Starting phenix.real_space_refine on Sun Mar 17 01:07:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/03_2024/6rib_4887_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/03_2024/6rib_4887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/03_2024/6rib_4887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/03_2024/6rib_4887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/03_2024/6rib_4887_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/03_2024/6rib_4887_neut.pdb" } resolution = 4.2 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= 1.000 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 10208 2.51 5 N 2926 2.21 5 O 3212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 24": "OD1" <-> "OD2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "C ASP 24": "OD1" <-> "OD2" Residue "C ARG 26": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "D ASP 24": "OD1" <-> "OD2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "E ASP 24": "OD1" <-> "OD2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F ARG 26": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 63": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "G ASP 24": "OD1" <-> "OD2" Residue "G ARG 26": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 59": "NH1" <-> "NH2" Residue "G ARG 63": "NH1" <-> "NH2" Residue "G ARG 87": "NH1" <-> "NH2" Residue "H ASP 24": "OD1" <-> "OD2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H ARG 32": "NH1" <-> "NH2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H GLU 44": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H ARG 59": "NH1" <-> "NH2" Residue "H ARG 63": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "I ASP 24": "OD1" <-> "OD2" Residue "I ARG 26": "NH1" <-> "NH2" Residue "I ARG 32": "NH1" <-> "NH2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 63": "NH1" <-> "NH2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "J ASP 24": "OD1" <-> "OD2" Residue "J ARG 26": "NH1" <-> "NH2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "J GLU 44": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ARG 59": "NH1" <-> "NH2" Residue "J ARG 63": "NH1" <-> "NH2" Residue "J ARG 87": "NH1" <-> "NH2" Residue "K ASP 24": "OD1" <-> "OD2" Residue "K ARG 26": "NH1" <-> "NH2" Residue "K ARG 32": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K GLU 44": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 59": "NH1" <-> "NH2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ARG 87": "NH1" <-> "NH2" Residue "L ASP 24": "OD1" <-> "OD2" Residue "L ARG 26": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L ARG 38": "NH1" <-> "NH2" Residue "L GLU 44": "OE1" <-> "OE2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 59": "NH1" <-> "NH2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "L ARG 87": "NH1" <-> "NH2" Residue "M ASP 24": "OD1" <-> "OD2" Residue "M ARG 26": "NH1" <-> "NH2" Residue "M ARG 32": "NH1" <-> "NH2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 87": "NH1" <-> "NH2" Residue "N ASP 24": "OD1" <-> "OD2" Residue "N ARG 26": "NH1" <-> "NH2" Residue "N ARG 32": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 87": "NH1" <-> "NH2" Residue "O ASP 24": "OD1" <-> "OD2" Residue "O ARG 26": "NH1" <-> "NH2" Residue "O ARG 32": "NH1" <-> "NH2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O GLU 44": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "O ARG 59": "NH1" <-> "NH2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 87": "NH1" <-> "NH2" Residue "P ASP 24": "OD1" <-> "OD2" Residue "P ARG 26": "NH1" <-> "NH2" Residue "P ARG 32": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P GLU 46": "OE1" <-> "OE2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 59": "NH1" <-> "NH2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 87": "NH1" <-> "NH2" Residue "Q ASP 24": "OD1" <-> "OD2" Residue "Q ARG 26": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 38": "NH1" <-> "NH2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q GLU 46": "OE1" <-> "OE2" Residue "Q ARG 54": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q ARG 63": "NH1" <-> "NH2" Residue "Q ARG 87": "NH1" <-> "NH2" Residue "R ASP 24": "OD1" <-> "OD2" Residue "R ARG 26": "NH1" <-> "NH2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R GLU 44": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R ARG 54": "NH1" <-> "NH2" Residue "R ARG 59": "NH1" <-> "NH2" Residue "R ARG 63": "NH1" <-> "NH2" Residue "R ARG 87": "NH1" <-> "NH2" Residue "S ASP 24": "OD1" <-> "OD2" Residue "S ARG 26": "NH1" <-> "NH2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S ARG 38": "NH1" <-> "NH2" Residue "S GLU 44": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S ARG 54": "NH1" <-> "NH2" Residue "S ARG 59": "NH1" <-> "NH2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "S ARG 87": "NH1" <-> "NH2" Residue "T ASP 24": "OD1" <-> "OD2" Residue "T ARG 26": "NH1" <-> "NH2" Residue "T ARG 32": "NH1" <-> "NH2" Residue "T ARG 38": "NH1" <-> "NH2" Residue "T GLU 44": "OE1" <-> "OE2" Residue "T GLU 46": "OE1" <-> "OE2" Residue "T ARG 54": "NH1" <-> "NH2" Residue "T ARG 59": "NH1" <-> "NH2" Residue "T ARG 63": "NH1" <-> "NH2" Residue "T ARG 87": "NH1" <-> "NH2" Residue "U ASP 24": "OD1" <-> "OD2" Residue "U ARG 26": "NH1" <-> "NH2" Residue "U ARG 32": "NH1" <-> "NH2" Residue "U ARG 38": "NH1" <-> "NH2" Residue "U GLU 44": "OE1" <-> "OE2" Residue "U GLU 46": "OE1" <-> "OE2" Residue "U ARG 54": "NH1" <-> "NH2" Residue "U ARG 59": "NH1" <-> "NH2" Residue "U ARG 63": "NH1" <-> "NH2" Residue "U ARG 87": "NH1" <-> "NH2" Residue "V ASP 24": "OD1" <-> "OD2" Residue "V ARG 