Starting phenix.real_space_refine on Thu Jul 18 17:10:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/07_2024/8b3a_15824.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/07_2024/8b3a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/07_2024/8b3a_15824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/07_2024/8b3a_15824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/07_2024/8b3a_15824.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/07_2024/8b3a_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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 1.17, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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 229.7 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: 0.23 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: 0.07 Time building geometry restraints manager: 1.11 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: 99.98 - 106.27: 160 106.27 - 112.56: 1088 112.56 - 118.85: 537 118.85 - 125.14: 795 125.14 - 131.43: 90 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.730 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.050 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.644 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 1.7640 time to fit residues: 4.5874 Evaluate side-chains 0 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 1.1945 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= 5.579 Angle : 5.877 32.688 2670 Z= 2.780 Chirality : 0.406 1.312 330 Planarity : 0.055 0.183 300 Dihedral : 10.599 30.688 270 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 283.58 Ramachandran Plot: Outliers : 60.00 % Allowed : 28.67 % Favored : 11.33 % Rotamer: Outliers : 41.90 % Allowed : 23.81 % Favored : 34.29 % Cbeta Deviations : 8.57 % 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: -10.67 (0.09), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.13 (0.07), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.050 0.014 HIS P 4 ARG 0.012 0.002 ARG d 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 88 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 0 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.7682 (t-170) REVERT: B 2 HIS cc_start: 0.8311 (OUTLIER) cc_final: 0.7696 (t-170) REVERT: B 5 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7915 (tt) REVERT: E 5 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8183 (tt) REVERT: F 5 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8128 (tt) REVERT: G 5 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8273 (tt) REVERT: H 5 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8216 (tt) REVERT: I 6 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8071 (ttt180) REVERT: K 5 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8697 (tt) REVERT: L 5 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8630 (tt) REVERT: M 2 HIS cc_start: 0.9176 (OUTLIER) cc_final: 0.8795 (t-170) REVERT: M 5 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8618 (tt) REVERT: N 2 HIS cc_start: 0.9157 (OUTLIER) cc_final: 0.8776 (t-170) REVERT: N 5 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8673 (tt) REVERT: O 4 HIS cc_start: 0.9286 (OUTLIER) cc_final: 0.8879 (m90) REVERT: P 2 HIS cc_start: 0.8978 (OUTLIER) cc_final: 0.8141 (t-170) REVERT: P 4 HIS cc_start: 0.9242 (OUTLIER) cc_final: 0.8284 (t70) REVERT: Q 5 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8908 (tt) REVERT: R 5 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8813 (tt) REVERT: X 4 HIS cc_start: 0.9159 (OUTLIER) cc_final: 0.8655 (t70) REVERT: Z 6 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8081 (ttt-90) REVERT: a 6 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7549 (ttt-90) outliers start: 88 outliers final: 33 residues processed: 88 average time/residue: 0.1530 time to fit residues: 15.2939 Evaluate side-chains 55 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 0 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain 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 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 4 HIS Chi-restraints excluded: chain K residue 5 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 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 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 Q residue 5 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 4 HIS 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 4 HIS Chi-restraints excluded: chain c residue 2 HIS 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: 0.7980 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 1.