Starting phenix.real_space_refine on Mon Feb 10 19:51:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b3a_15824/02_2025/8b3a_15824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b3a_15824/02_2025/8b3a_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_15824/02_2025/8b3a_15824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b3a_15824/02_2025/8b3a_15824.map" model { file = "/net/cci-nas-00/data/ceres_data/8b3a_15824/02_2025/8b3a_15824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b3a_15824/02_2025/8b3a_15824.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 1.04, per 1000 atoms: 0.52 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: 1.05 Conformation dependent library (CDL) restraints added in 160.0 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: 0.31 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: 0.09 Time building geometry restraints manager: 1.02 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: 322 3.03 - 4.55: 182 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'b' 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: 0.350 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.010 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 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 : 0.010 0.053 2010 Z= 0.677 Angle : 1.900 7.587 2670 Z= 1.076 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.001 HIS G 2 ARG 0.002 0.000 ARG c 6 *********************** 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 : 0.218 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.8514 time to fit residues: 2.1263 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 : 0.240 ------------------------------------------------------------------------------- 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: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4203 r_free = 0.4203 target = 0.082966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.067026 restraints weight = 7429.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.068274 restraints weight = 5045.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.069297 restraints weight = 3798.090| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4988 moved from start: 1.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.259 2010 Z= 5.600 Angle : 5.842 33.338 2670 Z= 2.796 Chirality : 0.401 1.292 330 Planarity : 0.054 0.182 300 Dihedral : 12.031 32.166 270 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 288.86 Ramachandran Plot: Outliers : 42.00 % Allowed : 48.67 % Favored : 9.33 % Rotamer: Outliers : 40.00 % Allowed : 17.14 % Favored : 42.86 % Cbeta Deviations : 10.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.66 (0.09), 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 HIS 0.052 0.013 HIS O 4 ARG 0.009 0.002 ARG O 6 *********************** 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 84 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 0 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 1 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5503 (pt) REVERT: A 5 LEU cc_start: 0.5760 (OUTLIER) cc_final: 0.5295 (tt) REVERT: B 1 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.5513 (pt) REVERT: B 5 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5333 (tt) REVERT: C 5 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5660 (tt) REVERT: D 5 LEU cc_start: 0.5848 (OUTLIER) cc_final: 0.5539 (tt) REVERT: E 5 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5590 (tt) REVERT: F 5 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5625 (tt) REVERT: G 5 LEU cc_start: 0.5590 (OUTLIER) cc_final: 0.5199 (tt) REVERT: H 5 LEU cc_start: 0.5567 (OUTLIER) cc_final: 0.5180 (tt) REVERT: K 5 LEU cc_start: 0.5706 (OUTLIER) cc_final: 0.5404 (tt) REVERT: L 5 LEU cc_start: 0.5699 (OUTLIER) cc_final: 0.5379 (tt) REVERT: M 5 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.5210 (tt) REVERT: N 5 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.5252 (tt) REVERT: O 4 HIS cc_start: 0.4970 (OUTLIER) cc_final: 0.4138 (m90) REVERT: O 5 LEU cc_start: 0.5784 (OUTLIER) cc_final: 0.5567 (tt) REVERT: P 4 HIS cc_start: 0.4898 (OUTLIER) cc_final: 0.4168 (m90) REVERT: Q 5 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.5514 (tt) REVERT: R 5 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5461 (tt) REVERT: W 5 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.6074 (tt) REVERT: X 5 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5760 (tt) outliers start: 84 outliers final: 37 residues processed: 84 average time/residue: 0.0815 time to fit residues: 9.0305 Evaluate side-chains 58 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 0 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 F residue 5 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 L residue 5 LEU 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 1 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: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 2 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 = 0.4237 r_free = 0.4237 target = 0.083789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.067548 restraints weight = 7425.