7 residue 1 PHE Chi-restraints excluded: chain 7 residue 2 LYS Chi-restraints excluded: chain 7 residue 5 PHE Chi-restraints excluded: chain 7 residue 8 GLU Chi-restraints excluded: chain AB residue 1 PHE Chi-restraints excluded: chain AB residue 6 LYS Chi-restraints excluded: chain AE residue 1 PHE Chi-restraints excluded: chain AE residue 2 LYS Chi-restraints excluded: chain AE residue 5 PHE Chi-restraints excluded: chain AF residue 1 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AI residue 1 PHE Chi-restraints excluded: chain AI residue 2 LYS Chi-restraints excluded: chain AI residue 3 PHE Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain AI residue 7 PHE Chi-restraints excluded: chain AL residue 2 LYS Chi-restraints excluded: chain AL residue 8 GLU Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 2 LYS Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 8 GLU 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 = 0.3166 r_free = 0.3166 target = 0.095179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.072506 restraints weight = 7354.766| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.28 r_work: 0.2647 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9295 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.288 3362 Z= 3.146 Angle : 3.341 32.808 4264 Z= 1.460 Chirality : 0.210 0.579 287 Planarity : 0.012 0.054 533 Dihedral : 36.435 179.885 369 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 24.30 Ramachandran Plot: Outliers : 6.91 % Allowed : 30.08 % Favored : 63.01 % Rotamer: Outliers : 22.30 % Allowed : 22.30 % Favored : 55.40 % Cbeta Deviations : 3.48 % 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: -5.67 (0.39), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.32 (0.29), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.058 0.008 PHEAE 5 Details of bonding type rmsd/Z covalent geometry : bond 0.07893 / 3.16 ( 3321) covalent geometry : angle 3.34071 / 1.46 ( 4264) hydrogen bonds : bond 0.10441 / 6.15 ( 20) hydrogen bonds : angle 6.77537 / 4.69 ( 60) Misc. bond : bond 0.00941 / 0.59 ( 41) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 68 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 PHE cc_start: 0.9515 (OUTLIER) cc_final: 0.8758 (t80) REVERT: Y 6 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8199 (mmmm) REVERT: Z 6 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8845 (tptm) REVERT: Z 8 GLU cc_start: 0.9324 (tt0) cc_final: 0.9027 (tt0) REVERT: b 6 LYS cc_start: 0.8950 (mttt) cc_final: 0.8497 (ttmm) REVERT: d 2 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9035 (tttt) REVERT: Q 1 PHE cc_start: 0.9505 (OUTLIER) cc_final: 0.8780 (t80) REVERT: Q 8 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: l 6 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8962 (tttm) REVERT: l 8 GLU cc_start: 0.9349 (tt0) cc_final: 0.9084 (tt0) REVERT: n 1 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8834 (m-80) REVERT: n 2 LYS cc_start: 0.8306 (tttt) cc_final: 0.7606 (mtmm) REVERT: n 6 LYS cc_start: 0.8862 (mttt) cc_final: 0.8442 (ttmm) REVERT: p 2 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8942 (tttt) REVERT: 1 6 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8979 (tttm) REVERT: 1 8 GLU cc_start: 0.9341 (tt0) cc_final: 0.9087 (tt0) REVERT: 3 6 LYS cc_start: 0.8883 (mttt) cc_final: 0.8438 (ttmm) REVERT: 6 2 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8982 (tttt) REVERT: AB 1 PHE cc_start: 0.9500 (OUTLIER) cc_final: 0.8780 (t80) REVERT: AE 6 LYS cc_start: 0.8865 (mttt) cc_final: 0.8422 (ttmm) REVERT: AG 6 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8988 (tttm) REVERT: AG 8 GLU cc_start: 0.9316 (tt0) cc_final: 0.9027 (tt0) REVERT: AI 6 LYS cc_start: 0.8886 (mttt) cc_final: 0.8437 (ttmm) REVERT: AL 2 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9062 (tttt) outliers start: 64 outliers final: 48 residues processed: 114 average time/residue: 0.7835 time to fit residues: 90.8901 Evaluate side-chains 129 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 68 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain Y residue 1 PHE Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain b residue 1 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d 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 5 PHE Chi-restraints excluded: chain e residue 8 GLU Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain Q