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.275 2010 Z= 5.467 Angle : 5.769 34.060 2670 Z= 2.665 Chirality : 0.413 1.330 330 Planarity : 0.052 0.164 300 Dihedral : 10.476 33.197 270 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 278.44 Ramachandran Plot: Outliers : 50.00 % Allowed : 46.00 % Favored : 4.00 % Rotamer: Outliers : 51.43 % Allowed : 20.48 % Favored : 28.10 % Cbeta Deviations : 13.33 % 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: -10.76 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.20 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.052 0.013 HIS D 4 ARG 0.010 0.002 ARG F 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 108 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 0 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.7917 (t-170) REVERT: A 5 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8042 (tt) REVERT: B 2 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.7760 (t-170) REVERT: B 5 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8034 (tt) REVERT: C 2 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7443 (t-170) REVERT: C 4 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.7425 (m90) REVERT: C 5 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7969 (tt) REVERT: D 2 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7127 (t-170) REVERT: D 4 HIS cc_start: 0.8575 (OUTLIER) cc_final: 0.7151 (m90) REVERT: E 2 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7809 (t-170) REVERT: F 2 HIS cc_start: 0.8259 (OUTLIER) cc_final: 0.7911 (t-170) REVERT: G 5 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7971 (tt) REVERT: H 5 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7967 (tt) REVERT: K 5 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8679 (tt) REVERT: L 5 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8678 (tt) REVERT: M 2 HIS cc_start: 0.9209 (OUTLIER) cc_final: 0.8816 (t-170) REVERT: M 5 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8571 (tt) REVERT: N 2 HIS cc_start: 0.9186 (OUTLIER) cc_final: 0.8794 (t-170) REVERT: N 5 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8597 (tt) REVERT: O 2 HIS cc_start: 0.9102 (OUTLIER) cc_final: 0.8342 (t-170) REVERT: O 4 HIS cc_start: 0.9426 (OUTLIER) cc_final: 0.8438 (t70) REVERT: P 2 HIS cc_start: 0.9052 (OUTLIER) cc_final: 0.8240 (t-170) REVERT: P 4 HIS cc_start: 0.9241 (OUTLIER) cc_final: 0.8229 (t70) REVERT: S 6 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8358 (ttt-90) REVERT: T 6 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8249 (ttt-90) REVERT: Y 2 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.8211 (t-170) REVERT: Z 2 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.8181 (t-170) REVERT: a 4 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.7528 (t70) REVERT: b 4 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.7330 (t70) outliers start: 108 outliers final: 53 residues processed: 108 average time/residue: 0.1650 time to fit residues: 19.9108 Evaluate side-chains 82 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 0 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 A residue 6 ARG 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 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 E residue 2 HIS Chi-restraints excluded: chain F residue 2 HIS 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 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 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 5 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 6 ARG 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 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS 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 4 HIS Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain V residue 6 ARG 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 2 HIS Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 2 HIS Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 2 HIS Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain 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 d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS 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** ** G 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 1.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.285 2010 Z= 5.411 Angle : 5.784 33.582 2670 Z= 2.709 Chirality : 0.414 1.316 330 Planarity : 0.052 0.175 300 Dihedral : 10.390 35.095 270 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 287.68 Ramachandran Plot: Outliers : 44.67 % Allowed : 50.67 % Favored : 4.67 % Rotamer: Outliers : 54.76 % Allowed : 16.19 % Favored : 29.05 % 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: -10.74 (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 0.051 0.013 HIS C 4 ARG 0.012 0.002 ARG F 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 115 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 0 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.7849 (t-170) REVERT: B 2 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.7887 (t-170) REVERT: B 5 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7904 (tt) REVERT: C 2 HIS cc_start: 0.7989 (OUTLIER) cc_final: 0.7443 (t-170) REVERT: C 4 HIS cc_start: 0.8483 (OUTLIER) cc_final: 0.7542 (m90) REVERT: D 2 HIS cc_start: 0.7992 (OUTLIER) cc_final: 0.6708 (t-170) REVERT: E 2 HIS cc_start: 0.8207 (OUTLIER) cc_final: 0.7887 (t-170) REVERT: F 2 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.7925 (t-170) REVERT: G 5 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8136 (tt) REVERT: H 5 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8026 (tt) REVERT: I 4 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.8367 (t70) REVERT: J 6 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8404 (ttt180) REVERT: K 5 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8674 (tt) REVERT: M 2 HIS cc_start: 0.9175 (OUTLIER) cc_final: 0.8796 (t-170) REVERT: M 5 