Starting phenix.real_space_refine on Wed Jul 1 20:45:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b3a_15824/07_2026/8b3a_15824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b3a_15824/07_2026/8b3a_15824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b3a_15824/07_2026/8b3a_15824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b3a_15824/07_2026/8b3a_15824.map" model { file = "/net/cci-nas-00/data/ceres_data/8b3a_15824/07_2026/8b3a_15824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b3a_15824/07_2026/8b3a_15824.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8b3a_15824/07_2026/8b3a_15824.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b3a_15824/07_2026/8b3a_15824.cif" } resolution = 3.8 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= 0.000 sd= 0.002 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 1320 2.51 5 N 450 2.21 5 O 240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2010 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} 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: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} 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: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} 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: "c" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 6} Chain: "d" 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: 0.67, per 1000 atoms: 0.33 Number of scatterers: 2010 At special positions: 0 Unit cell: (90.48, 49.92, 37.44, 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 240 8.00 N 450 7.00 C 1320 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=30, symmetry=0 Number of additional bonds: simple=30, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 55.1 milliseconds 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 420 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 47.6% 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 'A' and resid 2 through 4 removed outlier: 6.335A pdb=" N LEU A 3 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU G 3 " --> pdb=" O HIS M 4 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU M 3 " --> pdb=" O HIS S 4 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU S 3 " --> pdb=" O HIS Y 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 4 removed outlier: 6.335A pdb=" N LEU B 3 " --> pdb=" O HIS H 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU H 3 " --> pdb=" O HIS N 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU N 3 " --> pdb=" O HIS T 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU T 3 " --> pdb=" O HIS Z 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 6 removed outlier: 6.270A pdb=" N LEU C 3 " --> pdb=" O HIS I 4 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ARG I 6 " --> pdb=" O LEU C 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU C 5 " --> pdb=" O ARG I 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU I 3 " --> pdb=" O HIS O 4 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ARG O 6 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU I 5 " --> pdb=" O ARG O 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU O 3 " --> pdb=" O HIS U 4 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ARG U 6 " --> pdb=" O LEU O 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU O 5 " --> pdb=" O ARG U 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU U 3 " --> pdb=" O HIS a 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG a 6 " --> pdb=" O LEU U 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU U 5 " --> pdb=" O ARG a 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 6 removed outlier: 6.270A pdb=" N LEU D 3 " --> pdb=" O HIS J 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG J 6 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU D 5 " --> pdb=" O ARG J 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU J 3 " --> pdb=" O HIS P 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG P 6 " --> pdb=" O LEU J 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU J 5 " --> pdb=" O ARG P 6 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU P 3 " --> pdb=" O HIS V 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG V 6 " --> pdb=" O LEU P 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU P 5 " --> pdb=" O ARG V 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU V 3 " --> pdb=" O HIS b 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG b 6 " --> pdb=" O LEU V 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU V 5 " --> pdb=" O ARG b 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 6 removed outlier: 6.372A pdb=" N LEU E 3 " --> pdb=" O HIS K 4 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ARG K 6 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU E 5 " --> pdb=" O ARG K 6 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU K 3 " --> pdb=" O HIS Q 4 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ARG Q 6 " --> pdb=" O LEU K 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU K 5 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU Q 3 " --> pdb=" O HIS W 4 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ARG W 6 " --> pdb=" O LEU Q 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU Q 5 " --> pdb=" O ARG W 6 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU W 3 " --> pdb=" O HIS c 4 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ARG c 6 " --> pdb=" O LEU W 3 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU W 5 " --> pdb=" O ARG c 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 6 removed outlier: 6.372A pdb=" N LEU F 3 " --> pdb=" O HIS L 4 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ARG L 6 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU F 5 " --> pdb=" O ARG L 6 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU L 3 " --> pdb=" O HIS R 4 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ARG R 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU L 5 " --> pdb=" O ARG R 6 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU R 3 " --> pdb=" O HIS X 4 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ARG X 6 " --> pdb=" O LEU R 3 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU R 5 " --> pdb=" O ARG X 6 