Starting phenix.real_space_refine on Mon Sep 23 11:48:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/09_2024/8b3a_15824.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/09_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_15824/09_2024/8b3a_15824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/09_2024/8b3a_15824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/09_2024/8b3a_15824.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/09_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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 1.38, per 1000 atoms: 0.69 Number of scatterers: 2010 At special positions: 0 Unit cell: (90.48, 49.92, 37.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 240 8.00 N 450 7.00 C 1320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=30, symmetry=0 Number of additional bonds: simple=30, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 203.1 milliseconds 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 420 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 47.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 6.335A pdb=" N LEU A 3 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU G 3 " --> pdb=" O HIS M 4 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU M 3 " --> pdb=" O HIS S 4 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU S 3 " --> pdb=" O HIS Y 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 4 removed outlier: 6.335A pdb=" N LEU B 3 " --> pdb=" O HIS H 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU H 3 " --> pdb=" O HIS N 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU N 3 " --> pdb=" O HIS T 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU T 3 " --> pdb=" O HIS Z 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 6 removed outlier: 6.270A pdb=" N LEU C 3 " --> pdb=" O HIS I 4 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ARG I 6 " --> pdb=" O LEU C 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU C 5 " --> pdb=" O ARG I 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU I 3 " --> pdb=" O HIS O 4 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ARG O 6 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU I 5 " --> pdb=" O ARG O 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU O 3 " --> pdb=" O HIS U 4 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ARG U 6 " --> pdb=" O LEU O 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU O 5 " --> pdb=" O ARG U 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU U 3 " --> pdb=" O HIS a 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG a 6 " --> pdb=" O LEU U 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU U 5 " --> pdb=" O ARG a 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 6 removed outlier: 6.270A pdb=" N LEU D 3 " --> pdb=" O HIS J 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG J 6 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU D 5 " --> pdb=" O ARG J 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU J 3 " --> pdb=" O HIS P 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG P 6 " --> pdb=" O LEU J 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU J 5 " --> pdb=" O ARG P 6 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU P 3 " --> pdb=" O HIS V 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG V 6 " --> pdb=" O LEU P 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU P 5 " --> pdb=" O ARG V 6 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU V 3 " --> pdb=" O HIS b 4 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ARG b 6 " --> pdb=" O LEU V 3 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU V 5 " --> pdb=" O ARG b 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 6 removed outlier: 6.372A pdb=" N LEU E 3 " --> pdb=" O HIS K 4 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ARG K 6 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU E 5 " --> pdb=" O ARG K 6 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU K 3 " --> pdb=" O HIS Q 4 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ARG Q 6 " --> pdb=" O LEU K 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU K 5 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU Q 3 " --> pdb=" O HIS W 4 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ARG W 6 " --> pdb=" O LEU Q 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU Q 5 " --> pdb=" O ARG W 6 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU W 3 " --> pdb=" O HIS c 4 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ARG c 6 " --> pdb=" O LEU W 3 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU W 5 " --> pdb=" O ARG c 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 6 removed outlier: 6.372A pdb=" N LEU F 3 " --> pdb=" O HIS L 4 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ARG L 6 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU F 5 " --> pdb=" O ARG L 6 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU L 3 " --> pdb=" O HIS R 4 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ARG R 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU L 5 " --> pdb=" O ARG R 6 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU R 3 " --> pdb=" O HIS X 4 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ARG X 6 " --> pdb=" O LEU R 3 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU R 5 " --> pdb=" O ARG X 6 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU X 3 " --> pdb=" O HIS d 4 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ARG d 6 " --> pdb=" O LEU X 3 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU X 5 " --> pdb=" O ARG d 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.09 