26": "NH1" <-> "NH2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V ARG 38": "NH1" <-> "NH2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V GLU 46": "OE1" <-> "OE2" Residue "V ARG 54": "NH1" <-> "NH2" Residue "V ARG 59": "NH1" <-> "NH2" Residue "V ARG 63": "NH1" <-> "NH2" Residue "V ARG 87": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16368 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "B" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "C" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "E" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "F" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "G" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "I" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "J" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "K" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "L" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "M" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "N" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "O" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "P" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "Q" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "R" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "S" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "T" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "U" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "V" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Time building chain proxies: 8.59, per 1000 atoms: 0.52 Number of scatterers: 16368 At special positions: 0 Unit cell: (49.22, 78.11, 337.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 3212 8.00 N 2926 7.00 C 10208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.83 Conformation dependent library (CDL) restraints added in 3.1 seconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 88 sheets defined 0.0% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing sheet with id= A, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU A 36 " --> pdb=" O VAL A 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU A 42 " --> pdb=" O ALA A 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER A 64 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 49 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 66 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS A 79 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE A 67 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 81 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA A 96 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU A 70 " --> pdb=" O VAL A 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU B 36 " --> pdb=" O VAL B 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU B 42 " --> pdb=" O ALA B 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER B 64 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL B 49 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 66 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS B 79 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE B 67 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 81 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA B 96 " --> pdb=" O VAL B 80 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 54 through 56 removed outlier: 7.484A pdb=" N GLU B 70 " --> pdb=" O VAL B 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU C 36 " --> pdb=" O VAL C 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU C 42 " --> pdb=" O ALA C 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER C 64 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL C 49 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU C 66 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS C 79 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE C 67 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL C 81 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA C 96 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU C 70 " --> pdb=" O VAL C 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU D 36 " --> pdb=" O VAL D 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU D 42 " --> pdb=" O ALA D 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER D 64 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL D 49 " --> pdb=" O SER D 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU D 66 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS D 79 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE D 67 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL D 81 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA D 96 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU D 70 " --> pdb=" O VAL D 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU E 36 " --> pdb=" O VAL E 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU E 42 " --> pdb=" O ALA E 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER E 64 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL E 49 " --> pdb=" O SER E 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU E 66 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS E 79 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE E 67 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL E 81 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA E 96 " --> pdb=" O VAL E 80 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU E 70 " --> pdb=" O VAL E 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU F 36 " --> pdb=" O VAL F 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'F' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU F 42 " --> pdb=" O ALA F 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER F 64 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL F 49 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU F 66 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS F 79 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE F 67 " --> pdb=" O LYS F 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL F 81 " --> pdb=" O ILE F 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA F 96 " --> pdb=" O VAL F 80 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU F 70 " --> pdb=" O VAL F 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU G 36 " --> pdb=" O VAL G 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'G' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU G 42 " --> pdb=" O ALA G 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'G' and resid 31 through 33 removed outlier: 6.075A pdb=" N SER G 64 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL G 49 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU G 66 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS G 79 " --> pdb=" O VAL G 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE G 67 " --> pdb=" O LYS G 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL G 81 " --> pdb=" O ILE G 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA G 96 " --> pdb=" O VAL G 80 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU G 70 " --> pdb=" O VAL G 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU H 36 " --> pdb=" O VAL H 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'H' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU H 42 " --> pdb=" O ALA H 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'H' and resid 31 through 33 removed outlier: 6.078A pdb=" N SER H 64 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL H 49 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU H 66 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS H 79 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE H 67 " --> pdb=" O LYS H 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL H 81 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA H 96 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU H 70 " --> pdb=" O VAL H 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU I 36 " --> pdb=" O VAL I 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'I' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU I 42 " --> pdb=" O ALA I 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'I' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER I 64 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL I 49 " --> pdb=" O SER I 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU I 66 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS I 79 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE I 67 " --> pdb=" O LYS I 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL I 81 " --> pdb=" O ILE I 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA I 96 " --> pdb=" O VAL I 80 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU I 70 " --> pdb=" O VAL I 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'J' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU J 36 " --> pdb=" O VAL J 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'J' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU J 42 " --> pdb=" O ALA J 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'J' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER J 64 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL J 49 " --> pdb=" O SER J 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU J 66 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS J 79 " --> pdb=" O VAL J 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE J 67 " --> pdb=" O LYS J 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL J 81 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA J 96 " --> pdb=" O VAL J 80 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'J' and resid 54 through 56 removed outlier: 7.484A pdb=" N GLU J 70 " --> pdb=" O VAL J 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'K' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU K 36 " --> pdb=" O VAL K 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'K' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU K 42 " --> pdb=" O ALA K 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'K' and resid 31 through 33 removed outlier: 6.075A pdb=" N SER K 64 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL K 49 " --> pdb=" O SER K 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU K 66 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS K 79 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE K 67 " --> pdb=" O LYS K 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL K 81 " --> pdb=" O ILE K 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA K 96 " --> pdb=" O VAL K 80 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'K' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU K 70 " --> pdb=" O VAL K 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU L 36 " --> pdb=" O VAL L 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'L' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU L 42 " --> pdb=" O ALA L 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'L' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER L 64 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL L 49 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU L 66 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS L 79 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE L 67 " --> pdb=" O LYS L 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL L 81 