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU X 3 " --> pdb=" O HIS d 4 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ARG d 6 " --> pdb=" O LEU X 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU X 5 " --> pdb=" O ARG d 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 No hydrogen bonds 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: 0.03 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 240 1.27 - 1.34: 420 1.34 - 1.41: 180 1.41 - 1.47: 240 1.47 - 1.54: 930 Bond restraints: 2010 Sorted by residual: bond pdb=" C HIS I 4 " pdb=" N LEU I 5 " ideal model delta sigma weight residual 1.331 1.278 0.053 1.55e-02 4.16e+03 1.16e+01 bond pdb=" C HIS U 4 " pdb=" N LEU U 5 " ideal model delta sigma weight residual 1.331 1.278 0.053 1.55e-02 4.16e+03 1.15e+01 bond pdb=" C HIS a 4 " pdb=" N LEU a 5 " ideal model delta sigma weight residual 1.331 1.279 0.052 1.55e-02 4.16e+03 1.15e+01 bond pdb=" C HIS L 4 " pdb=" N LEU L 5 " ideal model delta sigma weight residual 1.331 1.279 0.052 1.55e-02 4.16e+03 1.15e+01 bond pdb=" C HIS J 4 " pdb=" N LEU J 5 " ideal model delta sigma weight residual 1.331 1.279 0.052 1.55e-02 4.16e+03 1.14e+01 ... (remaining 2005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 2018 1.52 - 3.03: 299 3.03 - 4.55: 205 4.55 - 6.07: 88 6.07 - 7.59: 60 Bond angle restraints: 2670 Sorted by residual: angle pdb=" N LEU N 3 " pdb=" CA LEU N 3 " pdb=" C LEU N 3 " ideal model delta sigma weight residual 108.96 102.19 6.77 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU M 3 " pdb=" CA LEU M 3 " pdb=" C LEU M 3 " ideal model delta sigma weight residual 108.96 102.19 6.77 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU Y 3 " pdb=" CA LEU Y 3 " pdb=" C LEU Y 3 " ideal model delta sigma weight residual 108.96 102.20 6.76 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU G 3 " pdb=" CA LEU G 3 " pdb=" C LEU G 3 " ideal model delta sigma weight residual 108.96 102.20 6.76 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU S 3 " pdb=" CA LEU S 3 " pdb=" C LEU S 3 " ideal model delta sigma weight residual 108.96 102.20 6.76 1.59e+00 3.96e-01 1.81e+01 ... (remaining 2665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.64: 860 18.64 - 37.29: 220 37.29 - 55.93: 60 55.93 - 74.57: 0 74.57 - 93.22: 30 Dihedral angle restraints: 1170 sinusoidal: 570 harmonic: 600 Sorted by residual: dihedral pdb=" CH3 ACE W 0 " pdb=" C ACE W 0 " pdb=" N LEU W 1 " pdb=" CA LEU W 1 " ideal model delta sinusoidal sigma weight residual -180.00 -86.78 -93.22 1 5.00e+00 4.00e-02 4.06e+02 dihedral pdb=" CH3 ACE K 0 " pdb=" C ACE K 0 " pdb=" N LEU K 1 " pdb=" CA LEU K 1 " ideal model delta sinusoidal sigma weight residual -180.00 -86.80 -93.20 1 5.00e+00 4.00e-02 4.05e+02 dihedral pdb=" CH3 ACE c 0 " pdb=" C ACE c 0 " pdb=" N LEU c 1 " pdb=" CA LEU c 1 " ideal model delta sinusoidal sigma weight residual -180.00 -86.82 -93.18 1 5.00e+00 4.00e-02 4.05e+02 ... (remaining 1167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 170 0.041 - 0.082: 40 0.082 - 0.123: 30 0.123 - 0.164: 17 0.164 - 0.205: 73 Chirality restraints: 330 Sorted by residual: chirality pdb=" CA HIS V 4 " pdb=" N HIS V 4 " pdb=" C HIS V 4 " pdb=" CB HIS V 4 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA HIS F 4 " pdb=" N HIS F 4 " pdb=" C HIS F 4 " pdb=" CB HIS F 4 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA HIS U 4 " pdb=" N HIS U 4 " pdb=" C HIS U 4 " pdb=" CB HIS U 4 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 327 not shown) Planarity restraints: 300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE J 0 " 0.089 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" O ACE J 0 " -0.104 2.00e-02 2.50e+03 pdb=" CH3 ACE J 0 " -0.175 2.00e-02 2.50e+03 pdb=" N LEU J 1 " 0.556 2.00e-02 2.50e+03 pdb=" CA LEU J 1 " -0.366 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE V 0 " 0.089 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" O ACE V 0 " -0.104 2.00e-02 2.50e+03 pdb=" CH3 ACE V 0 " -0.175 2.00e-02 2.50e+03 pdb=" N LEU V 1 " 0.556 2.00e-02 2.50e+03 pdb=" CA LEU V 1 " -0.366 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE P 0 " 0.089 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" O ACE P 0 " -0.104 2.00e-02 2.50e+03 pdb=" CH3 ACE P 0 " -0.175 2.00e-02 2.50e+03 pdb=" N LEU P 1 " 0.556 2.00e-02 2.50e+03 pdb=" CA LEU P 1 " -0.366 2.00e-02 2.50e+03 ... (remaining 297 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 758 3.07 - 3.53: 2022 3.53 - 3.99: 2661 3.99 - 4.44: 3385 4.44 - 4.90: 6093 Nonbonded interactions: 14919 Sorted by model distance: nonbonded pdb=" N LEU Y 5 " pdb=" O LEU Y 5 " model vdw 2.613 2.496 nonbonded pdb=" N LEU A 5 " pdb=" O LEU A 5 " model vdw 2.614 2.496 nonbonded pdb=" N LEU B 5 " pdb=" O LEU B 5 " model vdw 2.614 2.496 nonbonded pdb=" N LEU Z 5 " pdb=" O LEU Z 5 " model vdw 2.614 2.496 nonbonded pdb=" N LEU M 5 " pdb=" O LEU M 5 " model vdw 2.614 2.496 ... (remaining 14914 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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 group one per residue 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: 0.810 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.640 Find NCS groups from input model: 0.040 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:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 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 : 0.015 0.102 2040 Z= 1.379 Angle : 1.913 7.587 2670 Z= 1.079 Chirality : 0.104 0.205 330 Planarity : 0.098 0.314 300 Dihedral : 27.060 93.216 750 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 42.86 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.71 (0.30), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.23), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG c 6 HIS 0.002 0.001 HIS G 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00955 / 0.64 ( 2010) covalent geometry : angle 1.91261 / 1.08 ( 2670) Misc. bond : bond 0.10093 / 6.75 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.082 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.4295 time to fit residues: 1.0159 Evaluate side-chains 0 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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... ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.083117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.067295 restraints weight = 7266.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.068490 restraints weight = 4989.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.069451 restraints weight = 3777.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.070050 restraints weight = 3052.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.070822 restraints weight = 2657.229| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4942 moved from start: 1.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.260 2040 Z= 4.119 Angle : 5.868 33.681 2670 Z= 2.805 Chirality : 0.401 1.321 330 Planarity : 0.055 0.183 300 Dihedral : 12.102 31.974 270 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 291.25 Ramachandran Plot: Outliers : 44.00 % Allowed : 46.67 % Favored : 9.33 % Rotamer: Outliers : 39.05 % Allowed : 18.10 % Favored : 42.86 % Cbeta Deviations : 9.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % 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: -10.65 (0.10), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.12 (0.07), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG c 6 HIS 0.050 0.014 HIS O 4 Details of bonding type rmsd/Z covalent geometry : bond 0.08146 / 4.15 ( 2010) covalent geometry : angle 5.86849 / 2.80 ( 2670) Misc. bond : bond 0.00587 / 0.39 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 0 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: A 1 LEU cc_start: 0.5819 (OUTLIER) cc_final: 0.5466 (pt) REVERT: A 5 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5271 (tt) REVERT: B 1 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.5488 (pt) REVERT: B 5 LEU cc_start: 0.5754 (OUTLIER) cc_final: 0.5306 (tt) REVERT: C 5 LEU cc_start: 0.5960 (OUTLIER) cc_final: 0.5662 (tt) REVERT: D 5 LEU cc_start: 0.5838 (OUTLIER) cc_final: 0.5532 (tt) REVERT: E 5 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5569 (tt) REVERT: G 5 LEU cc_start: 0.5515 (OUTLIER) cc_final: 0.5116 (tt) REVERT: H 5 LEU cc_start: 0.5539 (OUTLIER) cc_final: 0.5154 (tt) REVERT: K 5 LEU cc_start: 0.5687 (OUTLIER) cc_final: 0.5386 (tt) REVERT: M 5 LEU cc_start: 0.5683 (OUTLIER) cc_final: 0.5219 (tt) REVERT: N 5 LEU cc_start: 0.5662 (OUTLIER) cc_final: 0.5220 (tt) REVERT: O 4 HIS cc_start: 0.4842 (OUTLIER) cc_final: 0.4031 (m90) REVERT: O 5 LEU cc_start: 0.5749 (OUTLIER) cc_final: 0.5544 (tt) REVERT: P 4 HIS cc_start: 0.4897 (OUTLIER) cc_final: 0.4185 (m90) REVERT: Q 5 LEU cc_start: 0.5843 (OUTLIER) cc_final: 0.5477 (tt) REVERT: R 5 LEU cc_start: 0.5783 (OUTLIER) cc_final: 0.5425 (tt) REVERT: W 5 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.6052 (tt) REVERT: X 5 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.5894 (tt) outliers start: 82 outliers final: 36 residues processed: 82 average time/residue: 0.0274 time to fit residues: 3.0196 Evaluate side-chains 55 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 0 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 1 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.083373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.067036 restraints weight = 8000.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.068333 restraints weight = 5339.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.069373 restraints weight = 4000.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.069987 restraints weight = 3196.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.070687 restraints weight = 2770.267| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4987 moved from start: 1.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.272 2040 Z= 4.014 Angle : 5.700 34.143 2670 Z= 2.691 Chirality : 0.406 1.310 330 Planarity : 0.051 0.163 300 Dihedral : 11.489 31.577 270 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 280.61 Ramachandran Plot: Outliers : 36.00 % Allowed : 60.00 % Favored : 4.00 % Rotamer: Outliers : 47.62 % Allowed : 20.00 % Favored : 32.38 % Cbeta Deviations : 12.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -10.75 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.19 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG O 6 HIS 0.051 0.014 HIS C 4 Details of bonding type rmsd/Z covalent geometry : bond 0.08068 / 4.04 ( 2010) covalent geometry : angle 5.70032 / 2.69 ( 2670) Misc. bond : bond 0.00557 / 0.38 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 0 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: A 2 HIS cc_start: 0.5558 (OUTLIER) cc_final: 0.5284 (t-170) REVERT: A 5 LEU cc_start: 0.5784 (OUTLIER) cc_final: 0.5360 (tt) REVERT: B 2 HIS cc_start: 0.5582 (OUTLIER) cc_final: 0.5266 (t-170) REVERT: B 5 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.5281 (tt) REVERT: C 4 HIS cc_start: 0.5183 (OUTLIER) cc_final: 0.4461 (m90) REVERT: C 5 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5522 (tt) REVERT: D 4 HIS cc_start: 0.5861 (OUTLIER) cc_final: 0.4965 (m90) REVERT: D 5 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5648 (tt) REVERT: E 5 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5842 (tt) REVERT: F 5 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5882 (tt) REVERT: G 5 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5411 (tt) REVERT: H 5 LEU cc_start: 0.5874 (OUTLIER) cc_final: 0.5470 (tt) REVERT: I 5 LEU cc_start: 0.5687 (OUTLIER) cc_final: 0.5442 (tt) REVERT: K 5 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5618 (tt) REVERT: M 5 LEU cc_start: 0.5537 (OUTLIER) cc_final: 0.5036 (tt) REVERT: N 5 LEU cc_start: 0.5553 (OUTLIER) cc_final: 0.5045 (tt) REVERT: O 2 HIS cc_start: 0.4899 (OUTLIER) cc_final: 0.4369 (t-170) REVERT: O 4 HIS cc_start: 0.5339 (OUTLIER) cc_final: 0.4281 (t70) REVERT: P 2 HIS cc_start: 0.4859 (OUTLIER) cc_final: 0.4388 (t-170) REVERT: P 4 HIS cc_start: 0.5389 (OUTLIER) cc_final: 0.4409 (t70) REVERT: P 5 LEU cc_start: 0.5703 (OUTLIER) cc_final: 0.5481 (tt) REVERT: Q 1 LEU cc_start: 0.5734 (OUTLIER) cc_final: 0.5522 (pt) REVERT: Q 5 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5580 (tt) REVERT: R 5 LEU cc_start: 0.5833 (OUTLIER) cc_final: 0.5443 (tt) REVERT: W 5 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.6042 (tt) REVERT: X 4 HIS cc_start: 0.5699 (OUTLIER) cc_final: 0.5465 (t70) REVERT: X 5 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5804 (tt) REVERT: c 5 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6550 (tt) REVERT: d 5 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6405 (tt) outliers start: 100 outliers final: 46 residues processed: 100 average time/residue: 0.0268 time to fit residues: 3.5769 Evaluate side-chains 75 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 0 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 HIS Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 2 HIS Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU 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... ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.083437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.066822 restraints weight = 8333.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.068110 restraints weight = 5518.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.069184 restraints weight = 4126.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.069837 restraints weight = 3284.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.070458 restraints weight = 2816.971| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4911 moved from start: 1.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.278 2040 Z= 4.010 Angle : 5.713 34.160 2670 Z= 2.708 Chirality : 0.409 1.321 330 Planarity : 0.051 0.152 300 Dihedral : 11.220 31.533 270 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 279.20 Ramachandran Plot: Outliers : 34.00 % Allowed : 62.00 % Favored : 4.00 % Rotamer: Outliers : 50.00 % Allowed : 18.10 % Favored : 31.90 % Cbeta Deviations : 13.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % 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: -10.74 (0.09), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG c 6 HIS 0.051 0.013 HIS C 4 Details of bonding type rmsd/Z covalent geometry : bond 0.08016 / 4.04 ( 2010) covalent geometry : angle 5.71291 / 2.71 ( 2670) Misc. bond : bond 0.00549 / 0.37 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 0 time to evaluate : 0.097 Fit side-chains REVERT: A 5 LEU cc_start: 0.5677 (OUTLIER) cc_final: 0.5219 (tt) REVERT: B 2 HIS cc_start: 0.5566 (OUTLIER) cc_final: 0.5352 (t-170) REVERT: B 5 LEU cc_start: 0.5679 (OUTLIER) cc_final: 0.5221 (tt) REVERT: C 4 HIS cc_start: 0.5181 (OUTLIER) cc_final: 0.4491 (m90) REVERT: C 5 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5427 (tt) REVERT: D 2 HIS cc_start: 0.5488 (OUTLIER) cc_final: 0.5112 (t-170) REVERT: D 5 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5455 (tt) REVERT: E 5 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5783 (tt) REVERT: F 5 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5739 (tt) REVERT: G 5 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5446 (tt) REVERT: H 5 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5439 (tt) REVERT: I 5 LEU cc_start: 0.5619 (OUTLIER) cc_final: 0.5355 (tt) REVERT: I 6 ARG cc_start: 0.5407 (OUTLIER) cc_final: 0.4783 (ttt180) REVERT: K 5 LEU cc_start: 0.5787 (OUTLIER) cc_final: 0.5546 (tt) REVERT: M 5 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.5204 (tt) REVERT: N 5 LEU cc_start: 0.5649 (OUTLIER) cc_final: 0.5207 (tt) REVERT: O 2 HIS cc_start: 0.4821 (OUTLIER) cc_final: 0.4373 (t-170) REVERT: O 4 HIS cc_start: 0.5400 (OUTLIER) cc_final: 0.4409 (t70) REVERT: P 2 HIS cc_start: 0.4654 (OUTLIER) cc_final: 0.4155 (t-170) REVERT: P 4 HIS cc_start: 0.5355 (OUTLIER) cc_final: 0.4311 (t70) REVERT: P 5 LEU cc_start: 0.5731 (OUTLIER) cc_final: 0.5487 (tt) REVERT: Q 5 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5666 (tt) REVERT: R 5 LEU cc_start: 0.5724 (OUTLIER) cc_final: 0.5425 (tt) REVERT: U 4 HIS cc_start: 0.4651 (OUTLIER) cc_final: 0.4305 (t70) REVERT: W 4 HIS cc_start: 0.5688 (OUTLIER) cc_final: 0.5429 (t70) REVERT: W 5 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.6092 (tt) REVERT: X 5 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5689 (tt) REVERT: a 6 ARG cc_start: 0.5749 (OUTLIER) cc_final: 0.5008 (ttm170) REVERT: c 5 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6421 (tt) REVERT: d 5 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6361 (tt) outliers start: 105 outliers final: 58 residues processed: 105 average time/residue: 0.0407 time to fit residues: 5.2365 Evaluate side-chains 88 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 0 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 2 HIS Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 2 HIS Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 HIS Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 2 HIS Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 2 HIS Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 2 HIS Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.083543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.067047 restraints weight = 7780.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.068370 restraints weight = 5227.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.069410 restraints weight = 3934.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.070103 restraints weight = 3138.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.070881 restraints weight = 2694.847| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4697 moved from start: 1.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.272 2040 Z= 4.004 Angle : 5.741 34.303 2670 Z= 2.720 Chirality : 0.410 1.324 330 Planarity : 0.050 0.147 300 Dihedral : 11.096 31.831 270 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 278.49 Ramachandran Plot: Outliers : 33.33 % Allowed : 62.00 % Favored : 4.67 % Rotamer: Outliers : 55.71 % Allowed : 13.33 % Favored : 30.95 % Cbeta Deviations : 12.