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 240 1.27 - 1.34: 420 1.34 - 1.41: 180 1.41 - 1.47: 240 1.47 - 1.54: 930 Bond restraints: 2010 Sorted by residual: bond pdb=" C HIS I 4 " pdb=" N LEU I 5 " ideal model delta sigma weight residual 1.331 1.278 0.053 1.55e-02 4.16e+03 1.16e+01 bond pdb=" C HIS U 4 " pdb=" N LEU U 5 " ideal model delta sigma weight residual 1.331 1.278 0.053 1.55e-02 4.16e+03 1.15e+01 bond pdb=" C HIS a 4 " pdb=" N LEU a 5 " ideal model delta sigma weight residual 1.331 1.279 0.052 1.55e-02 4.16e+03 1.15e+01 bond pdb=" C HIS L 4 " pdb=" N LEU L 5 " ideal model delta sigma weight residual 1.331 1.279 0.052 1.55e-02 4.16e+03 1.15e+01 bond pdb=" C HIS J 4 " pdb=" N LEU J 5 " ideal model delta sigma weight residual 1.331 1.279 0.052 1.55e-02 4.16e+03 1.14e+01 ... (remaining 2005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 2018 1.52 - 3.03: 322 3.03 - 4.55: 182 4.55 - 6.07: 88 6.07 - 7.59: 60 Bond angle restraints: 2670 Sorted by residual: angle pdb=" N LEU N 3 " pdb=" CA LEU N 3 " pdb=" C LEU N 3 " ideal model delta sigma weight residual 108.96 102.19 6.77 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU M 3 " pdb=" CA LEU M 3 " pdb=" C LEU M 3 " ideal model delta sigma weight residual 108.96 102.19 6.77 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU Y 3 " pdb=" CA LEU Y 3 " pdb=" C LEU Y 3 " ideal model delta sigma weight residual 108.96 102.20 6.76 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU G 3 " pdb=" CA LEU G 3 " pdb=" C LEU G 3 " ideal model delta sigma weight residual 108.96 102.20 6.76 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU S 3 " pdb=" CA LEU S 3 " pdb=" C LEU S 3 " ideal model delta sigma weight residual 108.96 102.20 6.76 1.59e+00 3.96e-01 1.81e+01 ... (remaining 2665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.64: 860 18.64 - 37.29: 220 37.29 - 55.93: 60 55.93 - 74.57: 0 74.57 - 93.22: 30 Dihedral angle restraints: 1170 sinusoidal: 570 harmonic: 600 Sorted by residual: dihedral pdb=" CH3 ACE W 0 " pdb=" C ACE W 0 " pdb=" N LEU W 1 " pdb=" CA LEU W 1 " ideal model delta sinusoidal sigma weight residual -180.00 -86.78 -93.22 1 5.00e+00 4.00e-02 4.06e+02 dihedral pdb=" CH3 ACE K 0 " pdb=" C ACE K 0 " pdb=" N LEU K 1 " pdb=" CA LEU K 1 " ideal model delta sinusoidal sigma weight residual -180.00 -86.80 -93.20 1 5.00e+00 4.00e-02 4.05e+02 dihedral pdb=" CH3 ACE c 0 " pdb=" C ACE c 0 " pdb=" N LEU c 1 " pdb=" CA LEU c 1 " ideal model delta sinusoidal sigma weight residual -180.00 -86.82 -93.18 1 5.00e+00 4.00e-02 4.05e+02 ... (remaining 1167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 170 0.041 - 0.082: 40 0.082 - 0.123: 30 0.123 - 0.164: 17 0.164 - 0.205: 73 Chirality restraints: 330 Sorted by residual: chirality pdb=" CA HIS V 4 " pdb=" N HIS V 4 " pdb=" C HIS V 4 " pdb=" CB HIS V 4 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA HIS F 4 " pdb=" N HIS F 4 " pdb=" C HIS F 4 " pdb=" CB HIS F 4 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA HIS U 4 " pdb=" N HIS U 4 " pdb=" C HIS U 4 " pdb=" CB HIS U 4 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 327 not shown) Planarity restraints: 300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE J 0 " 0.089 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" O ACE J 0 " -0.104 2.00e-02 2.50e+03 pdb=" CH3 ACE J 0 " -0.175 2.00e-02 2.50e+03 pdb=" N LEU J 1 " 0.556 2.00e-02 2.50e+03 pdb=" CA LEU J 1 " -0.366 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE V 0 " 0.089 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" O ACE V 0 " -0.104 2.00e-02 2.50e+03 pdb=" CH3 ACE V 0 " -0.175 2.00e-02 2.50e+03 pdb=" N LEU V 1 " 0.556 2.00e-02 2.50e+03 pdb=" CA LEU V 1 " -0.366 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE P 0 " 0.089 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" O ACE P 0 " -0.104 2.00e-02 2.50e+03 pdb=" CH3 ACE P 0 " -0.175 2.00e-02 2.50e+03 pdb=" N LEU P 1 " 0.556 2.00e-02 2.50e+03 pdb=" CA LEU P 1 " -0.366 2.00e-02 2.50e+03 ... (remaining 297 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 758 3.07 - 3.53: 2022 3.53 - 3.99: 2661 3.99 - 4.44: 3385 4.44 - 4.90: 6093 Nonbonded interactions: 14919 Sorted by model distance: nonbonded pdb=" N LEU Y 5 " pdb=" O LEU Y 5 " model vdw 2.613 2.496 nonbonded pdb=" N LEU A 5 " pdb=" O LEU A 5 " model vdw 2.614 2.496 nonbonded pdb=" N LEU B 5 " pdb=" O LEU B 5 " model vdw 2.614 2.496 nonbonded pdb=" N LEU Z 5 " pdb=" O LEU Z 5 " model vdw 2.614 2.496 nonbonded pdb=" N LEU M 5 " pdb=" O LEU M 5 " model vdw 2.614 2.496 ... (remaining 14914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.910 Find NCS groups from input model: 0.140 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.360 ------------------------------------------------------------------------------- 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 : 0.233 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.8626 time to fit residues: 2.1559 Evaluate side-chains 0 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 1.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.259 2010 Z= 5.600 Angle : 5.842 33.338 2670 Z= 2.796 Chirality : 0.401 1.292 330 Planarity : 0.054 0.182 300 Dihedral : 12.031 32.166 270 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 288.86 Ramachandran Plot: Outliers : 42.00 % Allowed : 48.67 % Favored : 9.33 % Rotamer: Outliers : 40.00 % Allowed : 17.14 % Favored : 42.86 % Cbeta Deviations : 10.