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.068892 restraints weight = 4997.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.069945 restraints weight = 3733.076| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5647 moved from start: 1.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.273 2010 Z= 5.574 Angle : 5.698 34.006 2670 Z= 2.689 Chirality : 0.407 1.316 330 Planarity : 0.051 0.162 300 Dihedral : 11.533 31.208 270 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 283.41 Ramachandran Plot: Outliers : 36.67 % Allowed : 59.33 % Favored : 4.00 % Rotamer: Outliers : 46.67 % Allowed : 20.00 % Favored : 33.33 % Cbeta Deviations : 12.86 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.051 0.014 HIS C 4 ARG 0.010 0.002 ARG c 6 *********************** 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 98 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 0 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 2 HIS cc_start: 0.5997 (OUTLIER) cc_final: 0.5678 (t-170) REVERT: A 5 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5747 (tt) REVERT: B 2 HIS cc_start: 0.6040 (OUTLIER) cc_final: 0.5667 (t-170) REVERT: B 5 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5768 (tt) REVERT: C 4 HIS cc_start: 0.5792 (OUTLIER) cc_final: 0.4908 (m90) REVERT: C 5 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5898 (tt) REVERT: D 4 HIS cc_start: 0.6324 (OUTLIER) cc_final: 0.5269 (m90) REVERT: D 5 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.5997 (tt) REVERT: E 5 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6267 (tt) REVERT: F 5 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6369 (tt) REVERT: G 5 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.5951 (tt) REVERT: H 5 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.5953 (tt) REVERT: I 5 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5979 (tt) REVERT: K 5 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.6096 (tt) REVERT: L 5 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.6010 (tt) REVERT: M 5 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5749 (tt) REVERT: N 5 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.5762 (tt) REVERT: O 2 HIS cc_start: 0.5758 (OUTLIER) cc_final: 0.5129 (t-170) REVERT: O 4 HIS cc_start: 0.6262 (OUTLIER) cc_final: 0.5145 (t70) REVERT: P 2 HIS cc_start: 0.5765 (OUTLIER) cc_final: 0.5167 (t-170) REVERT: P 4 HIS cc_start: 0.6392 (OUTLIER) cc_final: 0.5232 (t70) REVERT: P 5 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.6152 (tt) REVERT: Q 1 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.6028 (pt) REVERT: Q 5 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6223 (tt) REVERT: R 1 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6172 (pt) REVERT: R 5 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6071 (tt) REVERT: W 4 HIS cc_start: 0.6664 (OUTLIER) cc_final: 0.6433 (t70) REVERT: W 5 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6495 (tt) REVERT: X 4 HIS cc_start: 0.6563 (OUTLIER) cc_final: 0.6281 (t70) REVERT: X 5 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6250 (tt) REVERT: c 5 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6961 (tt) REVERT: d 5 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6835 (tt) outliers start: 98 outliers final: 47 residues processed: 98 average time/residue: 0.0617 time to fit residues: 7.7642 Evaluate side-chains 79 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 0 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 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 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 L residue 5 LEU 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 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 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 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 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 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: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.083591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.066822 restraints weight = 8423.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.068181 restraints weight = 5552.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.069355 restraints weight = 4100.122| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5052 moved from start: 1.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.279 2010 Z= 5.513 Angle : 5.689 34.359 2670 Z= 2.701 Chirality : 0.408 1.329 330 Planarity : 0.051 0.155 300 Dihedral : 11.283 31.397 270 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 281.75 Ramachandran Plot: Outliers : 36.00 % Allowed : 60.00 % Favored : 4.00 % Rotamer: Outliers : 50.95 % Allowed : 16.67 % Favored : 32.38 % Cbeta Deviations : 13.