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA L 96 " --> pdb=" O VAL L 80 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'L' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU L 70 " --> pdb=" O VAL L 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'M' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU M 36 " --> pdb=" O VAL M 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'M' and resid 26 through 28 removed outlier: 6.281A pdb=" N LEU M 42 " --> pdb=" O ALA M 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'M' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER M 64 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL M 49 " --> pdb=" O SER M 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU M 66 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS M 79 " --> pdb=" O VAL M 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE M 67 " --> pdb=" O LYS M 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL M 81 " --> pdb=" O ILE M 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA M 96 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'M' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU M 70 " --> pdb=" O VAL M 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'N' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU N 36 " --> pdb=" O VAL N 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'N' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU N 42 " --> pdb=" O ALA N 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BB Processing sheet with id= BC, first strand: chain 'N' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER N 64 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL N 49 " --> pdb=" O SER N 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU N 66 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS N 79 " --> pdb=" O VAL N 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE N 67 " --> pdb=" O LYS N 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL N 81 " --> pdb=" O ILE N 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA N 96 " --> pdb=" O VAL N 80 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'N' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU N 70 " --> pdb=" O VAL N 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'O' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU O 36 " --> pdb=" O VAL O 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain 'O' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU O 42 " --> pdb=" O ALA O 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BF Processing sheet with id= BG, first strand: chain 'O' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER O 64 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL O 49 " --> pdb=" O SER O 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU O 66 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS O 79 " --> pdb=" O VAL O 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE O 67 " --> pdb=" O LYS O 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL O 81 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA O 96 " --> pdb=" O VAL O 80 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'O' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU O 70 " --> pdb=" O VAL O 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'P' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU P 36 " --> pdb=" O VAL P 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'P' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU P 42 " --> pdb=" O ALA P 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BJ Processing sheet with id= BK, first strand: chain 'P' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER P 64 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL P 49 " --> pdb=" O SER P 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU P 66 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS P 79 " --> pdb=" O VAL P 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE P 67 " --> pdb=" O LYS P 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL P 81 " --> pdb=" O ILE P 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA P 96 " --> pdb=" O VAL P 80 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'P' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU P 70 " --> pdb=" O VAL P 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BL Processing sheet with id= BM, first strand: chain 'Q' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU Q 36 " --> pdb=" O VAL Q 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'Q' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU Q 42 " --> pdb=" O ALA Q 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain 'Q' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER Q 64 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL Q 49 " --> pdb=" O SER Q 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU Q 66 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS Q 79 " --> pdb=" O VAL Q 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE Q 67 " --> pdb=" O LYS Q 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL Q 81 " --> pdb=" O ILE Q 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA Q 96 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'Q' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU Q 70 " --> pdb=" O VAL Q 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BP Processing sheet with id= BQ, first strand: chain 'R' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU R 36 " --> pdb=" O VAL R 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BQ Processing sheet with id= BR, first strand: chain 'R' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU R 42 " --> pdb=" O ALA R 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BR Processing sheet with id= BS, first strand: chain 'R' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER R 64 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL R 49 " --> pdb=" O SER R 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU R 66 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS R 79 " --> pdb=" O VAL R 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE R 67 " --> pdb=" O LYS R 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL R 81 " --> pdb=" O ILE R 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA R 96 " --> pdb=" O VAL R 80 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'R' and resid 54 through 56 removed outlier: 7.484A pdb=" N GLU R 70 " --> pdb=" O VAL R 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BT Processing sheet with id= BU, first strand: chain 'S' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU S 36 " --> pdb=" O VAL S 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'S' and resid 26 through 28 removed outlier: 6.281A pdb=" N LEU S 42 " --> pdb=" O ALA S 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'S' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER S 64 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL S 49 " --> pdb=" O SER S 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU S 66 " --> pdb=" O VAL S 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS S 79 " --> pdb=" O VAL S 65 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE S 67 " --> pdb=" O LYS S 79 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL S 81 " --> pdb=" O ILE S 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA S 96 " --> pdb=" O VAL S 80 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'S' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU S 70 " --> pdb=" O VAL S 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BX Processing sheet with id= BY, first strand: chain 'T' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU T 36 " --> pdb=" O VAL T 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BY Processing sheet with id= BZ, first strand: chain 'T' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU T 42 " --> pdb=" O ALA T 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BZ Processing sheet with id= CA, first strand: chain 'T' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER T 64 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL T 49 " --> pdb=" O SER T 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU T 66 " --> pdb=" O VAL T 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS T 79 " --> pdb=" O VAL T 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE T 67 " --> pdb=" O LYS T 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL T 81 " --> pdb=" O ILE T 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA T 96 " --> pdb=" O VAL T 80 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'T' and resid 54 through 56 removed outlier: 7.484A pdb=" N GLU T 70 " --> pdb=" O VAL T 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= CB Processing sheet with id= CC, first strand: chain 'U' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU U 36 " --> pdb=" O VAL U 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= CC Processing sheet with id= CD, first strand: chain 'U' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU U 42 " --> pdb=" O ALA U 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= CD Processing sheet with id= CE, first strand: chain 'U' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER U 64 " --> pdb=" O LEU U 47 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL U 49 " --> pdb=" O SER U 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU U 66 " --> pdb=" O VAL U 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS U 79 " --> pdb=" O VAL U 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE U 67 " --> pdb=" O LYS U 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL U 81 " --> pdb=" O ILE U 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA U 96 " --> pdb=" O VAL U 80 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'U' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU U 70 " --> pdb=" O VAL U 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= CF Processing sheet with id= CG, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU V 36 " --> pdb=" O VAL V 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= CG Processing sheet with id= CH, first strand: chain 'V' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU V 42 " --> pdb=" O ALA V 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= CH Processing sheet with id= CI, first strand: chain 'V' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER V 64 " --> pdb=" O LEU V 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL V 49 " --> pdb=" O SER V 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU V 66 " --> pdb=" O VAL V 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS V 79 " --> pdb=" O VAL V 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE V 67 " --> pdb=" O LYS V 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL V 81 " --> pdb=" O ILE V 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA V 96 " --> pdb=" O VAL V 80 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'V' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU V 70 " --> pdb=" O VAL V 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= CJ 66 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 6.