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.66 (0.09), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.12 (0.07), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.052 0.013 HIS O 4 ARG 0.009 0.002 ARG O 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 0 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 1 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8190 (pt) REVERT: A 2 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.7732 (t-170) REVERT: A 5 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7922 (tt) REVERT: B 1 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8110 (pt) REVERT: B 2 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7777 (t-170) REVERT: B 5 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7980 (tt) REVERT: E 2 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7570 (t70) REVERT: E 5 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8174 (tt) REVERT: F 2 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7580 (t70) REVERT: F 5 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8152 (tt) REVERT: G 5 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8262 (tt) REVERT: H 5 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8260 (tt) REVERT: K 5 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8742 (tt) REVERT: L 5 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8711 (tt) REVERT: M 2 HIS cc_start: 0.9160 (OUTLIER) cc_final: 0.8817 (t-170) REVERT: M 5 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8648 (tt) REVERT: N 2 HIS cc_start: 0.9143 (OUTLIER) cc_final: 0.8795 (t-170) REVERT: N 5 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8704 (tt) REVERT: O 4 HIS cc_start: 0.9253 (OUTLIER) cc_final: 0.8378 (m90) REVERT: P 4 HIS cc_start: 0.9207 (OUTLIER) cc_final: 0.8481 (m90) REVERT: Q 5 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8904 (tt) REVERT: R 5 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8824 (tt) outliers start: 84 outliers final: 37 residues processed: 84 average time/residue: 0.0721 time to fit residues: 7.7622 Evaluate side-chains 59 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 0 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 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 E residue 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 5 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 4 HIS Chi-restraints excluded: chain Q residue 1 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 1 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 1.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.276 2010 Z= 5.542 Angle : 5.717 34.558 2670 Z= 2.697 Chirality : 0.408 1.332 330 Planarity : 0.051 0.163 300 Dihedral : 11.559 31.481 270 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 278.91 Ramachandran Plot: Outliers : 36.00 % Allowed : 60.00 % Favored : 4.00 % Rotamer: Outliers : 47.62 % Allowed : 19.05 % Favored : 33.33 % Cbeta Deviations : 13.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.75 (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 0.014 HIS C 4 ARG 0.010 0.002 ARG A 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 100 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 0 time to evaluate : 0.260 Fit side-chains REVERT: A 2 HIS cc_start: 0.8358 (OUTLIER) cc_final: 0.7865 (t-170) REVERT: A 5 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8052 (tt) REVERT: B 2 HIS cc_start: 0.8319 (OUTLIER) cc_final: 0.7820 (t-170) REVERT: B 5 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8033 (tt) REVERT: C 2 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7483 (t-170) REVERT: C 4 HIS cc_start: 0.8441 (OUTLIER) cc_final: 0.7417 (m90) REVERT: C 5 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7876 (tt) REVERT: D 4 HIS cc_start: 0.8511 (OUTLIER) cc_final: 0.7319 (m90) REVERT: D 5 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7975 (tt) REVERT: E 2 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7651 (t70) REVERT: F 2 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7737 (t70) REVERT: G 5 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7973 (tt) REVERT: H 5 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7944 (tt) REVERT: K 5 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8678 (tt) REVERT: L 5 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8721 (tt) REVERT: M 2 HIS cc_start: 0.9201 (OUTLIER) cc_final: 0.8846 (t-170) REVERT: M 5 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8584 (tt) REVERT: N 2 HIS cc_start: 0.9182 (OUTLIER) cc_final: 0.8839 (t-170) REVERT: N 5 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8589 (tt) REVERT: O 2 HIS cc_start: 0.9045 (OUTLIER) cc_final: 0.8360 (t-170) REVERT: O 4 HIS cc_start: 0.9310 (OUTLIER) cc_final: 0.8383 (t70) REVERT: P 2 HIS cc_start: 0.9041 (OUTLIER) cc_final: 0.8353 (t-170) REVERT: P 4 HIS cc_start: 0.9320 (OUTLIER) cc_final: 0.8370 (t70) REVERT: Q 5 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8988 (tt) REVERT: R 5 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8917 (tt) REVERT: V 4 HIS cc_start: 0.8916 (OUTLIER) cc_final: 0.8658 (t70) REVERT: W 4 HIS cc_start: 0.9070 (OUTLIER) cc_final: 0.8717 (t70) outliers start: 100 outliers final: 46 residues processed: 100 average time/residue: 0.0647 time to fit residues: 8.3698 Evaluate side-chains 73 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 0 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain F residue 1 LEU 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 1 LEU 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 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 Q residue 5 LEU Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 2 HIS Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain 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** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 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: 0.8162 moved from start: 1.