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.051 0.013 HIS C 4 ARG 0.009 0.002 ARG O 6 *********************** 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 107 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 0 time to evaluate : 0.268 Fit side-chains REVERT: A 5 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5309 (tt) REVERT: B 2 HIS cc_start: 0.5638 (OUTLIER) cc_final: 0.5421 (t-170) REVERT: B 5 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5321 (tt) REVERT: C 2 HIS cc_start: 0.5525 (OUTLIER) cc_final: 0.5114 (t-170) REVERT: C 4 HIS cc_start: 0.5262 (OUTLIER) cc_final: 0.4434 (m90) REVERT: C 5 LEU cc_start: 0.5846 (OUTLIER) cc_final: 0.5532 (tt) REVERT: D 5 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5605 (tt) REVERT: E 5 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5849 (tt) REVERT: F 5 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5897 (tt) REVERT: G 5 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5534 (tt) REVERT: H 5 LEU cc_start: 0.5933 (OUTLIER) cc_final: 0.5536 (tt) REVERT: I 5 LEU cc_start: 0.5706 (OUTLIER) cc_final: 0.5434 (tt) REVERT: I 6 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.4798 (ttt180) REVERT: K 5 LEU cc_start: 0.5886 (OUTLIER) cc_final: 0.5637 (tt) REVERT: L 5 LEU cc_start: 0.5885 (OUTLIER) cc_final: 0.5611 (tt) REVERT: M 5 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5328 (tt) REVERT: N 5 LEU cc_start: 0.5796 (OUTLIER) cc_final: 0.5340 (tt) REVERT: O 2 HIS cc_start: 0.4965 (OUTLIER) cc_final: 0.4446 (t-170) REVERT: O 4 HIS cc_start: 0.5533 (OUTLIER) cc_final: 0.4428 (t70) REVERT: P 2 HIS cc_start: 0.4787 (OUTLIER) cc_final: 0.4250 (t-170) REVERT: P 4 HIS cc_start: 0.5533 (OUTLIER) cc_final: 0.4457 (t70) REVERT: P 5 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.5625 (tt) REVERT: Q 5 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5861 (tt) REVERT: R 5 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5520 (tt) REVERT: U 4 HIS cc_start: 0.4824 (OUTLIER) cc_final: 0.4408 (t70) REVERT: W 5 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6178 (tt) REVERT: X 5 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5798 (tt) REVERT: a 6 ARG cc_start: 0.5874 (OUTLIER) cc_final: 0.5113 (ttm170) REVERT: c 5 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6522 (tt) REVERT: d 5 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6439 (tt) outliers start: 107 outliers final: 54 residues processed: 107 average time/residue: 0.1034 time to fit residues: 13.1170 Evaluate side-chains 85 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 1 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 5 LEU 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 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 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 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: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4204 r_free = 0.4204 target = 0.083456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.066886 restraints weight = 8045.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.068192 restraints weight = 5351.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.069306 restraints weight = 4015.162| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5071 moved from start: 1.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.270 2010 Z= 5.532 Angle : 5.740 34.481 2670 Z= 2.718 Chirality : 0.410 1.333 330 Planarity : 0.050 0.148 300 Dihedral : 11.179 32.725 270 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 279.86 Ramachandran Plot: Outliers : 30.67 % Allowed : 64.67 % Favored : 4.67 % Rotamer: Outliers : 53.81 % Allowed : 14.29 % Favored : 31.90 % Cbeta Deviations : 12.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.052 0.013 HIS C 4 ARG 0.015 0.002 ARG O 6 *********************** 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 113 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 0 time to evaluate : 0.256 Fit side-chains REVERT: A 5 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5324 (tt) REVERT: B 2 HIS cc_start: 0.5716 (OUTLIER) cc_final: 0.5467 (t-170) REVERT: B 5 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5301 (tt) REVERT: C 2 HIS cc_start: 0.5524 (OUTLIER) cc_final: 0.5121 (t-170) REVERT: C 4 HIS cc_start: 0.5432 (OUTLIER) cc_final: 0.4600 (m90) REVERT: C 5 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5621 (tt) REVERT: D 5 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5713 (tt) REVERT: E 5 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5891 (tt) REVERT: F 5 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.5975 (tt) REVERT: G 5 LEU cc_start: 0.5957 (OUTLIER) cc_final: 0.5533 (tt) REVERT: H 5 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5527 (tt) REVERT: I 5 LEU cc_start: 0.5649 (OUTLIER) cc_final: 0.5429 (tt) REVERT: I 6 ARG cc_start: 0.5459 (OUTLIER) cc_final: 0.4791 (ttt180) REVERT: J 6 ARG cc_start: 0.5568 (OUTLIER) cc_final: 0.4887 (ttt180) REVERT: K 5 LEU cc_start: 