Starting phenix.real_space_refine on Thu Oct 22 18:03:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pdt_71543/10_2026/9pdt_71543.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pdt_71543/10_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_71543/10_2026/9pdt_71543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pdt_71543/10_2026/9pdt_71543.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pdt_71543/10_2026/9pdt_71543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pdt_71543/10_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-2.3rc1-6221/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: 0.84, per 1000 atoms: 0.26 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: 0.35 Conformation dependent library (CDL) restraints added in 50.4 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: 0.08 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: 0.37 Time building geometry restraints manager: 0.37 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: 0.550 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.640 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.410 ------------------------------------------------------------------------------- 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 : 0.126 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: 1.0372 time to fit residues: 62.1162 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 : 0.097 ------------------------------------------------------------------------------- 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: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.145542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122441 restraints weight = 4231.005| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.13 r_work: 0.3375 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3362 Z= 0.114 Angle : 0.613 5.487 4264 Z= 0.290 Chirality : 0.029 0.092 287 Planarity : 0.002 0.007 533 Dihedral : 54.201 179.973 378 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.81 % Allowed : 11.38 % Favored : 87.80 % Rotamer: Outliers : 4.53 % Allowed : 25.44 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.08 (0.44), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE b 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 3321) covalent geometry : angle 0.61270 / 0.29 ( 4264) hydrogen bonds : bond 0.01525 / 0.83 ( 20) hydrogen bonds : angle 4.13476 / 2.83 ( 60) Misc. bond : bond 0.00021 / 0.01 ( 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 60 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.105 Fit side-chains REVERT: Y 2 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6826 (tmtt) REVERT: b 8 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7625 (mt-10) REVERT: n 8 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7583 (mt-10) REVERT: AE 2 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6953 (tmtt) REVERT: AI 8 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7638 (mt-10) outliers start: 13 outliers final: 0 residues processed: 60 average time/residue: 1.0477 time to fit residues: 63.7342 Evaluate side-chains 49 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain AE residue 2 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.098476 restraints weight = 5368.060| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.41 r_work: 0.3038 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.074 3362 Z= 0.452 Angle : 0.902 7.138 4264 Z= 0.431 Chirality : 0.035 0.120 287 Planarity : 0.004 0.017 533 Dihedral : 54.481 179.985 369 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.41 % Allowed : 35.77 % Favored : 63.82 % Rotamer: Outliers : 15.33 % Allowed : 19.51 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.54 (0.40), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.31), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.039 0.003 PHE 3 7 Details of bonding type rmsd/Z covalent geometry : bond 0.01188 / 0.45 ( 3321) covalent geometry : angle 0.90239 / 0.43 ( 4264) hydrogen bonds : bond 0.02995 / 1.72 ( 20) hydrogen bonds : angle 5.48399 / 3.76 ( 60) Misc. bond : bond 0.00131 / 0.08 ( 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 88 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 44 time to evaluate : 0.106 Fit side-chains REVERT: Z 6 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8455 (tptm) REVERT: b 5 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8716 (m-10) REVERT: n 5 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8711 (m-10) REVERT: AI 5 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8718 (m-10) outliers start: 44 outliers final: 15 residues processed: 85 average time/residue: 0.7409 time to fit residues: 64.2248 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 : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain e residue 1 PHE 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 2 residue 2 LYS Chi-restraints excluded: chain 3 residue 3 PHE Chi-restraints excluded: chain 7 residue 1 PHE Chi-restraints excluded: chain AE residue 5 PHE Chi-restraints excluded: chain AH residue 2 LYS Chi-restraints excluded: chain AI residue 3 PHE Chi-restraints excluded: chain AI residue 5 PHE Chi-restraints excluded: chain AM residue 1 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110302 restraints weight = 5353.773| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.51 r_work: 0.3167 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3362 Z= 0.113 Angle : 0.603 4.885 4264 Z= 0.289 Chirality : 0.030 0.091 287 Planarity : 0.002 0.007 533 Dihedral : 54.698 179.997 369 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 4.07 % Allowed : 8.54 % Favored : 87.40 % Rotamer: Outliers : 1.74 % Allowed : 30.66 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.33 (0.42), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.32), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHEAE 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 3321) covalent geometry : angle 0.60261 / 0.29 ( 4264) hydrogen bonds : bond 0.01749 / 0.97 ( 20) hydrogen bonds : angle 4.41938 / 3.04 ( 60) Misc. bond : bond 0.00021 / 0.01 ( 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 49 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.145 Fit side-chains REVERT: d 6 LYS cc_start: 0.9106 (tttp) cc_final: 0.8890 (tptt) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 1.0533 time to fit residues: 52.4345 Evaluate side-chains 46 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 2 LYS Chi-restraints excluded: chain AH residue 2 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.096674 restraints weight = 6687.067| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.71 r_work: 0.3008 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.063 3362 Z= 0.446 Angle : 0.843 6.764 4264 Z= 0.404 Chirality : 0.032 0.091 287 Planarity : 0.003 0.015 533 Dihedral : 54.586 179.941 369 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 1.63 % Allowed : 35.37 % Favored : 63.01 % Rotamer: Outliers : 11.15 % Allowed : 23.00 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.56 (0.39), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.30), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.033 0.002 PHE Y 7 Details of bonding type rmsd/Z covalent geometry : bond 0.01161 / 0.45 ( 3321) covalent geometry : angle 0.84338 / 0.40 ( 4264) hydrogen bonds : bond 0.02536 / 1.45 ( 20) hydrogen bonds : angle 5.51194 / 3.77 ( 60) Misc. bond : bond 0.00141 / 0.09 ( 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 76 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 44 time to evaluate : 0.085 Fit side-chains REVERT: l 6 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8188 (tptm) REVERT: l 8 GLU cc_start: 0.8755 (tt0) cc_final: 0.8550 (tt0) REVERT: 1 6 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8251 (tptm) REVERT: AG 6 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8346 (tptm) outliers start: 32 outliers final: 9 residues processed: 73 average time/residue: 0.7151 time to fit residues: 53.2948 Evaluate side-chains 56 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain e 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 q residue 1 PHE Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 2 residue 2 LYS Chi-restraints excluded: chain 3 residue 3 PHE Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AH residue 2 LYS Chi-restraints excluded: chain AI residue 3 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108763 restraints weight = 5522.021| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.46 r_work: 0.3208 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3362 Z= 0.106 Angle : 0.585 4.853 4264 Z= 0.283 Chirality : 0.029 0.064 287 Planarity : 0.002 0.006 533 Dihedral : 54.686 179.997 369 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 4.07 % Allowed : 11.79 % Favored : 84.15 % Rotamer: Outliers : 2.44 % Allowed : 33.45 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.27 (0.42), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.32), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE 7 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 3321) covalent geometry : angle 0.58475 / 0.28 ( 4264) hydrogen bonds : bond 0.01696 / 0.96 ( 20) hydrogen bonds : angle 4.31028 / 3.01 ( 60) Misc. bond : bond 0.00020 / 0.01 ( 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 51 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.108 Fit side-chains REVERT: l 6 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8336 (tptm) REVERT: 1 6 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8311 (tptm) outliers start: 7 outliers final: 2 residues processed: 48 average time/residue: 1.0034 time to fit residues: 48.8755 Evaluate side-chains 48 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 2 residue 2 LYS Chi-restraints excluded: chain AH residue 2 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.097574 restraints weight = 6565.726| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.72 r_work: 0.3002 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.062 3362 Z= 0.448 Angle : 0.827 6.779 4264 Z= 0.396 Chirality : 0.032 0.073 287 Planarity : 0.003 0.014 533 Dihedral : 54.597 179.993 369 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 4.07 % Allowed : 32.93 % Favored : 63.01 % Rotamer: Outliers : 9.41 % Allowed : 26.48 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.44 (0.40), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.30), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.031 0.002 PHE Y 7 Details of bonding type rmsd/Z covalent geometry : bond 0.01165 / 0.45 ( 3321) covalent geometry : angle 0.82703 / 0.40 ( 4264) hydrogen bonds : bond 0.02486 / 1.42 ( 20) hydrogen bonds : angle 5.65667 / 3.88 ( 60) Misc. bond : bond 0.00131 / 0.08 ( 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 71 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 44 time to evaluate : 0.134 Fit side-chains REVERT: l 6 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8200 (tptm) REVERT: 1 6 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8304 (tptm) REVERT: 6 6 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8644 (tptm) outliers start: 27 outliers final: 7 residues processed: 68 average time/residue: 0.7967 time to fit residues: 55.2077 Evaluate side-chains 54 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 2 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain n residue 3 PHE Chi-restraints excluded: chain q residue 1 PHE Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 2 residue 2 LYS Chi-restraints excluded: chain 6 residue 6 LYS Chi-restraints excluded: chain AH residue 2 LYS Chi-restraints excluded: chain AI residue 3 