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.271 2010 Z= 5.462 Angle : 5.696 34.495 2670 Z= 2.719 Chirality : 0.410 1.335 330 Planarity : 0.052 0.155 300 Dihedral : 11.128 32.952 270 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 280.57 Ramachandran Plot: Outliers : 33.33 % Allowed : 62.67 % Favored : 4.00 % Rotamer: Outliers : 47.14 % Allowed : 20.48 % Favored : 32.38 % Cbeta Deviations : 11.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.052 0.013 HIS C 4 ARG 0.009 0.002 ARG A 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 99 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 0 time to evaluate : 0.267 Fit side-chains REVERT: A 2 HIS cc_start: 0.8354 (OUTLIER) cc_final: 0.7838 (t-170) REVERT: A 5 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8017 (tt) REVERT: B 2 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7862 (t-170) REVERT: B 5 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8015 (tt) REVERT: B 6 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7906 (ttt-90) REVERT: C 2 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7440 (t-170) REVERT: C 4 HIS cc_start: 0.8480 (OUTLIER) cc_final: 0.7571 (m90) REVERT: D 2 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.7254 (t-170) REVERT: D 4 HIS cc_start: 0.8562 (OUTLIER) cc_final: 0.7379 (m90) REVERT: E 2 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7722 (t70) REVERT: E 5 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8352 (tt) REVERT: F 2 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.7798 (t70) REVERT: F 5 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8285 (tt) REVERT: G 5 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8047 (tt) REVERT: H 5 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8032 (tt) REVERT: K 5 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8673 (tt) REVERT: L 5 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8670 (tt) REVERT: M 2 HIS cc_start: 0.9183 (OUTLIER) cc_final: 0.8835 (t-170) REVERT: M 5 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8569 (tt) REVERT: N 2 HIS cc_start: 0.9170 (OUTLIER) cc_final: 0.8746 (t-170) REVERT: N 5 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8572 (tt) REVERT: O 4 HIS cc_start: 0.9354 (OUTLIER) cc_final: 0.8573 (m90) REVERT: P 2 HIS cc_start: 0.9039 (OUTLIER) cc_final: 0.8302 (t-170) REVERT: P 4 HIS cc_start: 0.9314 (OUTLIER) cc_final: 0.8332 (t70) REVERT: U 4 HIS cc_start: 0.8919 (OUTLIER) cc_final: 0.8188 (t70) outliers start: 99 outliers final: 55 residues processed: 99 average time/residue: 0.0922 time to fit residues: 11.0559 Evaluate side-chains 80 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 0 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain 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 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 2 HIS Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 2 HIS Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain 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 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 T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 2 HIS Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain 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=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** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 2 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: 0.8161 moved from start: 1.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.279 2010 Z= 5.497 Angle : 5.732 34.653 2670 Z= 2.731 Chirality : 0.411 1.332 330 Planarity : 0.051 0.149 300 Dihedral : 10.959 31.030 270 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 282.46 Ramachandran Plot: Outliers : 32.67 % Allowed : 63.33 % Favored : 4.00 % 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 : 1.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.053 0.013 HIS C 4 ARG 0.010 0.002 ARG a 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 104 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 0 time to evaluate : 0.357 Fit side-chains REVERT: A 2 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.7812 (t-170) REVERT: A 5 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8027 (tt) REVERT: B 2 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.7802 (t-170) REVERT: B 5 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8003 (tt) REVERT: C 2 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7435 (t-170) REVERT: C 4 HIS cc_start: 0.8461 (OUTLIER) cc_final: 0.7546 (m90) REVERT: C 5 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8013 (tt) REVERT: D 2 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7229 (t-170) REVERT: D 4 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.7392 (m90) REVERT: D 5 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8150 (tt) REVERT: E 2 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7783 (t70) REVERT: F 2 HIS cc_start: 0.8260 (OUTLIER) cc_final: 0.7826 (t70) REVERT: G 5 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8020 (tt) REVERT: H 5 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7998 (tt) REVERT: M 2 HIS cc_start: 0.9191 (OUTLIER) cc_final: 0.8356 (t-170) REVERT: M 4 HIS cc_start: 0.9093 (OUTLIER) cc_final: 0.7931 (t70) REVERT: M 5 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8691 (tt) REVERT: N 2 HIS cc_start: 0.9171 (OUTLIER) cc_final: 0.8338 (t-170) REVERT: N 4 HIS cc_start: 0.9089 (OUTLIER) cc_final: 0.7919 (t70) REVERT: N 5 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8696 (tt) REVERT: O 4 HIS cc_start: 0.9326 (OUTLIER) cc_final: 0.8725 (m90) REVERT: O 6 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8369 (ttm170) REVERT: P 2 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8188 (t-170) REVERT: P 4 HIS cc_start: 0.9312 (OUTLIER) cc_final: 0.8331 (t70) REVERT: U 4 HIS cc_start: 0.9036 (OUTLIER) cc_final: 0.8158 (t70) REVERT: a 4 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.8245 (t70) REVERT: b 6 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7433 (ttt180) outliers start: 104 outliers final: 52 residues processed: 104 average time/residue: 0.1301 time to fit residues: 15.9107 Evaluate side-chains 79 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 0 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain F residue 1 LEU 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 2 HIS Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 2 HIS Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain 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 T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain X residue 1 LEU 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 Z residue 1 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 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 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: 0.7980 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** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 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 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 2 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: 0.8155 moved from start: 1.3148 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= 5.464 Angle : 5.760 34.418 2670 Z= 2.749 Chirality : 0.413 1.333 330 Planarity : 0.049 0.143 300 Dihedral : 10.749 32.698 270 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 287.20 Ramachandran Plot: Outliers : 31.33 % Allowed : 64.67 % Favored : 4.00 % Rotamer: Outliers : 48.10 % Allowed : 22.38 % Favored : 29.52 % Cbeta Deviations : 10.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.73 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.053 0.013 HIS C 4 ARG 0.010 0.002 ARG O 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 101 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 0 time to evaluate : 0.253 Fit side-chains REVERT: A 2 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.7831 (t-170) REVERT: A 5 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7972 (tt) REVERT: B 2 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.7756 (t-170) REVERT: B 5 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8008 (tt) REVERT: C 2 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.7486 (t-170) REVERT: C 4 HIS cc_start: 0.8499 (OUTLIER) cc_final: 0.7621 (m90) REVERT: C 5 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8153 (tt) REVERT: D 2 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7326 (t-170) REVERT: D 4 HIS cc_start: 0.8675 (OUTLIER) cc_final: 0.7459 (m90) REVERT: D 5 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8047 (tt) REVERT: E 2 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7836 (t70) REVERT: F 2 HIS cc_start: 0.8273 (OUTLIER) cc_final: 0.7934 (t70) REVERT: G 5 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8013 (tt) REVERT: H 5 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8013 (tt) REVERT: M 2 HIS cc_start: 0.9191 (OUTLIER) cc_final: 0.8352 (t-170) REVERT: M 4 HIS cc_start: 0.9096 (OUTLIER) cc_final: 0.7935 (t70) REVERT: M 5 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8706 (tt) REVERT: N 2 HIS cc_start: 0.9172 (OUTLIER) cc_final: 0.8328 (t-170) REVERT: N 4 HIS cc_start: 0.9087 (OUTLIER) cc_final: 0.7905 (t70) REVERT: N 5 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8694 (tt) REVERT: O 4 HIS cc_start: 0.9329 (OUTLIER) cc_final: 0.8762 (m90) REVERT: O 6 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8371 (ttm170) REVERT: P 4 HIS cc_start: 0.9354 (OUTLIER) cc_final: 0.8619 (m90) REVERT: Q 5 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8947 (tt) REVERT: R 4 HIS cc_start: 0.9351 (OUTLIER) cc_final: 0.8735 (m90) REVERT: S 6 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8252 (ttt-90) REVERT: U 4 HIS cc_start: 0.8990 (OUTLIER) cc_final: 0.8165 (t70) REVERT: V 6 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8033 (ttt180) REVERT: b 6 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7345 (ttt180) outliers start: 101 outliers final: 55 residues processed: 101 average time/residue: 0.1252 time to fit residues: 14.7043 Evaluate side-chains 84 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 0 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain 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 2 HIS Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain 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 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 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 d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS 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** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 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** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 2 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: 0.8150 moved from start: 1.3254 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= 5.477 Angle : 5.763 34.575 2670 Z= 2.753 Chirality : 0.412 1.338 330 Planarity : 0.049 0.141 300 Dihedral : 10.806 33.045 270 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 286.49 Ramachandran Plot: Outliers : 31.33 % Allowed : 64.67 % Favored : 4.00 % Rotamer: Outliers : 50.00 % Allowed : 18.57 % Favored : 31.43 % Cbeta Deviations : 10.