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % 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: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG O 6 HIS 0.052 0.013 HIS C 4 Details of bonding type rmsd/Z covalent geometry : bond 0.08023 / 4.03 ( 2010) covalent geometry : angle 5.74086 / 2.72 ( 2670) Misc. bond : bond 0.00545 / 0.38 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 0 time to evaluate : 0.089 Fit side-chains REVERT: A 5 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.5056 (tt) REVERT: B 2 HIS cc_start: 0.5455 (OUTLIER) cc_final: 0.5239 (t-170) REVERT: B 5 LEU cc_start: 0.5490 (OUTLIER) cc_final: 0.5053 (tt) REVERT: C 2 HIS cc_start: 0.5347 (OUTLIER) cc_final: 0.4921 (t-170) REVERT: C 4 HIS cc_start: 0.5240 (OUTLIER) cc_final: 0.4497 (m90) REVERT: C 5 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5520 (tt) REVERT: D 5 LEU cc_start: 0.5568 (OUTLIER) cc_final: 0.5345 (tt) REVERT: E 5 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5630 (tt) REVERT: F 5 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5672 (tt) REVERT: G 5 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5270 (tt) REVERT: H 5 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.5257 (tt) REVERT: I 6 ARG cc_start: 0.5188 (OUTLIER) cc_final: 0.4676 (ttt180) REVERT: J 6 ARG cc_start: 0.5215 (OUTLIER) cc_final: 0.4559 (ttt180) REVERT: K 5 LEU cc_start: 0.5622 (OUTLIER) cc_final: 0.5395 (tt) REVERT: M 4 HIS cc_start: 0.4446 (OUTLIER) cc_final: 0.3590 (t70) REVERT: M 5 LEU cc_start: 0.5371 (OUTLIER) cc_final: 0.5091 (tt) REVERT: N 2 HIS cc_start: 0.3760 (OUTLIER) cc_final: 0.2997 (t-170) REVERT: N 4 HIS cc_start: 0.4429 (OUTLIER) cc_final: 0.3519 (t70) REVERT: N 5 LEU cc_start: 0.5395 (OUTLIER) cc_final: 0.5074 (tt) REVERT: O 6 ARG cc_start: 0.5164 (OUTLIER) cc_final: 0.4371 (ttm170) REVERT: P 2 HIS cc_start: 0.4327 (OUTLIER) cc_final: 0.3863 (t-170) REVERT: P 4 HIS cc_start: 0.5026 (OUTLIER) cc_final: 0.4072 (t70) REVERT: P 5 LEU cc_start: 0.5563 (OUTLIER) cc_final: 0.5344 (tt) REVERT: Q 5 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5633 (tt) REVERT: R 5 LEU cc_start: 0.5536 (OUTLIER) cc_final: 0.5199 (tt) REVERT: U 6 ARG cc_start: 0.5328 (OUTLIER) cc_final: 0.4961 (ttt180) REVERT: V 6 ARG cc_start: 0.5454 (OUTLIER) cc_final: 0.5158 (ttt180) REVERT: W 5 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5775 (tt) REVERT: X 5 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5539 (tt) REVERT: a 6 ARG cc_start: 0.5432 (OUTLIER) cc_final: 0.4725 (ttt180) REVERT: b 6 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.4882 (ttm170) REVERT: c 5 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6277 (tt) REVERT: d 5 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6257 (tt) outliers start: 117 outliers final: 55 residues processed: 117 average time/residue: 0.0595 time to fit residues: 8.0084 Evaluate side-chains 89 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 2 HIS Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 2 HIS Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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... ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.082625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.067395 restraints weight = 9064.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.068636 restraints weight = 5793.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.069447 restraints weight = 4239.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.070335 restraints weight = 3493.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.071024 restraints weight = 2881.051| |-----------------------------------------------------------------------------| r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4587 moved from start: 1.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.274 2040 Z= 3.985 Angle : 5.742 34.418 2670 Z= 2.727 Chirality : 0.412 1.330 330 Planarity : 0.049 0.144 300 Dihedral : 11.026 33.034 270 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 276.36 Ramachandran Plot: Outliers : 32.00 % Allowed : 63.33 % Favored : 4.67 % Rotamer: Outliers : 50.95 % Allowed : 18.57 % Favored : 30.48 % Cbeta Deviations : 11.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.67 % 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: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG P 6 HIS 0.052 0.013 HIS C 4 Details of bonding type rmsd/Z covalent geometry : bond 0.07985 / 4.01 ( 2010) covalent geometry : angle 5.74190 / 2.73 ( 2670) Misc. bond : bond 0.00553 / 0.38 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 0 time to evaluate : 0.094 Fit side-chains REVERT: A 5 LEU cc_start: 0.5396 (OUTLIER) cc_final: 0.4979 (tt) REVERT: B 2 HIS cc_start: 0.5380 (OUTLIER) cc_final: 0.5162 (t-170) REVERT: B 5 LEU cc_start: 0.5386 (OUTLIER) cc_final: 0.4962 (tt) REVERT: C 2 HIS cc_start: 0.5207 (OUTLIER) cc_final: 0.4808 (t-170) REVERT: C 4 HIS cc_start: 0.5029 (OUTLIER) cc_final: 0.4329 (m90) REVERT: C 5 LEU cc_start: 0.5610 (OUTLIER) cc_final: 0.5296 (tt) REVERT: D 5 LEU cc_start: 0.5508 (OUTLIER) cc_final: 0.5276 (tt) REVERT: E 5 LEU cc_start: 0.5860 (OUTLIER) cc_final: 0.5562 (tt) REVERT: F 5 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5539 (tt) REVERT: G 5 LEU cc_start: 0.5566 (OUTLIER) cc_final: 0.5190 (tt) REVERT: H 5 LEU cc_start: 0.5552 (OUTLIER) cc_final: 0.5177 (tt) REVERT: I 6 ARG cc_start: 0.4999 (OUTLIER) cc_final: 0.4497 (ttt180) REVERT: J 6 ARG cc_start: 0.5095 (OUTLIER) cc_final: 0.4446 (ttt180) REVERT: M 4 HIS cc_start: 0.4255 (OUTLIER) cc_final: 0.3443 (t70) REVERT: M 5 LEU cc_start: 0.5263 (OUTLIER) cc_final: 0.4996 (tt) REVERT: N 2 HIS cc_start: 0.3613 (OUTLIER) cc_final: 0.2868 (t-170) REVERT: N 4 HIS cc_start: 0.4288 (OUTLIER) cc_final: 0.3375 (t70) REVERT: N 5 LEU cc_start: 0.5280 (OUTLIER) cc_final: 0.4973 (tt) REVERT: O 6 ARG cc_start: 0.4941 (OUTLIER) cc_final: 0.4268 (ttm170) REVERT: P 2 HIS cc_start: 0.4311 (OUTLIER) cc_final: 0.3930 (t-170) REVERT: P 4 HIS cc_start: 0.4833 (OUTLIER) cc_final: 0.3902 (t70) REVERT: Q 5 LEU cc_start: 0.5863 (OUTLIER) cc_final: 0.5570 (tt) REVERT: R 5 LEU cc_start: 0.5592 (OUTLIER) cc_final: 0.5305 (tt) REVERT: S 6 ARG cc_start: 0.5852 (OUTLIER) cc_final: 0.5571 (ttt-90) REVERT: T 6 ARG cc_start: 0.5902 (OUTLIER) cc_final: 0.4851 (ttm170) REVERT: U 6 ARG cc_start: 0.5111 (OUTLIER) cc_final: 0.4688 (ttt180) REVERT: V 6 ARG cc_start: 0.5415 (OUTLIER) cc_final: 0.4960 (ttt180) REVERT: W 5 LEU cc_start: 0.5873 (OUTLIER) cc_final: 0.5623 (tt) REVERT: X 5 LEU cc_start: 0.5791 (OUTLIER) cc_final: 0.5545 (tt) REVERT: a 6 ARG cc_start: 0.5240 (OUTLIER) cc_final: 0.4610 (ttt180) REVERT: b 6 ARG cc_start: 0.5485 (OUTLIER) cc_final: 0.4830 (ttm-80) REVERT: c 5 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6295 (tt) REVERT: d 5 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6237 (tt) outliers start: 107 outliers final: 56 residues processed: 107 average time/residue: 0.0634 time to fit residues: 7.7783 Evaluate side-chains 89 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 0 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 2 HIS Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 2 HIS Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU 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... ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.083862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.066880 restraints weight = 8454.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.068289 restraints weight = 5559.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.069420 restraints weight = 4102.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.070268 restraints weight = 3231.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.071013 restraints weight = 2696.079| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5075 moved from start: 1.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.274 2040 Z= 3.979 Angle : 5.759 34.431 2670 Z= 2.735 Chirality : 0.413 1.330 330 Planarity : 0.049 0.142 300 Dihedral : 11.000 33.442 270 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 275.65 Ramachandran Plot: Outliers : 32.00 % Allowed : 63.33 % Favored : 4.67 % Rotamer: Outliers : 51.43 % Allowed : 17.14 % Favored : 31.43 % Cbeta Deviations : 11.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.67 % 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: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG T 6 HIS 0.053 0.013 HIS C 4 Details of bonding type rmsd/Z covalent geometry : bond 0.07983 / 4.01 ( 2010) covalent geometry : angle 5.75945 / 2.74 ( 2670) Misc. bond : bond 0.00556 / 0.39 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 0 time to evaluate : 0.088 Fit side-chains REVERT: A 5 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5424 (tt) REVERT: B 2 HIS cc_start: 0.5730 (OUTLIER) cc_final: 0.5479 (t-170) REVERT: B 5 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5337 (tt) REVERT: C 2 HIS cc_start: 0.5548 (OUTLIER) cc_final: 0.5090 (t-170) REVERT: C 4 HIS cc_start: 0.5531 (OUTLIER) cc_final: 0.4696 (m90) REVERT: C 5 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5789 (tt) REVERT: D 5 LEU cc_start: 0.5879 (OUTLIER) cc_final: 0.5548 (tt) REVERT: E 5 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.5890 (tt) REVERT: F 5 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.5918 (tt) REVERT: G 5 LEU cc_start: 0.5979 (OUTLIER) cc_final: 0.5553 (tt) REVERT: H 5 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5537 (tt) REVERT: I 6 ARG cc_start: 0.5449 (OUTLIER) cc_final: 0.4778 (ttt180) REVERT: J 6 ARG cc_start: 0.5473 (OUTLIER) cc_final: 0.4688 (ttt180) REVERT: M 4 HIS cc_start: 0.5070 (OUTLIER) cc_final: 0.4096 (t70) REVERT: M 5 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5523 (tt) REVERT: N 2 HIS cc_start: 0.4462 (OUTLIER) cc_final: 0.3626 (t-170) REVERT: N 4 HIS cc_start: 0.5084 (OUTLIER) cc_final: 0.4011 (t70) REVERT: N 5 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5465 (tt) REVERT: O 6 ARG cc_start: 0.5406 (OUTLIER) cc_final: 0.4687 (ttm170) REVERT: P 2 HIS cc_start: 0.4884 (OUTLIER) cc_final: 0.4295 (t-170) REVERT: P 4 HIS cc_start: 0.5643 (OUTLIER) cc_final: 0.4529 (t70) REVERT: Q 5 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5967 (tt) REVERT: R 5 LEU cc_start: 0.5903 (OUTLIER) cc_final: 0.5601 (tt) REVERT: U 6 ARG cc_start: 0.5569 (OUTLIER) cc_final: 0.4890 (ttt180) REVERT: V 6 ARG cc_start: 0.5836 (OUTLIER) cc_final: 0.5234 (ttt180) REVERT: W 5 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5968 (tt) REVERT: X 5 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.6030 (tt) REVERT: Y 6 ARG cc_start: 0.6372 (OUTLIER) cc_final: 0.5114 (ttm170) REVERT: Z 6 ARG cc_start: 0.6396 (OUTLIER) cc_final: 0.5082 (ttm170) REVERT: a 4 HIS cc_start: 0.5634 (OUTLIER) cc_final: 0.4978 (t70) REVERT: b 6 ARG cc_start: 0.5852 (OUTLIER) cc_final: 0.5065 (ttm-80) REVERT: c 5 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6578 (tt) REVERT: d 5 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6625 (tt) outliers start: 108 outliers final: 59 residues processed: 108 average time/residue: 0.0745 time to fit residues: 9.0876 Evaluate side-chains 93 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 2 HIS Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 2 HIS Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.083834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.066940 restraints weight = 8218.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.068343 restraints weight = 5424.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.069435 restraints weight = 4034.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.070325 restraints weight = 3193.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.071062 restraints weight = 2659.992| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5104 moved from start: 1.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.277 2040 Z= 3.972 Angle : 5.775 34.461 2670 Z= 2.739 Chirality : 0.413 1.334 330 Planarity : 0.049 0.140 300 Dihedral : 11.081 33.460 270 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 276.83 Ramachandran Plot: Outliers : 31.33 % Allowed : 64.00 % Favored : 4.67 % Rotamer: Outliers : 50.48 % Allowed : 20.95 % Favored : 28.57 % Cbeta Deviations : 11.