0.5905 (OUTLIER) cc_final: 0.5650 (tt) REVERT: L 5 LEU cc_start: 0.5904 (OUTLIER) cc_final: 0.5668 (tt) REVERT: M 4 HIS cc_start: 0.5054 (OUTLIER) cc_final: 0.4069 (t70) REVERT: M 5 LEU cc_start: 0.5790 (OUTLIER) cc_final: 0.5456 (tt) REVERT: N 4 HIS cc_start: 0.5115 (OUTLIER) cc_final: 0.4121 (t70) REVERT: N 5 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5460 (tt) REVERT: O 6 ARG cc_start: 0.5530 (OUTLIER) cc_final: 0.4674 (ttm170) REVERT: P 2 HIS cc_start: 0.4877 (OUTLIER) cc_final: 0.4361 (t-170) REVERT: P 4 HIS cc_start: 0.5662 (OUTLIER) cc_final: 0.4638 (t70) REVERT: P 5 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5684 (tt) REVERT: Q 5 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5821 (tt) REVERT: R 5 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5530 (tt) REVERT: U 4 HIS cc_start: 0.4902 (OUTLIER) cc_final: 0.4647 (t70) REVERT: U 6 ARG cc_start: 0.5648 (OUTLIER) cc_final: 0.5157 (ttt180) REVERT: V 6 ARG cc_start: 0.5774 (OUTLIER) cc_final: 0.5347 (ttt180) REVERT: W 5 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6211 (tt) REVERT: X 5 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5837 (tt) REVERT: a 6 ARG cc_start: 0.5823 (OUTLIER) cc_final: 0.4984 (ttt180) REVERT: b 6 ARG cc_start: 0.5821 (OUTLIER) cc_final: 0.5054 (ttm170) REVERT: c 5 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6507 (tt) REVERT: d 5 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6457 (tt) outliers start: 113 outliers final: 56 residues processed: 113 average time/residue: 0.1498 time to fit residues: 19.3443 Evaluate side-chains 92 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 1 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 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 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 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 L residue 5 LEU 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 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 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 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 2 HIS 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 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: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 = 0.4204 r_free = 0.4204 target = 0.083595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.066630 restraints weight = 8868.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.068031 restraints weight = 5732.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.069186 restraints weight = 4197.362| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4898 moved from start: 1.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.274 2010 Z= 5.515 Angle : 5.745 34.443 2670 Z= 2.727 Chirality : 0.412 1.331 330 Planarity : 0.049 0.145 300 Dihedral : 11.130 32.824 270 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 277.25 Ramachandran Plot: Outliers : 30.67 % Allowed : 64.67 % Favored : 4.67 % Rotamer: Outliers : 52.86 % Allowed : 18.10 % Favored : 29.05 % Cbeta Deviations : 11.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.052 0.013 HIS C 4 ARG 0.016 0.002 ARG T 6 *********************** 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 111 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 0 time to evaluate : 0.261 Fit side-chains REVERT: A 5 LEU cc_start: 0.5634 (OUTLIER) cc_final: 0.5192 (tt) REVERT: B 2 HIS cc_start: 0.5577 (OUTLIER) cc_final: 0.5347 (t-170) REVERT: B 5 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5183 (tt) REVERT: C 2 HIS cc_start: 0.5385 (OUTLIER) cc_final: 0.4995 (t-170) REVERT: C 4 HIS cc_start: 0.5319 (OUTLIER) cc_final: 0.4528 (m90) REVERT: C 5 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5517 (tt) REVERT: D 5 LEU cc_start: 0.5720 (OUTLIER) cc_final: 0.5441 (tt) REVERT: E 5 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5752 (tt) REVERT: F 5 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5767 (tt) REVERT: G 5 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5400 (tt) REVERT: H 5 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5382 (tt) REVERT: I 6 ARG cc_start: 0.5263 (OUTLIER) cc_final: 0.4715 (ttt180) REVERT: J 6 ARG cc_start: 0.5331 (OUTLIER) cc_final: 0.4607 (ttt180) REVERT: K 5 LEU cc_start: 0.5760 (OUTLIER) cc_final: 0.5527 (tt) REVERT: L 5 LEU cc_start: 0.5748 (OUTLIER) cc_final: 0.5517 (tt) REVERT: M 4 HIS cc_start: 0.4739 (OUTLIER) cc_final: 0.3853 (t70) REVERT: M 5 LEU cc_start: 0.5599 (OUTLIER) cc_final: 0.5290 (tt) REVERT: N 4 HIS cc_start: 0.4799 (OUTLIER) cc_final: 0.3890 (t70) REVERT: N 5 LEU cc_start: 0.5593 (OUTLIER) cc_final: 0.5276 (tt) REVERT: O 6 ARG cc_start: 0.5192 (OUTLIER) cc_final: 0.4479 (ttm170) REVERT: P 2 HIS cc_start: 0.4771 (OUTLIER) cc_final: 0.4350 (t-170) REVERT: P 4 HIS cc_start: 0.5450 (OUTLIER) cc_final: 0.4412 (t70) REVERT: Q 5 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5660 (tt) REVERT: R 5 LEU cc_start: 0.5731 (OUTLIER) cc_final: 0.5374 (tt) REVERT: S 6 ARG cc_start: 0.6081 (OUTLIER) cc_final: 0.5812 (ttt-90) REVERT: T 6 ARG cc_start: 0.6132 (OUTLIER) cc_final: 0.5056 (ttm170) REVERT: U 6 ARG cc_start: 0.5507 (OUTLIER) cc_final: 0.4782 (ttm170) REVERT: V 6 ARG cc_start: 0.5574 (OUTLIER) cc_final: 0.5145 (ttt180) REVERT: W 5 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5874 (tt) REVERT: X 5 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5751 (tt) REVERT: Z 6 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.4900 (ttm170) REVERT: a 6 ARG cc_start: 0.5597 (OUTLIER) cc_final: 0.4820 (ttt180) REVERT: b 6 ARG cc_start: 0.5680 (OUTLIER) cc_final: 0.4958 (ttm170) REVERT: c 5 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6424 (tt) REVERT: d 5 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6393 (tt) outliers start: 111 outliers final: 59 residues processed: 111 average time/residue: 0.1550 time to fit residues: 19.4120 Evaluate side-chains 94 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 0 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 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 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 L residue 5 LEU 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 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 2 HIS 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 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=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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4208 r_free = 0.4208 target = 0.083734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.066764 restraints weight = 8618.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.068169 restraints weight = 5627.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.069311 restraints weight = 4152.505| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5085 moved from start: 1.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.274 2010 Z= 5.493 Angle : 5.751 34.516 2670 Z= 2.738 Chirality : 0.412 1.333 330 Planarity : 0.049 0.144 300 Dihedral : 11.099 33.229 270 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 277.49 Ramachandran Plot: Outliers : 31.33 % Allowed : 64.00 % Favored : 4.67 % Rotamer: Outliers : 52.38 % Allowed : 17.14 % Favored : 30.48 % Cbeta Deviations : 11.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.052 0.013 HIS C 4 ARG 0.012 0.002 ARG T 6 *********************** 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 110 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 0 time to evaluate : 0.284 Fit side-chains REVERT: A 5 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5418 (tt) REVERT: B 2 HIS cc_start: 0.5715 (OUTLIER) cc_final: 0.5470 (t-170) REVERT: B 5 LEU cc_start: 0.5807 (OUTLIER) cc_final: 0.5339 (tt) REVERT: C 2 HIS cc_start: 0.5527 (OUTLIER) cc_final: 0.5059 (t-170) REVERT: C 4 HIS cc_start: 0.5501 (OUTLIER) cc_final: 0.4674 (m90) REVERT: C 5 LEU cc_start: 0.6178 (OUTLIER) cc_final: 0.5771 (tt) REVERT: D 5 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5490 (tt) REVERT: E 5 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5938 (tt) REVERT: F 5 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.6009 (tt) REVERT: G 5 LEU cc_start: 0.5979 (OUTLIER) cc_final: 0.5552 (tt) REVERT: H 5 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5533 (tt) REVERT: I 6 ARG cc_start: 0.5365 (OUTLIER) cc_final: 0.4713 (ttt180) REVERT: J 6 ARG cc_start: 0.5452 (OUTLIER) cc_final: 0.4660 (ttt180) REVERT: K 5 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5710 (tt) REVERT: L 5 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5712 (tt) REVERT: M 4 HIS cc_start: 0.5073 (OUTLIER) cc_final: 0.4113 (t70) REVERT: M 5 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5536 (tt) REVERT: N 4 HIS cc_start: 0.5150 (OUTLIER) cc_final: 0.4162 (t70) REVERT: N 5 LEU cc_start: 0.5851 (OUTLIER) cc_final: 0.5527 (tt) REVERT: O 2 HIS cc_start: 0.5132 (OUTLIER) cc_final: 0.4923 (t-170) REVERT: P 2 HIS cc_start: 0.4929 (OUTLIER) cc_final: 0.4370 (t-170) REVERT: P 4 HIS cc_start: 0.5639 (OUTLIER) cc_final: 0.4534 (t70) REVERT: Q 5 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5852 (tt) REVERT: R 5 LEU cc_start: 0.5978 (OUTLIER) cc_final: 0.5661 (tt) REVERT: S 6 ARG cc_start: 0.6244 (OUTLIER) cc_final: 0.5961 (ttt-90) REVERT: U 6 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.4985 (ttt180) REVERT: V 6 ARG cc_start: 0.5764 (OUTLIER) cc_final: 0.5303 (ttt180) REVERT: W 5 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.5999 (tt) REVERT: X 5 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5903 (tt) REVERT: a 6 ARG cc_start: 0.5674 (OUTLIER) cc_final: 0.4815 (ttt180) REVERT: b 6 ARG cc_start: 0.5850 (OUTLIER) cc_final: 0.5090 (ttt180) REVERT: c 5 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6589 (tt) REVERT: d 5 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6535 (tt) outliers start: 110 outliers final: 62 residues processed: 110 average time/residue: 