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.053 0.013 HIS C 4 ARG 0.011 0.002 ARG c 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 105 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 0 time to evaluate : 0.262 Fit side-chains REVERT: A 2 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.7854 (t-170) REVERT: A 5 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7969 (tt) REVERT: B 2 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.7757 (t-170) REVERT: B 5 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7994 (tt) REVERT: C 2 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.7494 (t-170) REVERT: C 4 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.7670 (m90) REVERT: C 5 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8127 (tt) REVERT: D 2 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.7331 (t-170) REVERT: D 4 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.7566 (m90) REVERT: D 5 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8149 (tt) REVERT: E 2 HIS cc_start: 0.8271 (OUTLIER) cc_final: 0.7927 (t70) REVERT: F 2 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7913 (t70) REVERT: G 5 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8021 (tt) REVERT: H 5 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7981 (tt) REVERT: I 5 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8626 (tt) REVERT: M 2 HIS cc_start: 0.9205 (OUTLIER) cc_final: 0.8350 (t-170) REVERT: M 4 HIS cc_start: 0.9097 (OUTLIER) cc_final: 0.7934 (t70) REVERT: M 5 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8701 (tt) REVERT: N 2 HIS cc_start: 0.9175 (OUTLIER) cc_final: 0.8351 (t-170) REVERT: N 4 HIS cc_start: 0.9087 (OUTLIER) cc_final: 0.7911 (t70) REVERT: N 5 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8680 (tt) REVERT: O 4 HIS cc_start: 0.9310 (OUTLIER) cc_final: 0.8765 (m90) REVERT: O 6 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8356 (ttm170) REVERT: P 4 HIS cc_start: 0.9338 (OUTLIER) cc_final: 0.8830 (m90) REVERT: P 6 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8271 (ttm170) REVERT: Q 5 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8897 (tt) REVERT: R 5 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8848 (tt) REVERT: S 6 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8056 (ttt-90) REVERT: U 4 HIS cc_start: 0.9060 (OUTLIER) cc_final: 0.8281 (t70) REVERT: V 6 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.8050 (ttt180) REVERT: Z 6 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7761 (ttm170) REVERT: b 4 HIS cc_start: 0.8494 (OUTLIER) cc_final: 0.7539 (t70) REVERT: b 6 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7453 (ttt-90) outliers start: 105 outliers final: 54 residues processed: 105 average time/residue: 0.1154 time to fit residues: 13.9362 Evaluate side-chains 87 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 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 B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain F residue 1 LEU 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 I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain X residue 1 LEU 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 Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 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 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 2 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: 0.8151 moved from start: 1.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.277 2010 Z= 5.481 Angle : 5.798 34.554 2670 Z= 2.765 Chirality : 0.414 1.338 330 Planarity : 0.049 0.140 300 Dihedral : 10.797 33.237 270 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 284.60 Ramachandran Plot: Outliers : 29.33 % Allowed : 66.67 % Favored : 4.00 % Rotamer: Outliers : 47.14 % Allowed : 20.48 % Favored : 32.38 % Cbeta Deviations : 11.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.053 0.014 HIS C 4 ARG 0.011 0.002 ARG O 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 99 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 0 time to evaluate : 0.272 Fit side-chains REVERT: A 2 HIS cc_start: 0.8374 (OUTLIER) cc_final: 0.7877 (t-170) REVERT: A 5 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7943 (tt) REVERT: A 6 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7840 (ttt-90) REVERT: B 2 HIS cc_start: 0.8323 (OUTLIER) cc_final: 0.7773 (t-170) REVERT: B 5 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7997 (tt) REVERT: B 6 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7904 (ttt-90) REVERT: C 2 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7459 (t-170) REVERT: C 4 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.7699 (m90) REVERT: D 2 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.7267 (t-170) REVERT: D 4 HIS cc_start: 0.8695 (OUTLIER) cc_final: 0.7543 (m90) REVERT: D 5 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8164 (tt) REVERT: E 2 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7931 (t70) REVERT: F 2 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7926 (t70) REVERT: G 5 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8011 (tt) REVERT: H 5 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7978 (tt) REVERT: J 5 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8666 (tt) REVERT: M 2 HIS cc_start: 0.9206 (OUTLIER) cc_final: 0.8353 (t-170) REVERT: M 4 HIS cc_start: 0.9087 (OUTLIER) cc_final: 0.7933 (t70) REVERT: M 5 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8695 (tt) REVERT: N 2 HIS cc_start: 0.9177 (OUTLIER) cc_final: 0.8277 (t-170) REVERT: N 4 HIS cc_start: 0.9088 (OUTLIER) cc_final: 0.7930 (t70) REVERT: N 5 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8666 (tt) REVERT: O 4 HIS cc_start: 