residue 8 GLU Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain p residue 2 LYS Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain q residue 1 PHE Chi-restraints excluded: chain q residue 5 PHE Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain z residue 1 PHE Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 3 residue 1 PHE Chi-restraints excluded: chain 3 residue 3 PHE Chi-restraints excluded: chain 3 residue 5 PHE Chi-restraints excluded: chain 3 residue 7 PHE Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 6 residue 8 GLU Chi-restraints excluded: chain 7 residue 1 PHE Chi-restraints excluded: chain 7 residue 2 LYS Chi-restraints excluded: chain 7 residue 5 PHE Chi-restraints excluded: chain 7 residue 8 GLU Chi-restraints excluded: chain AB residue 1 PHE Chi-restraints excluded: chain AB residue 6 LYS Chi-restraints excluded: chain AE residue 1 PHE Chi-restraints excluded: chain AE residue 2 LYS Chi-restraints excluded: chain AE residue 5 PHE Chi-restraints excluded: chain AF residue 1 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AI residue 1 PHE Chi-restraints excluded: chain AI residue 2 LYS Chi-restraints excluded: chain AI residue 3 PHE Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain AI residue 7 PHE Chi-restraints excluded: chain AL residue 2 LYS Chi-restraints excluded: chain AL residue 8 GLU Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 2 LYS Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 8 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 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 = 0.3174 r_free = 0.3174 target = 0.095634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.073213 restraints weight = 7164.348| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.21 r_work: 0.2651 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9296 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.287 3362 Z= 3.147 Angle : 3.341 32.844 4264 Z= 1.460 Chirality : 0.210 0.580 287 Planarity : 0.012 0.054 533 Dihedral : 36.435 179.832 369 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 6.91 % Allowed : 30.08 % Favored : 63.01 % Rotamer: Outliers : 21.95 % Allowed : 24.04 % Favored : 54.01 % Cbeta Deviations : 3.48 % 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: -5.73 (0.38), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.36 (0.29), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.057 0.008 PHE Y 5 Details of bonding type rmsd/Z covalent geometry : bond 0.07896 / 3.16 ( 3321) covalent geometry : angle 3.34097 / 1.46 ( 4264) hydrogen bonds : bond 0.10384 / 6.12 ( 20) hydrogen bonds : angle 6.76879 / 4.69 ( 60) Misc. bond : bond 0.00935 / 0.59 ( 41) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 69 time to evaluate : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 1 PHE cc_start: 0.9514 (OUTLIER) cc_final: 0.8754 (t80) REVERT: Y 6 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8193 (mmmm) REVERT: Z 8 GLU cc_start: 0.9323 (tt0) cc_final: 0.9071 (tt0) REVERT: b 6 LYS cc_start: 0.8943 (mttt) cc_final: 0.8499 (ttmm) REVERT: d 2 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9053 (tttt) REVERT: Q 1 PHE cc_start: 0.9505 (OUTLIER) cc_final: 0.8781 (t80) REVERT: Q 8 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: l 6 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8975 (tttm) REVERT: n 1 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8835 (m-80) REVERT: n 2 LYS cc_start: 0.8320 (tttt) cc_final: 0.7607 (mtmm) REVERT: n 6 LYS cc_start: 0.8874 (mttt) cc_final: 0.8451 (ttmm) REVERT: p 2 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8948 (tttt) REVERT: q 2 LYS cc_start: 0.8195 (tttt) cc_final: 0.7726 (tttt) REVERT: 1 6 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8983 (tttm) REVERT: 1 8 GLU cc_start: 0.9337 (tt0) cc_final: 0.9093 (tt0) REVERT: 3 6 LYS cc_start: 0.8885 (mttt) cc_final: 0.8441 (ttmm) REVERT: 6 2 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8985 (tttt) REVERT: AB 1 PHE cc_start: 0.9499 (OUTLIER) cc_final: 0.8786 (t80) REVERT: AE 6 LYS cc_start: 0.8848 (mttt) cc_final: 0.8381 (mtpp) REVERT: AG 6 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8997 (tttm) REVERT: AI 6 LYS cc_start: 0.8875 (mttt) cc_final: 0.8440 (ttmm) REVERT: AL 2 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9039 (tttt) outliers start: 63 outliers final: 48 residues processed: 115 average time/residue: 