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8550 (tt) REVERT: N 2 HIS cc_start: 0.9157 (OUTLIER) cc_final: 0.8793 (t-170) REVERT: N 5 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8587 (tt) REVERT: O 2 HIS cc_start: 0.9086 (OUTLIER) cc_final: 0.8657 (t-170) REVERT: P 2 HIS cc_start: 0.8969 (OUTLIER) cc_final: 0.8447 (t-170) REVERT: Q 5 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8932 (tt) REVERT: S 6 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8335 (ttt-90) REVERT: T 6 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8259 (ttt-90) REVERT: a 4 HIS cc_start: 0.8700 (OUTLIER) cc_final: 0.7818 (t70) REVERT: b 4 HIS cc_start: 0.8474 (OUTLIER) cc_final: 0.7315 (t70) outliers start: 115 outliers final: 69 residues processed: 115 average time/residue: 0.1833 time to fit residues: 22.8608 Evaluate side-chains 93 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 0 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 6 ARG 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 D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS 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 G residue 6 ARG Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 6 ARG 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 O residue 7 LEU Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 6 ARG 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 V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS 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 X residue 6 ARG 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 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 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 1.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.288 2010 Z= 5.474 Angle : 5.736 33.569 2670 Z= 2.690 Chirality : 0.415 1.315 330 Planarity : 0.052 0.176 300 Dihedral : 10.342 35.270 270 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 288.39 Ramachandran Plot: Outliers : 46.67 % Allowed : 49.33 % Favored : 4.00 % Rotamer: Outliers : 55.24 % Allowed : 15.71 % Favored : 29.05 % 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: -10.75 (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 0.013 HIS C 4 ARG 0.009 0.002 ARG d 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 116 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 0 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.7856 (t-170) REVERT: A 5 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7977 (tt) REVERT: B 2 HIS cc_start: 0.8324 (OUTLIER) cc_final: 0.7806 (t-170) REVERT: B 5 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7937 (tt) REVERT: C 2 HIS cc_start: 0.7953 (OUTLIER) cc_final: 0.7387 (t-170) REVERT: C 4 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.7486 (m90) REVERT: D 2 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.6699 (t-170) REVERT: E 2 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7823 (t-170) REVERT: F 2 HIS cc_start: 0.8253 (OUTLIER) cc_final: 0.7883 (t-170) REVERT: G 5 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8022 (tt) REVERT: H 5 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8015 (tt) REVERT: I 4 HIS cc_start: 0.8910 (OUTLIER) cc_final: 0.8380 (t70) REVERT: M 2 HIS cc_start: 0.9187 (OUTLIER) cc_final: 0.8298 (t-170) REVERT: M 4 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.7918 (t70) REVERT: M 5 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8688 (tt) REVERT: N 2 HIS cc_start: 0.9173 (OUTLIER) cc_final: 0.8808 (t-170) REVERT: N 5 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8591 (tt) REVERT: O 2 HIS cc_start: 0.9095 (OUTLIER) cc_final: 0.8667 (t-170) REVERT: P 2 HIS cc_start: 0.8931 (OUTLIER) cc_final: 0.8051 (t-170) REVERT: P 4 HIS cc_start: 0.9257 (OUTLIER) cc_final: 0.8225 (t70) REVERT: S 6 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8346 (ttt-90) REVERT: T 6 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8292 (ttt-90) REVERT: V 6 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8125 (ttt180) REVERT: a 4 HIS cc_start: 0.8695 (OUTLIER) cc_final: 0.7883 (t70) REVERT: b 4 HIS cc_start: 0.8543 (OUTLIER) cc_final: 0.7473 (t70) outliers start: 116 outliers final: 66 residues processed: 116 average time/residue: 0.1754 time to fit residues: 22.1471 Evaluate side-chains 91 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 0 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 A residue 6 ARG 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 D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 6 ARG 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 M residue 6 ARG Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 6 ARG 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 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 6 ARG 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 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 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS 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 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 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS 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 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 2 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 1.