0.1475 time to fit residues: 18.3140 Evaluate side-chains 95 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 0 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 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 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 1 LEU 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 L residue 5 LEU 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 4 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 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 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 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=2.00 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 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 = 0.4184 r_free = 0.4184 target = 0.082659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.067249 restraints weight = 9787.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.068482 restraints weight = 6077.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.069568 restraints weight = 4443.852| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5123 moved from start: 1.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.277 2010 Z= 5.510 Angle : 5.787 34.565 2670 Z= 2.743 Chirality : 0.413 1.343 330 Planarity : 0.049 0.144 300 Dihedral : 11.126 33.568 270 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 276.07 Ramachandran Plot: Outliers : 31.33 % Allowed : 64.00 % Favored : 4.67 % Rotamer: Outliers : 52.38 % Allowed : 18.10 % Favored : 29.52 % Cbeta Deviations : 11.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.052 0.013 HIS C 4 ARG 0.012 0.002 ARG T 6 *********************** 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 110 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 0 time to evaluate : 0.275 Fit side-chains REVERT: A 5 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5466 (tt) REVERT: B 2 HIS cc_start: 0.5751 (OUTLIER) cc_final: 0.5453 (t-170) REVERT: B 5 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5394 (tt) REVERT: C 2 HIS cc_start: 0.5553 (OUTLIER) cc_final: 0.5083 (t-170) REVERT: C 4 HIS cc_start: 0.5531 (OUTLIER) cc_final: 0.4701 (m90) REVERT: C 5 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5779 (tt) REVERT: D 5 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.5519 (tt) REVERT: E 2 HIS cc_start: 0.6152 (OUTLIER) cc_final: 0.5938 (t70) REVERT: E 5 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5984 (tt) REVERT: F 5 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6070 (tt) REVERT: G 5 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5575 (tt) REVERT: H 5 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5579 (tt) REVERT: I 6 ARG cc_start: 0.5407 (OUTLIER) cc_final: 0.4754 (ttt180) REVERT: J 6 ARG cc_start: 0.5491 (OUTLIER) cc_final: 0.4708 (ttt180) REVERT: K 5 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5758 (tt) REVERT: L 5 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5771 (tt) REVERT: M 2 HIS cc_start: 0.4321 (OUTLIER) cc_final: 0.3486 (t-170) REVERT: M 4 HIS cc_start: 0.5273 (OUTLIER) cc_final: 0.4185 (t70) REVERT: M 5 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5555 (tt) REVERT: N 2 HIS cc_start: 0.4620 (OUTLIER) cc_final: 0.3697 (t-170) REVERT: N 4 HIS cc_start: 0.5370 (OUTLIER) cc_final: 0.4249 (t70) REVERT: N 5 LEU cc_start: 0.5886 (OUTLIER) cc_final: 0.5564 (tt) REVERT: O 2 HIS cc_start: 0.5210 (OUTLIER) cc_final: 0.5001 (t-170) REVERT: P 4 HIS cc_start: 0.5660 (OUTLIER) cc_final: 0.4850 (m90) REVERT: Q 5 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5926 (tt) REVERT: R 5 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5743 (tt) REVERT: S 6 ARG cc_start: 0.6305 (OUTLIER) cc_final: 0.6083 (ttt-90) REVERT: U 6 ARG cc_start: 0.5565 (OUTLIER) cc_final: 0.4822 (ttt180) REVERT: V 6 ARG cc_start: 0.5845 (OUTLIER) cc_final: 0.5284 (ttt180) REVERT: W 5 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.6054 (tt) REVERT: X 5 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6216 (tt) REVERT: Y 6 ARG cc_start: 0.6454 (OUTLIER) cc_final: 0.5109 (ttm170) REVERT: Z 6 ARG cc_start: 0.6375 (OUTLIER) cc_final: 0.5050 (ttm170) REVERT: a 4 HIS cc_start: 0.5670 (OUTLIER) cc_final: 0.4981 (t70) REVERT: b 6 ARG cc_start: 0.5897 (OUTLIER) cc_final: 0.5072 (ttt180) REVERT: c 5 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6714 (tt) REVERT: d 5 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6674 (tt) outliers start: 110 outliers final: 61 residues processed: 110 average time/residue: 0.1592 time to fit residues: 19.7189 Evaluate side-chains 99 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 1 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 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 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 1 LEU 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 L residue 5 LEU 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 2 HIS Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU 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 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=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... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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 = 0.4188 r_free = 0.4188 target = 0.082839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.067593 restraints weight = 9136.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.068869 restraints weight = 5825.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.069904 restraints weight = 4268.853| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4957 moved from start: 1.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.277 2010 Z= 5.506 Angle : 5.778 34.485 2670 Z= 2.744 Chirality : 0.413 1.336 330 Planarity : 0.049 0.141 300 Dihedral : 11.161 33.249 270 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 277.49 Ramachandran Plot: Outliers : 31.33 % Allowed : 64.00 % Favored : 4.67 % Rotamer: Outliers : 50.95 % Allowed : 20.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.052 0.013 HIS C 4 ARG 0.016 0.002 ARG A 6 *********************** 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 107 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 0 time to evaluate : 0.267 Fit side-chains REVERT: A 5 LEU cc_start: 0.5686 (OUTLIER) cc_final: 0.5242 (tt) REVERT: B 2 HIS cc_start: 0.5627 (OUTLIER) cc_final: 0.5345 (t-170) REVERT: B 5 LEU cc_start: 0.5716 (OUTLIER) cc_final: 0.5255 (tt) REVERT: C 2 HIS cc_start: 0.5408 (OUTLIER) cc_final: 0.4968 (t-170) REVERT: C 4 HIS cc_start: 0.5361 (OUTLIER) cc_final: 0.4578 (m90) REVERT: C 5 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5551 (tt) REVERT: D 2 HIS cc_start: 0.5785 (OUTLIER) cc_final: 0.5564 (t-170) REVERT: D 5 LEU cc_start: 0.5744 (OUTLIER) cc_final: 0.5406 (tt) REVERT: E 2 HIS cc_start: 0.6013 (OUTLIER) cc_final: 0.5799 (t70) REVERT: E 5 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5853 (tt) REVERT: F 5 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5874 (tt) REVERT: G 5 LEU cc_start: 0.5859 (OUTLIER) cc_final: 0.5447 (tt) REVERT: H 5 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5443 (tt) REVERT: I 6 ARG cc_start: 0.5302 (OUTLIER) cc_final: 0.4652 (ttt180) REVERT: J 6 ARG cc_start: 0.5358 (OUTLIER) cc_final: 0.4608 (ttt180) REVERT: K 5 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.5635 (tt) REVERT: L 5 LEU cc_start: 0.5867 (OUTLIER) cc_final: 0.5643 (tt) REVERT: M 4 HIS cc_start: 0.4825 (OUTLIER) cc_final: 0.3895 (t70) REVERT: M 5 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5398 (tt) REVERT: N 2 HIS cc_start: 0.4273 (OUTLIER) cc_final: 0.3419 (t-170) REVERT: N 4 HIS cc_start: 0.5085 (OUTLIER) cc_final: 0.4028 (t70) REVERT: N 5 LEU cc_start: 0.5699 (OUTLIER) cc_final: 0.5396 (tt) REVERT: P 6 ARG cc_start: 0.5376 (OUTLIER) cc_final: 0.4630 (ttm170) REVERT: Q 5 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5728 (tt) REVERT: R 5 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5628 (tt) REVERT: S 6 ARG cc_start: 0.6152 (OUTLIER) cc_final: 0.5941 (ttt-90) REVERT: U 6 ARG cc_start: 0.5531 (OUTLIER) cc_final: 0.4831 (ttt180) REVERT: V 6 ARG cc_start: 0.5681 (OUTLIER) cc_final: 0.5159 (ttt180) REVERT: W 5 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5924 (tt) REVERT: X 5 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6091 (tt) REVERT: Y 6 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.4989 (ttm170) REVERT: Z 6 ARG cc_start: 0.6208 (OUTLIER) cc_final: 0.4938 (ttm170) REVERT: a 4 HIS cc_start: 0.5481 (OUTLIER) cc_final: 0.4939 (t70) REVERT: b 6 ARG cc_start: 0.5675 (OUTLIER) cc_final: 0.4909 (ttt180) REVERT: c 5 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6626 (tt) REVERT: d 5 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6584 (tt) outliers start: 107 outliers final: 61 residues processed: 107 average time/residue: 0.1554 time to fit residues: 18.8373 Evaluate side-chains 97 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 0 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 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 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 1 LEU 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 L residue 5 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 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 = 0.4193 r_free = 0.4193 target = 0.082934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.067679 restraints weight = 9144.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.068950 restraints weight = 5839.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.069979 restraints weight = 4274.432| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4986 moved from start: 1.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.275 2010 Z= 5.489 Angle : 5.786 34.453 2670 Z= 2.745 Chirality : 0.414 1.331 330 Planarity : 0.049 0.140 300 Dihedral : 11.187 34.012 270 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 277.73 Ramachandran Plot: Outliers : 30.67 % Allowed : 64.67 % Favored : 4.67 % Rotamer: Outliers : 50.48 % Allowed : 20.00 % Favored : 29.52 % Cbeta Deviations : 10.