0.8334 time to fit residues: 97.4648 Evaluate side-chains 129 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 69 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Y residue 1 PHE Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain b residue 1 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d 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 5 PHE Chi-restraints excluded: chain e residue 8 GLU Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain Q residue 8 GLU Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain p residue 2 LYS Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain q residue 1 PHE Chi-restraints excluded: chain q residue 5 PHE Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain z residue 1 PHE Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 3 residue 1 PHE Chi-restraints excluded: chain 3 residue 3 PHE Chi-restraints excluded: chain 3 residue 5 PHE Chi-restraints excluded: chain 3 residue 7 PHE Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 6 residue 8 GLU Chi-restraints excluded: chain 7 residue 1 PHE Chi-restraints excluded: chain 7 residue 2 LYS Chi-restraints excluded: chain 7 residue 5 PHE Chi-restraints excluded: chain 7 residue 8 GLU Chi-restraints excluded: chain AB residue 1 PHE Chi-restraints excluded: chain AE residue 1 PHE Chi-restraints excluded: chain AE residue 2 LYS Chi-restraints excluded: chain AE residue 5 PHE Chi-restraints excluded: chain AF residue 1 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AI residue 1 PHE Chi-restraints excluded: chain AI residue 2 LYS Chi-restraints excluded: chain AI residue 3 PHE Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain AI residue 7 PHE Chi-restraints excluded: chain AL residue 2 LYS Chi-restraints excluded: chain AL residue 8 GLU Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 2 LYS Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 8 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.095700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.073684 restraints weight = 6364.321| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.08 r_work: 0.2657 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9294 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.288 3362 Z= 3.147 Angle : 3.340 32.811 4264 Z= 1.461 Chirality : 0.210 0.580 287 Planarity : 0.012 0.054 533 Dihedral : 36.449 179.952 369 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 25.10 Ramachandran Plot: Outliers : 6.91 % Allowed : 29.67 % Favored : 63.41 % Rotamer: Outliers : 22.65 % Allowed : 24.74 % Favored : 52.61 % Cbeta Deviations : 3.48 % 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: -5.76 (0.38), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.29), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.066 0.008 PHE Y 7 Details of bonding type rmsd/Z covalent geometry : bond 0.07896 / 3.16 ( 3321) covalent geometry : angle 3.34049 / 1.46 ( 4264) hydrogen bonds : bond 0.10396 / 6.12 ( 20) hydrogen bonds : angle 6.78095 / 4.69 ( 60) Misc. bond : bond 0.00922 / 0.58 ( 41) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 69 time to evaluate : 0.138 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: M 1 PHE cc_start: 0.9505 (OUTLIER) cc_final: 0.8749 (t80) REVERT: Y 6 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8208 (mmmm) REVERT: Z 6 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8831 (tptm) REVERT: Z 8 GLU cc_start: 0.9315 (tt0) cc_final: 0.9030 (tt0) REVERT: b 6 LYS cc_start: 0.8932 (mttt) cc_final: 0.8486 (ttmm) REVERT: d 2 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9015 (tttt) REVERT: Q 1 PHE cc_start: 0.9499 (OUTLIER) cc_final: 0.8785 (t80) REVERT: Q 8 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: l 6 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8955 (tttm) REVERT: n 1 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8832 (m-80) REVERT: n 2 LYS cc_start: 0.8297 (tttt) cc_final: 0.7614 (mtmm) REVERT: n 6 LYS cc_start: 0.8862 (mttt) cc_final: 0.8440 (ttmm) REVERT: p 2 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8944 (tttt) REVERT: q 2 LYS cc_start: 0.8197 (tttt) cc_final: 0.7741 (tttt) REVERT: 1 6 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8971 (tttm) REVERT: 1 8 GLU cc_start: 0.9333 (tt0) cc_final: 0.9084 (tt0) REVERT: 3 6 LYS cc_start: 0.8879 (mttt) cc_final: 0.8431 (ttmm) REVERT: 6 2 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8986 (tttt) REVERT: AB 1 PHE cc_start: 0.9490 (OUTLIER) cc_final: 0.8776 (t80) REVERT: AC 8 GLU cc_start: 0.9296 (tt0) cc_final: 0.9090 (tt0) REVERT: AE 6 LYS cc_start: 0.8817 (mttt) cc_final: 0.8370 (mtpp) REVERT: AG 6 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8980 (tttm) REVERT: AI 6 LYS cc_start: 0.8867 (mttt) cc_final: 0.8430 (ttmm) REVERT: AL 2 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.9034 (tttt) outliers start: 65 outliers final: 48 residues processed: 116 average time/residue: 0.8631 time to fit residues: 101.8845 Evaluate side-chains 130 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 69 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 1 PHE Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain Y residue 1 PHE Chi-restraints excluded: chain Y residue 5 PHE Chi-restraints excluded: chain N residue 1 PHE Chi-restraints excluded: chain Z residue 6 LYS Chi-restraints excluded: chain b residue 1 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d 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 5 PHE Chi-restraints excluded: chain e residue 8 GLU Chi-restraints excluded: chain Q residue 1 PHE Chi-restraints excluded: chain Q residue 6 LYS Chi-restraints excluded: chain Q residue 8 GLU Chi-restraints excluded: chain R residue 1 PHE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain n residue 1 PHE Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain n residue 5 PHE Chi-restraints excluded: chain n residue 7 PHE Chi-restraints excluded: chain p residue 2 LYS Chi-restraints excluded: chain p residue 8 GLU Chi-restraints excluded: chain q residue 1 PHE Chi-restraints excluded: chain q residue 5 PHE Chi-restraints excluded: chain q residue 8 GLU Chi-restraints excluded: chain z residue 1 PHE Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 3 residue 1 PHE Chi-restraints excluded: chain 3 residue 3 PHE Chi-restraints excluded: chain 3 residue 5 PHE Chi-restraints excluded: chain 3 residue 7 PHE Chi-restraints excluded: chain 3 residue 8 GLU Chi-restraints excluded: chain 6 residue 2 LYS Chi-restraints excluded: chain 6 residue 8 GLU Chi-restraints excluded: chain 7 residue 1 PHE Chi-restraints excluded: chain 7 residue 2 LYS Chi-restraints excluded: chain 7 residue 5 PHE Chi-restraints excluded: chain 7 residue 8 GLU Chi-restraints excluded: chain AB residue 1 PHE Chi-restraints excluded: chain AE residue 1 PHE Chi-restraints excluded: chain AE residue 2 LYS Chi-restraints excluded: chain AE residue 5 PHE Chi-restraints excluded: chain AF residue 1 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AI residue 1 PHE Chi-restraints excluded: chain AI residue 2 LYS Chi-restraints excluded: chain AI residue 3 PHE Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain AI residue 7 PHE Chi-restraints excluded: chain AL residue 2 LYS Chi-restraints excluded: chain AL residue 8 GLU Chi-restraints excluded: chain AM residue 1 PHE Chi-restraints excluded: chain AM residue 2 LYS Chi-restraints excluded: chain AM residue 5 PHE Chi-restraints excluded: chain AM residue 8 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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 = 0.3171 r_free = 0.3171 target = 0.095520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.072802 restraints weight = 7927.141| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.33 r_work: 0.2642 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9299 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.290 3362 Z= 3.146 Angle : 3.344 32.837 4264 Z= 1.462 Chirality : 0.210 0.580 287 Planarity : 0.012 0.054 533 Dihedral : 36.454 179.976 369 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 7.72 % Allowed : 29.67 % Favored : 62.60 % Rotamer: Outliers : 22.65 % Allowed : 25.44 % Favored : 51.92 % Cbeta Deviations : 3.48 % 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: -5.80 (0.38), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.42 (0.29), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.068 0.008 PHE Y 7 Details of bonding type rmsd/Z covalent geometry : bond 0.07895 / 3.16 ( 3321) covalent geometry : angle 3.34420 / 1.46 ( 4264) hydrogen bonds : bond 0.10372 / 6.11 ( 20) hydrogen bonds : angle 6.77038 / 4.68 ( 60) Misc. bond : bond 0.00923 / 0.58 ( 41) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1542.50 seconds wall clock time: 26 minutes 57.83 seconds (1617.83 seconds total)