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.67 % 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: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.003 ARG S 6 HIS 0.052 0.013 HIS C 4 Details of bonding type rmsd/Z covalent geometry : bond 0.07980 / 4.00 ( 2010) covalent geometry : angle 5.77462 / 2.74 ( 2670) Misc. bond : bond 0.00579 / 0.41 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 0 time to evaluate : 0.093 Fit side-chains REVERT: A 5 LEU cc_start: 0.5867 (OUTLIER) cc_final: 0.5452 (tt) REVERT: B 2 HIS cc_start: 0.5753 (OUTLIER) cc_final: 0.5498 (t-170) REVERT: B 5 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5366 (tt) REVERT: C 2 HIS cc_start: 0.5580 (OUTLIER) cc_final: 0.5135 (t-170) REVERT: C 4 HIS cc_start: 0.5567 (OUTLIER) cc_final: 0.4724 (m90) REVERT: C 5 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5703 (tt) REVERT: D 5 LEU cc_start: 0.5863 (OUTLIER) cc_final: 0.5513 (tt) REVERT: E 2 HIS cc_start: 0.6129 (OUTLIER) cc_final: 0.5914 (t70) REVERT: E 5 LEU cc_start: 0.6333 (OUTLIER) cc_final: 0.5928 (tt) REVERT: F 5 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.6024 (tt) REVERT: G 5 LEU cc_start: 0.6027 (OUTLIER) cc_final: 0.5598 (tt) REVERT: H 5 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5561 (tt) REVERT: I 6 ARG cc_start: 0.5499 (OUTLIER) cc_final: 0.4797 (ttt180) REVERT: J 6 ARG cc_start: 0.5486 (OUTLIER) cc_final: 0.4696 (ttt180) REVERT: M 2 HIS cc_start: 0.4367 (OUTLIER) cc_final: 0.3498 (t-170) REVERT: M 4 HIS cc_start: 0.5285 (OUTLIER) cc_final: 0.4177 (t70) REVERT: M 5 LEU cc_start: 0.5866 (OUTLIER) cc_final: 0.5558 (tt) REVERT: N 2 HIS cc_start: 0.4513 (OUTLIER) cc_final: 0.3669 (t-170) REVERT: N 4 HIS cc_start: 0.5129 (OUTLIER) cc_final: 0.4046 (t70) REVERT: N 5 LEU cc_start: 0.5866 (OUTLIER) cc_final: 0.5502 (tt) REVERT: O 6 ARG cc_start: 0.5430 (OUTLIER) cc_final: 0.4712 (ttm170) REVERT: P 2 HIS cc_start: 0.4842 (OUTLIER) cc_final: 0.4243 (t-170) REVERT: P 4 HIS cc_start: 0.5679 (OUTLIER) cc_final: 0.4514 (t70) REVERT: Q 5 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.5954 (tt) REVERT: R 5 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5720 (tt) REVERT: U 6 ARG cc_start: 0.5555 (OUTLIER) cc_final: 0.4675 (ttt180) REVERT: V 6 ARG cc_start: 0.5799 (OUTLIER) cc_final: 0.5270 (ttt180) REVERT: W 5 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.6001 (tt) REVERT: X 5 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6183 (tt) REVERT: Z 6 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.5084 (ttm170) REVERT: a 4 HIS cc_start: 0.5679 (OUTLIER) cc_final: 0.5054 (t70) REVERT: b 6 ARG cc_start: 0.5842 (OUTLIER) cc_final: 0.5023 (ttt180) REVERT: c 5 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6759 (tt) REVERT: d 5 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6650 (tt) outliers start: 106 outliers final: 59 residues processed: 106 average time/residue: 0.0658 time to fit residues: 7.9442 Evaluate side-chains 95 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 2 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 2 HIS Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.084040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.067216 restraints weight = 8027.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.068600 restraints weight = 5340.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.069721 restraints weight = 3965.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.070609 restraints weight = 3124.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.071286 restraints weight = 2602.576| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5132 moved from start: 1.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.276 2040 Z= 3.966 Angle : 5.788 34.496 2670 Z= 2.746 Chirality : 0.414 1.329 330 Planarity : 0.049 0.140 300 Dihedral : 11.100 33.748 270 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 278.25 Ramachandran Plot: Outliers : 32.00 % Allowed : 63.33 % Favored : 4.67 % Rotamer: Outliers : 48.57 % Allowed : 21.90 % Favored : 29.52 % Cbeta Deviations : 10.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.67 % 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: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG B 6 HIS 0.052 0.013 HIS C 4 Details of bonding type rmsd/Z covalent geometry : bond 0.07984 / 3.99 ( 2010) covalent geometry : angle 5.78796 / 2.75 ( 2670) Misc. bond : bond 0.00553 / 0.39 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 0 time to evaluate : 0.095 Fit side-chains REVERT: A 5 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5386 (tt) REVERT: B 2 HIS cc_start: 0.5783 (OUTLIER) cc_final: 0.5521 (t-170) REVERT: B 5 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5481 (tt) REVERT: C 2 HIS cc_start: 0.5605 (OUTLIER) cc_final: 0.5158 (t-170) REVERT: C 4 HIS cc_start: 0.5593 (OUTLIER) cc_final: 0.4747 (m90) REVERT: C 5 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5730 (tt) REVERT: D 5 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5579 (tt) REVERT: E 2 HIS cc_start: 0.6125 (OUTLIER) cc_final: 0.5921 (t70) REVERT: E 5 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.5927 (tt) REVERT: F 2 HIS cc_start: 0.6296 (OUTLIER) cc_final: 0.6080 (t70) REVERT: F 5 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6062 (tt) REVERT: G 5 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5507 (tt) REVERT: H 5 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5619 (tt) REVERT: H 6 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.5214 (ttm170) REVERT: I 6 ARG cc_start: 0.5531 (OUTLIER) cc_final: 0.4816 (ttt180) REVERT: J 6 ARG cc_start: 0.5539 (OUTLIER) cc_final: 0.4740 (ttt180) REVERT: M 2 HIS cc_start: 0.4401 (OUTLIER) cc_final: 0.3526 (t-170) REVERT: M 4 HIS cc_start: 0.5155 (OUTLIER) cc_final: 0.4122 (t70) REVERT: M 5 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5581 (tt) REVERT: N 2 HIS cc_start: 0.4558 (OUTLIER) cc_final: 0.3703 (t-170) REVERT: N 4 HIS cc_start: 0.5176 (OUTLIER) cc_final: 0.4079 (t70) REVERT: N 5 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5531 (tt) REVERT: O 6 ARG cc_start: 0.5433 (OUTLIER) cc_final: 0.4756 (ttm170) REVERT: P 6 ARG cc_start: 0.5626 (OUTLIER) cc_final: 0.4833 (ttm170) REVERT: Q 5 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5858 (tt) REVERT: R 5 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5839 (tt) REVERT: U 6 ARG cc_start: 0.5675 (OUTLIER) cc_final: 0.4826 (ttt180) REVERT: V 6 ARG cc_start: 0.5760 (OUTLIER) cc_final: 0.5026 (ttt180) REVERT: W 5 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.6029 (tt) REVERT: X 5 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6169 (tt) REVERT: Y 6 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.5094 (ttm170) REVERT: Z 6 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.5093 (ttm170) REVERT: a 4 HIS cc_start: 0.5687 (OUTLIER) cc_final: 0.5044 (t70) REVERT: b 4 HIS cc_start: 0.5740 (OUTLIER) cc_final: 0.4933 (t70) REVERT: c 5 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6777 (tt) REVERT: d 5 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6555 (tt) outliers start: 102 outliers final: 56 residues processed: 102 average time/residue: 0.0714 time to fit residues: 8.2400 Evaluate side-chains 92 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 0 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU 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... ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.084580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.067774 restraints weight = 8126.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.068883 restraints weight = 5380.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.070070 restraints weight = 4185.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.071005 restraints weight = 3296.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.071767 restraints weight = 2712.837| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5143 moved from start: 1.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.275 2040 Z= 3.965 Angle : 5.785 34.593 2670 Z= 2.745 Chirality : 0.414 1.335 330 Planarity : 0.049 0.138 300 Dihedral : 11.212 34.343 270 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 278.96 Ramachandran Plot: Outliers : 32.00 % Allowed : 63.33 % Favored : 4.67 % Rotamer: Outliers : 46.67 % Allowed : 23.33 % Favored : 30.00 % Cbeta Deviations : 10.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % 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: -10.73 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG S 6 HIS 0.053 0.013 HIS C 4 Details of bonding type rmsd/Z covalent geometry : bond 0.07974 / 3.99 ( 2010) covalent geometry : angle 5.78497 / 2.75 ( 2670) Misc. bond : bond 0.00552 / 0.39 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 0 time to evaluate : 0.109 Fit side-chains REVERT: A 5 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5392 (tt) REVERT: B 2 HIS cc_start: 0.5793 (OUTLIER) cc_final: 0.5535 (t-170) REVERT: B 5 LEU cc_start: 0.5850 (OUTLIER) cc_final: 0.5377 (tt) REVERT: C 2 HIS cc_start: 0.5617 (OUTLIER) cc_final: 0.5173 (t-170) REVERT: C 4 HIS cc_start: 0.5517 (OUTLIER) cc_final: 0.4746 (m90) REVERT: C 5 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5736 (tt) REVERT: D 5 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5819 (tt) REVERT: E 2 HIS cc_start: 0.6187 (OUTLIER) cc_final: 0.5978 (t70) REVERT: E 5 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.5945 (tt) REVERT: F 2 HIS cc_start: 0.6241 (OUTLIER) cc_final: 0.6024 (t70) REVERT: F 5 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.5973 (tt) REVERT: G 5 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5646 (tt) REVERT: H 5 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5628 (tt) REVERT: H 6 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.5238 (ttm170) REVERT: I 6 ARG cc_start: 0.5522 (OUTLIER) cc_final: 0.4803 (ttt180) REVERT: J 6 ARG cc_start: 0.5599 (OUTLIER) cc_final: 0.4769 (ttt180) REVERT: M 2 HIS cc_start: 0.4416 (OUTLIER) cc_final: 0.3554 (t-170) REVERT: M 4 HIS cc_start: 0.5165 (OUTLIER) cc_final: 0.4137 (t70) REVERT: M 5 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5555 (tt) REVERT: N 2 HIS cc_start: 0.4565 (OUTLIER) cc_final: 0.3708 (t-170) REVERT: N 4 HIS cc_start: 0.5180 (OUTLIER) cc_final: 0.4095 (t70) REVERT: N 5 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.5552 (tt) REVERT: O 6 ARG cc_start: 0.5450 (OUTLIER) cc_final: 0.4764 (ttm170) REVERT: P 6 ARG cc_start: 0.5608 (OUTLIER) cc_final: 0.4859 (ttm170) REVERT: Q 5 LEU cc_start: 0.6163 (OUTLIER) cc_final: 0.5873 (tt) REVERT: R 5 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5847 (tt) REVERT: U 6 ARG cc_start: 0.5692 (OUTLIER) cc_final: 0.4842 (ttt180) REVERT: V 6 ARG cc_start: 0.5707 (OUTLIER) cc_final: 0.4946 (ttt180) REVERT: W 5 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6162 (tt) REVERT: X 5 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6189 (tt) REVERT: Y 6 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.5106 (ttm170) REVERT: Z 6 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.5107 (ttm170) REVERT: a 4 HIS cc_start: 0.5785 (OUTLIER) cc_final: 0.5274 (t70) REVERT: b 4 HIS cc_start: 0.5729 (OUTLIER) cc_final: 0.5053 (t70) REVERT: c 5 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6790 (tt) REVERT: d 5 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6568 (tt) outliers start: 98 outliers final: 56 residues processed: 98 average time/residue: 0.0682 time to fit residues: 7.6185 Evaluate side-chains 92 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 0 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.084632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.067531 restraints weight = 8985.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.068909 restraints weight = 5739.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.070112 restraints weight = 4235.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.070986 restraints weight = 3311.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.071771 restraints weight = 2760.309| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5138 moved from start: 1.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.275 2040 Z= 3.964 Angle : 5.784 34.559 2670 Z= 2.745 Chirality : 0.414 1.332 330 Planarity : 0.049 0.138 300 Dihedral : 11.168 34.222 270 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 278.01 Ramachandran Plot: Outliers : 32.00 % Allowed : 63.33 % Favored : 4.67 % Rotamer: Outliers : 47.14 % Allowed : 22.86 % Favored : 30.00 % Cbeta Deviations : 10.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % 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: -10.73 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG S 6 HIS 0.053 0.013 HIS C 4 Details of bonding type rmsd/Z covalent geometry : bond 0.07970 / 3.99 ( 2010) covalent geometry : angle 5.78380 / 2.74 ( 2670) Misc. bond : bond 0.00554 / 0.39 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 363.16 seconds wall clock time: 7 minutes 25.11 seconds (445.11 seconds total)