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.287 2010 Z= 5.450 Angle : 5.735 33.703 2670 Z= 2.694 Chirality : 0.417 1.321 330 Planarity : 0.052 0.195 300 Dihedral : 10.453 36.633 270 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 285.55 Ramachandran Plot: Outliers : 45.33 % Allowed : 49.33 % Favored : 5.33 % Rotamer: Outliers : 55.24 % Allowed : 14.76 % 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: -10.75 (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 0.052 0.013 HIS C 4 ARG 0.012 0.002 ARG G 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 116 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 0 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.7847 (t-170) REVERT: A 5 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7989 (tt) REVERT: B 2 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.7788 (t-170) REVERT: B 5 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7933 (tt) REVERT: C 2 HIS cc_start: 0.7962 (OUTLIER) cc_final: 0.7366 (t-170) REVERT: C 4 HIS cc_start: 0.8480 (OUTLIER) cc_final: 0.7427 (m90) REVERT: C 5 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8048 (tt) REVERT: D 2 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.6646 (t-170) REVERT: E 2 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7923 (t-170) REVERT: F 2 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.7881 (t-170) REVERT: G 5 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8013 (tt) REVERT: H 5 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8002 (tt) REVERT: I 4 HIS cc_start: 0.8931 (OUTLIER) cc_final: 0.8353 (t70) REVERT: J 4 HIS cc_start: 0.9204 (OUTLIER) cc_final: 0.8618 (t70) REVERT: M 2 HIS cc_start: 0.9181 (OUTLIER) cc_final: 0.8293 (t-170) REVERT: M 4 HIS cc_start: 0.9078 (OUTLIER) cc_final: 0.7924 (t70) REVERT: M 5 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8686 (tt) REVERT: N 2 HIS cc_start: 0.9176 (OUTLIER) cc_final: 0.8322 (t-170) REVERT: N 4 HIS cc_start: 0.9084 (OUTLIER) cc_final: 0.7912 (t70) REVERT: N 5 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8698 (tt) REVERT: O 2 HIS cc_start: 0.9121 (OUTLIER) cc_final: 0.8664 (t-170) REVERT: P 2 HIS cc_start: 0.8975 (OUTLIER) cc_final: 0.8436 (t-170) REVERT: S 6 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8345 (ttt-90) REVERT: T 6 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8288 (ttt-90) REVERT: a 4 HIS cc_start: 0.8714 (OUTLIER) cc_final: 0.7998 (t70) REVERT: b 4 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.7651 (t70) outliers start: 116 outliers final: 72 residues processed: 116 average time/residue: 0.1804 time to fit residues: 22.6194 Evaluate side-chains 98 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 0 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 A residue 6 ARG 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 4 HIS Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS 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 G residue 6 ARG 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 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 6 ARG Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 6 ARG 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 M residue 6 ARG 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 N residue 6 ARG 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 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 6 ARG 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 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 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 6 ARG 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 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 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 6 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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** ** G 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 2 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 1.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.288 2010 Z= 5.450 Angle : 5.767 33.651 2670 Z= 2.703 Chirality : 0.417 1.315 330 Planarity : 0.053 0.182 300 Dihedral : 10.529 37.718 270 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 286.97 Ramachandran Plot: Outliers : 44.00 % Allowed : 50.67 % Favored : 5.33 % Rotamer: Outliers : 52.86 % Allowed : 17.62 % Favored : 29.52 % 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: -10.74 (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 0.052 0.013 HIS C 4 ARG 0.012 0.002 ARG Q 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 111 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 0 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8365 (OUTLIER) cc_final: 0.7841 (t-170) REVERT: A 5 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7986 (tt) REVERT: B 2 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.7786 (t-170) REVERT: B 5 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7923 (tt) REVERT: C 2 HIS cc_start: 0.7953 (OUTLIER) cc_final: 0.7372 (t-170) REVERT: C 4 HIS cc_start: 0.8477 (OUTLIER) cc_final: 0.7424 (m90) REVERT: C 5 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8053 (tt) REVERT: D 2 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.6650 (t-170) REVERT: E 2 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7935 (t-170) REVERT: F 2 HIS cc_start: 0.8270 (OUTLIER) cc_final: 0.7926 (t-170) REVERT: G 5 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8023 (tt) REVERT: H 5 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8067 (tt) REVERT: I 4 HIS cc_start: 0.8919 (OUTLIER) cc_final: 0.8322 (t70) REVERT: J 4 HIS cc_start: 0.9222 (OUTLIER) cc_final: 0.8573 (t70) REVERT: K 5 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8695 (tt) REVERT: M 2 HIS cc_start: 0.9180 (OUTLIER) cc_final: 0.8305 (t-170) REVERT: M 4 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.7923 (t70) REVERT: M 5 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8673 (tt) REVERT: N 2 HIS cc_start: 0.9177 (OUTLIER) cc_final: 0.8323 (t-170) REVERT: N 4 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.7917 (t70) REVERT: N 5 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8698 (tt) REVERT: O 2 HIS cc_start: 0.9094 (OUTLIER) cc_final: 0.8617 (t-170) REVERT: P 2 HIS cc_start: 0.8967 (OUTLIER) cc_final: 0.8443 (t-170) REVERT: S 6 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8346 (ttt-90) REVERT: T 6 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8281 (ttt-90) REVERT: a 4 HIS cc_start: 0.8720 (OUTLIER) cc_final: 0.8029 (t70) REVERT: b 4 HIS cc_start: 0.8572 (OUTLIER) cc_final: 0.7746 (t70) outliers start: 111 outliers final: 70 residues processed: 111 average time/residue: 0.2096 time to fit residues: 25.2230 Evaluate side-chains 97 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 0 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 A residue 6 ARG 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 4 HIS Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS 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 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 K residue 6 ARG Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 6 ARG 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 M residue 6 ARG 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 N residue 6 ARG 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 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 6 ARG 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 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 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 6 ARG 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 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 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 6 ARG 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** ** G 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 2 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 1.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.287 2010 Z= 5.430 Angle : 5.761 33.551 2670 Z= 2.703 Chirality : 0.418 1.313 330 Planarity : 0.053 0.187 300 Dihedral : 10.577 38.575 270 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 285.55 Ramachandran Plot: Outliers : 44.00 % Allowed : 50.67 % Favored : 5.33 % Rotamer: Outliers : 52.38 % Allowed : 17.14 % Favored : 30.48 % 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: -10.75 (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 0.052 0.013 HIS C 4 ARG 0.009 0.002 ARG R 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 fitting. rotamer outliers: 110 poor density : 0 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.7837 (t-170) REVERT: A 5 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7980 (tt) REVERT: B 2 HIS cc_start: 0.8330 (OUTLIER) cc_final: 0.7789 (t-170) REVERT: B 5 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7922 (tt) REVERT: C 2 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7363 (t-170) REVERT: C 4 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.7419 (m90) REVERT: C 5 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8205 (tt) REVERT: D 2 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.6628 (t-170) REVERT: E 2 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7937 (t-170) REVERT: F 2 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7884 (t-170) REVERT: G 5 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8028 (tt) REVERT: H 5 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8068 (tt) REVERT: I 4 HIS cc_start: 0.8923 (OUTLIER) cc_final: 0.8275 (t70) REVERT: J 4 HIS cc_start: 0.9204 (OUTLIER) cc_final: 0.8491 (t70) REVERT: M 2 HIS cc_start: 0.9173 (OUTLIER) cc_final: 0.8279 (t-170) REVERT: M 4 HIS cc_start: 0.9080 (OUTLIER) cc_final: 0.7918 (t70) REVERT: M 5 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8674 (tt) REVERT: N 2 HIS cc_start: 0.9173 (OUTLIER) cc_final: 0.8307 (t-170) REVERT: N 4 HIS cc_start: 0.9083 (OUTLIER) cc_final: 0.7914 (t70) REVERT: N 5 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8685 (tt) REVERT: O 2 HIS cc_start: 0.9078 (OUTLIER) cc_final: 0.8586 (t-170) REVERT: P 2 HIS cc_start: 0.8967 (OUTLIER) cc_final: 0.8442 (t-170) REVERT: S 6 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8312 (ttt-90) REVERT: T 6 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8281 (ttt-90) REVERT: a 4 HIS cc_start: 0.8756 (OUTLIER) cc_final: 0.8052 (t70) REVERT: b 4 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.7762 (t70) outliers start: 110 outliers final: 71 residues processed: 110 average time/residue: 