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.131921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108088 restraints weight = 5848.923| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.59 r_work: 0.3182 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3362 Z= 0.108 Angle : 0.582 4.820 4264 Z= 0.282 Chirality : 0.029 0.061 287 Planarity : 0.002 0.006 533 Dihedral : 54.625 179.998 369 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 4.07 % Allowed : 12.20 % Favored : 83.74 % Rotamer: Outliers : 1.74 % Allowed : 34.15 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.22 (0.42), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.32), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.001 PHE 3 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 3321) covalent geometry : angle 0.58249 / 0.28 ( 4264) hydrogen bonds : bond 0.01845 / 1.02 ( 20) hydrogen bonds : angle 4.33743 / 3.00 ( 60) Misc. bond : bond 0.00017 / 0.01 ( 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 49 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.125 Fit side-chains REVERT: l 6 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8322 (tptm) outliers start: 5 outliers final: 2 residues processed: 47 average time/residue: 1.0483 time to fit residues: 50.0455 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 : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain 2 residue 2 LYS Chi-restraints excluded: chain AH residue 2 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.120257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.097184 restraints weight = 5590.008| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.39 r_work: 0.3019 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.061 3362 Z= 0.447 Angle : 0.820 6.693 4264 Z= 0.391 Chirality : 0.033 0.073 287 Planarity : 0.003 0.014 533 Dihedral : 54.591 179.909 369 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 4.07 % Allowed : 32.11 % Favored : 63.82 % Rotamer: Outliers : 4.18 % Allowed : 31.71 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.34 (0.40), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.30), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.031 0.002 PHEAE 7 Details of bonding type rmsd/Z covalent geometry : bond 0.01159 / 0.45 ( 3321) covalent geometry : angle 0.81970 / 0.39 ( 4264) hydrogen bonds : bond 0.02420 / 1.37 ( 20) hydrogen bonds : angle 5.84525 / 3.99 ( 60) Misc. bond : bond 0.00133 / 0.08 ( 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 56 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.128 Fit side-chains REVERT: l 6 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8338 (tptm) REVERT: 1 6 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8461 (tptm) REVERT: 6 6 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8762 (tptm) outliers start: 12 outliers final: 3 residues processed: 53 average time/residue: 0.9634 time to fit residues: 51.9158 Evaluate side-chains 50 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 2 residue 2 LYS Chi-restraints excluded: chain 6 residue 6 LYS Chi-restraints excluded: chain AD residue 2 LYS Chi-restraints excluded: chain AH residue 2 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107619 restraints weight = 5487.175| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.49 r_work: 0.3160 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3362 Z= 0.111 Angle : 0.585 4.823 4264 Z= 0.285 Chirality : 0.029 0.061 287 Planarity : 0.002 0.007 533 Dihedral : 54.613 180.000 369 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 4.07 % Allowed : 12.20 % Favored : 83.74 % Rotamer: Outliers : 2.09 % Allowed : 34.15 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.16 (0.43), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.33), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE 3 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 3321) covalent geometry : angle 0.58548 / 0.28 ( 4264) hydrogen bonds : bond 0.01851 / 1.02 ( 20) hydrogen bonds : angle 4.43672 / 3.08 ( 60) Misc. bond : bond 0.00020 / 0.01 ( 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 50 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.130 Fit side-chains REVERT: l 6 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8300 (tptm) REVERT: 1 6 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8350 (tptm) REVERT: 6 6 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8660 (tptm) outliers start: 6 outliers final: 2 residues processed: 46 average time/residue: 1.0770 time to fit residues: 50.3012 Evaluate side-chains 49 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 6 LYS Chi-restraints excluded: chain 1 residue 6 LYS Chi-restraints excluded: chain 2 residue 2 LYS Chi-restraints excluded: chain 6 residue 6 LYS Chi-restraints excluded: chain AH residue 2 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.097546 restraints weight = 6401.383| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.67 r_work: 0.2999 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.061 3362 Z= 0.450 Angle : 0.828 6.706 4264 Z= 0.397 Chirality : 0.034 0.075 287 Planarity : 0.003 0.014 533 Dihedral : 54.606 179.944 369 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 4.07 % Allowed : 32.52 % Favored : 63.41 % Rotamer: Outliers : 3.14 % Allowed : 33.10 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.30 (0.40), residues: 246 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.31), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.031 0.002 PHEAE 7 Details of bonding type rmsd/Z covalent geometry : bond 0.01164 / 0.45 ( 3321) covalent geometry : angle 0.82847 / 0.40 ( 4264) hydrogen bonds : bond 0.02343 / 1.35 ( 20) hydrogen bonds : angle 5.90414 / 4.03 ( 60) Misc. bond : bond 0.00138 / 0.08 ( 41) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1127.30 seconds wall clock time: 19 minutes 58.93 seconds (1198.93 seconds total)