0.9297 (OUTLIER) cc_final: 0.8738 (m90) REVERT: O 6 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8345 (ttm170) REVERT: P 4 HIS cc_start: 0.9327 (OUTLIER) cc_final: 0.8767 (m90) REVERT: P 6 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8260 (ttm170) REVERT: S 6 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8087 (ttt-90) REVERT: U 4 HIS cc_start: 0.9070 (OUTLIER) cc_final: 0.8271 (t70) REVERT: V 6 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7998 (ttt180) REVERT: Y 6 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7836 (ttm170) REVERT: Z 6 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7804 (ttm170) REVERT: b 4 HIS cc_start: 0.8505 (OUTLIER) cc_final: 0.7594 (t70) REVERT: b 6 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7442 (ttt-90) outliers start: 99 outliers final: 54 residues processed: 99 average time/residue: 0.1462 time to fit residues: 16.4289 Evaluate side-chains 87 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 0 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain 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 J residue 5 LEU Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 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 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 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS 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** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 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** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 2 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: 0.8151 moved from start: 1.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.280 2010 Z= 5.494 Angle : 5.803 34.378 2670 Z= 2.769 Chirality : 0.415 1.332 330 Planarity : 0.049 0.141 300 Dihedral : 10.839 33.700 270 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 286.26 Ramachandran Plot: Outliers : 30.67 % Allowed : 65.33 % Favored : 4.00 % Rotamer: Outliers : 44.76 % Allowed : 23.81 % 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 : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.053 0.014 HIS C 4 ARG 0.010 0.002 ARG O 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 94 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 0 time to evaluate : 0.287 Fit side-chains REVERT: A 2 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7875 (t-170) REVERT: A 5 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7950 (tt) REVERT: A 6 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7744 (ttt-90) REVERT: B 2 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.7776 (t-170) REVERT: B 5 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7997 (tt) REVERT: B 6 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7939 (ttt-90) REVERT: C 2 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.7593 (t-170) REVERT: C 4 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.7668 (m90) REVERT: C 5 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8124 (tt) REVERT: D 2 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7347 (t-170) REVERT: D 4 HIS cc_start: 0.8698 (OUTLIER) cc_final: 0.7535 (m90) REVERT: D 5 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8153 (tt) REVERT: E 2 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.7931 (t70) REVERT: F 2 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7938 (t70) REVERT: G 5 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8007 (tt) REVERT: H 5 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7977 (tt) REVERT: I 5 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8605 (tt) REVERT: J 5 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8670 (tt) REVERT: M 2 HIS cc_start: 0.9207 (OUTLIER) cc_final: 0.8358 (t-170) REVERT: M 4 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.7919 (t70) REVERT: M 5 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8694 (tt) REVERT: N 2 HIS cc_start: 0.9177 (OUTLIER) cc_final: 0.8272 (t-170) REVERT: N 4 HIS cc_start: 0.9091 (OUTLIER) cc_final: 0.7921 (t70) REVERT: N 5 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8670 (tt) REVERT: O 4 HIS cc_start: 0.9273 (OUTLIER) cc_final: 0.8743 (m90) REVERT: O 6 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8359 (ttm170) REVERT: P 4 HIS cc_start: 0.9299 (OUTLIER) cc_final: 0.8792 (m90) REVERT: P 6 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8267 (ttm170) REVERT: S 6 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8221 (ttt-90) REVERT: U 4 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.8276 (t70) REVERT: V 6 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.8042 (ttt180) REVERT: Y 6 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7860 (ttm170) REVERT: Z 6 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7803 (ttm170) REVERT: b 4 HIS cc_start: 0.8490 (OUTLIER) cc_final: 0.7680 (t70) REVERT: b 6 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7408 (ttt-90) outliers start: 94 outliers final: 54 residues processed: 94 average time/residue: 0.1448 time to fit residues: 15.5063 Evaluate side-chains 89 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 0 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 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 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 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS 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** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 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** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 2 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: 0.8153 moved from start: 1.