0.1751 time to fit residues: 20.9495 Evaluate side-chains 97 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 0 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 A residue 6 ARG 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 4 HIS Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 6 ARG 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 M residue 6 ARG 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 N residue 6 ARG 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 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 6 ARG 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 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 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 6 ARG 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 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 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 6 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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 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 2 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 1.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.287 2010 Z= 5.445 Angle : 5.750 33.583 2670 Z= 2.702 Chirality : 0.417 1.316 330 Planarity : 0.053 0.188 300 Dihedral : 10.570 39.240 270 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 286.49 Ramachandran Plot: Outliers : 44.00 % Allowed : 50.67 % Favored : 5.33 % Rotamer: Outliers : 49.52 % Allowed : 19.05 % Favored : 31.43 % Cbeta Deviations : 11.43 % 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: -10.75 (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 0.052 0.013 HIS C 4 ARG 0.009 0.002 ARG R 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 104 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 0 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8355 (OUTLIER) cc_final: 0.7862 (t-170) REVERT: A 5 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7980 (tt) REVERT: B 2 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7799 (t-170) REVERT: B 5 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7934 (tt) REVERT: C 2 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.7356 (t-170) REVERT: C 4 HIS cc_start: 0.8491 (OUTLIER) cc_final: 0.7444 (m90) REVERT: C 5 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8208 (tt) REVERT: D 2 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.6632 (t-170) REVERT: E 2 HIS cc_start: 0.8234 (OUTLIER) cc_final: 0.7937 (t-170) REVERT: E 6 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7523 (ttt-90) REVERT: F 2 HIS cc_start: 0.8239 (OUTLIER) cc_final: 0.7886 (t-170) REVERT: G 5 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8019 (tt) REVERT: H 5 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8071 (tt) REVERT: I 4 HIS cc_start: 0.8941 (OUTLIER) cc_final: 0.8318 (t70) REVERT: J 4 HIS cc_start: 0.9170 (OUTLIER) cc_final: 0.8499 (t70) REVERT: M 2 HIS cc_start: 0.9175 (OUTLIER) cc_final: 0.8272 (t-170) REVERT: M 4 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.7911 (t70) REVERT: M 5 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8673 (tt) REVERT: N 2 HIS cc_start: 0.9173 (OUTLIER) cc_final: 0.8304 (t-170) REVERT: N 4 HIS cc_start: 0.9082 (OUTLIER) cc_final: 0.7916 (t70) REVERT: N 5 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8684 (tt) REVERT: O 2 HIS cc_start: 0.9077 (OUTLIER) cc_final: 0.8632 (t-170) REVERT: P 2 HIS cc_start: 0.8961 (OUTLIER) cc_final: 0.8468 (t-170) REVERT: S 6 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8316 (ttt-90) REVERT: T 6 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8280 (ttt-90) REVERT: V 6 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8035 (ttt180) REVERT: Y 2 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.8192 (t-170) REVERT: a 4 HIS cc_start: 0.8746 (OUTLIER) cc_final: 0.8075 (t70) REVERT: b 4 HIS cc_start: 0.8526 (OUTLIER) cc_final: 0.7818 (t70) outliers start: 104 outliers final: 69 residues processed: 104 average time/residue: 0.1913 time to fit residues: 21.5184 Evaluate side-chains 98 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 0 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 A residue 6 ARG 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 4 HIS Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS 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 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 6 ARG Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 6 ARG 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 M residue 6 ARG 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 N residue 6 ARG 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 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 6 ARG 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 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 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 6 ARG Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 2 HIS 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 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 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 6 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 2 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 1.