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.053 0.013 HIS C 4 ARG 0.013 0.002 ARG T 6 ********************** 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 106 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 0 time to evaluate : 0.275 Fit side-chains REVERT: A 5 LEU cc_start: 0.5710 (OUTLIER) cc_final: 0.5257 (tt) REVERT: B 2 HIS cc_start: 0.5647 (OUTLIER) cc_final: 0.5363 (t-170) REVERT: B 5 LEU cc_start: 0.5739 (OUTLIER) cc_final: 0.5264 (tt) REVERT: C 2 HIS cc_start: 0.5433 (OUTLIER) cc_final: 0.5009 (t-170) REVERT: C 4 HIS cc_start: 0.5390 (OUTLIER) cc_final: 0.4600 (m90) REVERT: C 5 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5570 (tt) REVERT: D 2 HIS cc_start: 0.5807 (OUTLIER) cc_final: 0.5555 (t-170) REVERT: D 5 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5462 (tt) REVERT: E 2 HIS cc_start: 0.6079 (OUTLIER) cc_final: 0.5863 (t70) REVERT: E 5 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5769 (tt) REVERT: F 5 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.5865 (tt) REVERT: G 5 LEU cc_start: 0.5887 (OUTLIER) cc_final: 0.5471 (tt) REVERT: H 5 LEU cc_start: 0.5881 (OUTLIER) cc_final: 0.5497 (tt) REVERT: H 6 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5118 (ttm170) REVERT: I 6 ARG cc_start: 0.5341 (OUTLIER) cc_final: 0.4684 (ttt180) REVERT: J 6 ARG cc_start: 0.5390 (OUTLIER) cc_final: 0.4654 (ttt180) REVERT: K 5 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5702 (tt) REVERT: L 5 LEU cc_start: 0.5888 (OUTLIER) cc_final: 0.5663 (tt) REVERT: M 2 HIS cc_start: 0.4255 (OUTLIER) cc_final: 0.3468 (t-170) REVERT: M 4 HIS cc_start: 0.5030 (OUTLIER) cc_final: 0.3963 (t70) REVERT: M 5 LEU cc_start: 0.5726 (OUTLIER) cc_final: 0.5429 (tt) REVERT: N 2 HIS cc_start: 0.4305 (OUTLIER) cc_final: 0.3454 (t-170) REVERT: N 4 HIS cc_start: 0.4978 (OUTLIER) cc_final: 0.3982 (t70) REVERT: N 5 LEU cc_start: 0.5743 (OUTLIER) cc_final: 0.5435 (tt) REVERT: P 6 ARG cc_start: 0.5327 (OUTLIER) cc_final: 0.4689 (ttm170) REVERT: Q 5 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5717 (tt) REVERT: R 5 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5630 (tt) REVERT: S 6 ARG cc_start: 0.6108 (OUTLIER) cc_final: 0.5857 (ttt-90) REVERT: U 6 ARG cc_start: 0.5667 (OUTLIER) cc_final: 0.4941 (ttt180) REVERT: V 6 ARG cc_start: 0.5650 (OUTLIER) cc_final: 0.4908 (ttt180) REVERT: W 5 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5941 (tt) REVERT: X 5 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6098 (tt) REVERT: Y 6 ARG cc_start: 0.6242 (OUTLIER) cc_final: 0.4988 (ttm170) REVERT: Z 6 ARG cc_start: 0.6242 (OUTLIER) cc_final: 0.4962 (ttm170) REVERT: a 4 HIS cc_start: 0.5505 (OUTLIER) cc_final: 0.4926 (t70) REVERT: b 4 HIS cc_start: 0.5570 (OUTLIER) cc_final: 0.4849 (t70) REVERT: c 5 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6715 (tt) REVERT: d 5 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6504 (tt) outliers start: 106 outliers final: 59 residues processed: 106 average time/residue: 0.1605 time to fit residues: 19.1137 Evaluate side-chains 97 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 0 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 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 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 H residue 6 ARG Chi-restraints excluded: chain I residue 1 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 1 LEU 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 4 HIS Chi-restraints excluded: chain L residue 5 LEU 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 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... Flipped N/Q/H residues before XYZ refinement: ** 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 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 = 0.4195 r_free = 0.4195 target = 0.082995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.067700 restraints weight = 9393.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.068992 restraints weight = 5939.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.070059 restraints weight = 4328.758| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5000 moved from start: 1.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.276 2010 Z= 5.486 Angle : 5.784 34.482 2670 Z= 2.744 Chirality : 0.414 1.337 330 Planarity : 0.049 0.139 300 Dihedral : 11.253 34.686 270 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 278.20 Ramachandran Plot: Outliers : 31.33 % Allowed : 64.00 % Favored : 4.67 % Rotamer: Outliers : 47.62 % Allowed : 22.38 % Favored : 30.00 % Cbeta Deviations : 10.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.053 0.013 HIS C 4 ARG 0.013 0.002 ARG b 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 534.60 seconds wall clock time: 11 minutes 12.61 seconds (672.61 seconds total)