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.273 2010 Z= 5.489 Angle : 5.799 34.603 2670 Z= 2.770 Chirality : 0.415 1.338 330 Planarity : 0.049 0.137 300 Dihedral : 10.902 33.779 270 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 284.60 Ramachandran Plot: Outliers : 29.33 % Allowed : 66.67 % Favored : 4.00 % Rotamer: Outliers : 45.71 % Allowed : 23.81 % Favored : 30.48 % 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 : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.053 0.014 HIS C 4 ARG 0.010 0.002 ARG O 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 96 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 0 time to evaluate : 0.384 Fit side-chains REVERT: A 2 HIS cc_start: 0.8371 (OUTLIER) cc_final: 0.7888 (t-170) REVERT: A 5 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7954 (tt) REVERT: A 6 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7832 (ttt-90) REVERT: B 2 HIS cc_start: 0.8319 (OUTLIER) cc_final: 0.7789 (t-170) REVERT: B 5 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7999 (tt) REVERT: B 6 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7952 (ttt-90) REVERT: C 2 HIS cc_start: 0.7936 (OUTLIER) cc_final: 0.7570 (t-170) REVERT: C 4 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.7656 (m90) REVERT: C 5 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8115 (tt) REVERT: D 2 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.7366 (t-170) REVERT: D 4 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.7535 (m90) REVERT: D 5 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8149 (tt) REVERT: E 2 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.7939 (t70) REVERT: F 2 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.7944 (t70) REVERT: G 5 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8042 (tt) REVERT: H 5 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7981 (tt) REVERT: H 6 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8128 (ttm170) REVERT: I 5 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8598 (tt) REVERT: J 5 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8631 (tt) REVERT: M 2 HIS cc_start: 0.9210 (OUTLIER) cc_final: 0.8348 (t-170) REVERT: M 4 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.7921 (t70) REVERT: M 5 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8697 (tt) REVERT: N 2 HIS cc_start: 0.9182 (OUTLIER) cc_final: 0.8235 (t-170) REVERT: N 4 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.7886 (t70) REVERT: N 5 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8658 (tt) REVERT: O 4 HIS cc_start: 0.9284 (OUTLIER) cc_final: 0.8723 (m90) REVERT: O 6 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8400 (ttm170) REVERT: P 4 HIS cc_start: 0.9307 (OUTLIER) cc_final: 0.8767 (m90) REVERT: P 6 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8266 (ttm170) REVERT: S 6 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8222 (ttt-90) REVERT: U 4 HIS cc_start: 0.9078 (OUTLIER) cc_final: 0.8221 (t70) REVERT: V 6 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8020 (ttt180) REVERT: Y 6 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7847 (ttm170) REVERT: Z 2 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.7962 (t70) REVERT: Z 6 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7804 (ttm170) REVERT: b 4 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.7663 (t70) REVERT: b 6 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7425 (ttt-90) outliers start: 96 outliers final: 54 residues processed: 96 average time/residue: 0.1651 time to fit residues: 17.9754 Evaluate side-chains 91 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 0 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 D residue 5 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain F residue 1 LEU Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain 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 5 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 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 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 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain X residue 1 LEU Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain 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 2 HIS Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS 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** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 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** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 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** ** b 2 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 = 0.4268 r_free = 0.4268 target = 0.085511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.068925 restraints weight = 8125.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.070428 restraints weight = 5325.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.071292 restraints weight = 3922.748| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5264 moved from start: 1.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.274 2010 Z= 5.489 Angle : 5.797 34.576 2670 Z= 2.769 Chirality : 0.415 1.336 330 Planarity : 0.049 0.137 300 Dihedral : 10.929 34.398 270 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 283.65 Ramachandran Plot: Outliers : 29.33 % Allowed : 66.67 % Favored : 4.00 % Rotamer: Outliers : 44.76 % Allowed : 24.29 % Favored : 30.95 % 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 : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.053 0.014 HIS C 4 ARG 0.010 0.002 ARG O 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 394.29 seconds wall clock time: 14 minutes 6.58 seconds (846.58 seconds total)