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.284 2010 Z= 5.434 Angle : 5.781 33.595 2670 Z= 2.712 Chirality : 0.418 1.317 330 Planarity : 0.053 0.195 300 Dihedral : 10.607 39.469 270 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 288.39 Ramachandran Plot: Outliers : 44.00 % Allowed : 50.67 % Favored : 5.33 % Rotamer: Outliers : 49.05 % Allowed : 19.05 % Favored : 31.90 % 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: -10.75 (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 0.052 0.013 HIS C 4 ARG 0.009 0.002 ARG R 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 103 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 0 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7860 (t-170) REVERT: A 5 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7970 (tt) REVERT: B 2 HIS cc_start: 0.8336 (OUTLIER) cc_final: 0.7780 (t-170) REVERT: B 5 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7937 (tt) REVERT: C 2 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7369 (t-170) REVERT: C 4 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.7441 (m90) REVERT: C 5 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8216 (tt) REVERT: D 2 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.6697 (t-170) REVERT: E 2 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7944 (t-170) REVERT: E 6 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7517 (ttt-90) REVERT: F 2 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.7890 (t-170) REVERT: G 5 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8018 (tt) REVERT: H 5 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8075 (tt) REVERT: I 4 HIS cc_start: 0.8893 (OUTLIER) cc_final: 0.8192 (t70) REVERT: J 4 HIS cc_start: 0.9170 (OUTLIER) cc_final: 0.8445 (t70) REVERT: M 2 HIS cc_start: 0.9177 (OUTLIER) cc_final: 0.8274 (t-170) REVERT: M 4 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.7910 (t70) REVERT: M 5 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8672 (tt) REVERT: N 2 HIS cc_start: 0.9179 (OUTLIER) cc_final: 0.8340 (t-170) REVERT: N 4 HIS cc_start: 0.9081 (OUTLIER) cc_final: 0.7932 (t70) REVERT: N 5 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8686 (tt) REVERT: O 2 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.8611 (t-170) REVERT: P 2 HIS cc_start: 0.8998 (OUTLIER) cc_final: 0.8478 (t-170) REVERT: S 6 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8303 (ttt-90) REVERT: T 6 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8274 (ttt-90) REVERT: V 6 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8045 (ttt180) REVERT: Y 2 HIS cc_start: 0.8516 (OUTLIER) cc_final: 0.8191 (t-170) REVERT: a 4 HIS cc_start: 0.8754 (OUTLIER) cc_final: 0.7993 (t70) REVERT: b 4 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.7736 (t70) outliers start: 103 outliers final: 69 residues processed: 103 average time/residue: 0.2142 time to fit residues: 23.8199 Evaluate side-chains 98 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 0 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 A residue 6 ARG 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 4 HIS Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS 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 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 6 ARG Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 6 ARG 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 M residue 6 ARG 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 N residue 6 ARG 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 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 6 ARG 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 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 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 2 HIS 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 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 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 6 ARG 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 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 2 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** ** 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 2 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 = 0.4337 r_free = 0.4337 target = 0.085045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.068131 restraints weight = 8218.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.069604 restraints weight = 5322.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.070854 restraints weight = 3918.937| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 1.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.284 2010 Z= 5.438 Angle : 5.772 33.599 2670 Z= 2.710 Chirality : 0.420 1.317 330 Planarity : 0.053 0.201 300 Dihedral : 10.613 39.730 270 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 287.44 Ramachandran Plot: Outliers : 44.00 % Allowed : 50.67 % Favored : 5.33 % Rotamer: Outliers : 49.05 % Allowed : 19.52 % Favored : 31.43 % Cbeta Deviations : 11.43 % 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: -10.74 (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 0.052 0.013 HIS C 4 ARG 0.009 0.002 ARG R 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 444.89 seconds wall clock time: 14 minutes 46.55 seconds (886.55 seconds total)