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5764 1.34 - 1.45: 1804 1.45 - 1.57: 8866 1.57 - 1.68: 0 1.68 - 1.80: 44 Bond restraints: 16478 Sorted by residual: bond pdb=" CA GLU S 74 " pdb=" CB GLU S 74 " ideal model delta sigma weight residual 1.524 1.499 0.024 1.33e-02 5.65e+03 3.35e+00 bond pdb=" CA GLU Q 74 " pdb=" CB GLU Q 74 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.33e-02 5.65e+03 3.27e+00 bond pdb=" CA GLU C 74 " pdb=" CB GLU C 74 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.33e-02 5.65e+03 3.26e+00 bond pdb=" CA GLU A 74 " pdb=" CB GLU A 74 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.33e-02 5.65e+03 3.26e+00 bond pdb=" CA GLU K 74 " pdb=" CB GLU K 74 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.33e-02 5.65e+03 3.25e+00 ... (remaining 16473 not shown) Histogram of bond angle deviations from ideal: 101.56 - 107.54: 760 107.54 - 113.51: 8899 113.51 - 119.49: 4197 119.49 - 125.47: 8276 125.47 - 131.44: 66 Bond angle restraints: 22198 Sorted by residual: angle pdb=" CA ARG I 59 " pdb=" CB ARG I 59 " pdb=" CG ARG I 59 " ideal model delta sigma weight residual 114.10 120.21 -6.11 2.00e+00 2.50e-01 9.32e+00 angle pdb=" CA ARG U 59 " pdb=" CB ARG U 59 " pdb=" CG ARG U 59 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.15e+00 angle pdb=" CA ARG E 59 " pdb=" CB ARG E 59 " pdb=" CG ARG E 59 " ideal model delta sigma weight residual 114.10 120.14 -6.04 2.00e+00 2.50e-01 9.13e+00 angle pdb=" CA ARG M 59 " pdb=" CB ARG M 59 " pdb=" CG ARG M 59 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.11e+00 angle pdb=" CA ARG Q 59 " pdb=" CB ARG Q 59 " pdb=" CG ARG Q 59 " ideal model delta sigma weight residual 114.10 120.12 -6.02 2.00e+00 2.50e-01 9.05e+00 ... (remaining 22193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 8680 17.17 - 34.33: 824 34.33 - 51.50: 242 51.50 - 68.66: 176 68.66 - 85.83: 44 Dihedral angle restraints: 9966 sinusoidal: 3916 harmonic: 6050 Sorted by residual: dihedral pdb=" CA ALA A 101 " pdb=" C ALA A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA H 101 " pdb=" C ALA H 101 " pdb=" N GLY H 102 " pdb=" CA GLY H 102 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA D 101 " pdb=" C ALA D 101 " pdb=" N GLY D 102 " pdb=" CA GLY D 102 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 9963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1368 0.032 - 0.065: 626 0.065 - 0.097: 367 0.097 - 0.130: 222 0.130 - 0.162: 101 Chirality restraints: 2684 Sorted by residual: chirality pdb=" CA VAL P 71 " pdb=" N VAL P 71 " pdb=" C VAL P 71 " pdb=" CB VAL P 71 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA VAL T 71 " pdb=" N VAL T 71 " pdb=" C VAL T 71 " pdb=" CB VAL T 71 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 2681 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 18 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ASP B 18 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP B 18 " 0.011 2.00e-02 2.50e+03 pdb=" N THR B 19 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP T 18 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C ASP T 18 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP T 18 " -0.011 2.00e-02 2.50e+03 pdb=" N THR T 19 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 18 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C ASP H 18 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP H 18 " -0.011 2.00e-02 2.50e+03 pdb=" N THR H 19 " -0.010 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 0.56 - 1.43: 20 1.43 - 2.30: 40 2.30 - 3.17: 12178 3.17 - 4.03: 42757 4.03 - 4.90: 78621 Warning: very small nonbonded interaction distances. Nonbonded interactions: 133616 Sorted by model distance: nonbonded pdb=" OE1 GLU A 98 " pdb=" O GLU T 100 " model vdw 0.563 3.040 nonbonded pdb=" O GLU P 100 " pdb=" OE1 GLU S 98 " model vdw 0.563 3.040 nonbonded pdb=" O GLU L 100 " pdb=" OE1 GLU O 98 " model vdw 0.563 3.040 nonbonded pdb=" O GLU D 100 " pdb=" OE1 GLU G 98 " model vdw 0.563 3.040 nonbonded pdb=" O GLU H 100 " pdb=" OE1 GLU K 98 " model vdw 0.564 3.040 ... (remaining 133611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.830 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 43.880 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.160 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 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 : 0.008 0.039 16478 Z= 0.511 Angle : 1.117 6.531 22198 Z= 0.630 Chirality : 0.058 0.162 2684 Planarity : 0.004 0.017 2904 Dihedral : 18.477 85.829 6138 Min Nonbonded Distance : 0.563 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 9.09 % Allowed : 11.69 % Favored : 79.22 % 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: -5.68 (0.13), residues: 2178 helix: None (None), residues: 0 sheet: -3.45 (0.12), residues: 1122 loop : -4.09 (0.13), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS J 68 PHE 0.008 0.003 PHE E 88 TYR 0.003 0.001 TYR O 14 ARG 0.006 0.001 ARG H 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 532 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 SER cc_start: 0.3394 (OUTLIER) cc_final: 0.3154 (t) REVERT: A 78 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: A 79 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7653 (tptt) REVERT: A 91 GLN cc_start: 0.6739 (mp10) cc_final: 0.5991 (tm-30) REVERT: B 40 SER cc_start: 0.3285 (OUTLIER) cc_final: 0.3023 (t) REVERT: B 78 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: B 79 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7811 (tptt) REVERT: B 91 GLN cc_start: 0.6945 (mp10) cc_final: 0.6494 (tm-30) REVERT: C 20 GLU cc_start: 0.7830 (mp0) cc_final: 0.7600 (mp0) REVERT: C 24 ASP cc_start: 0.6996 (m-30) cc_final: 0.6419 (t0) REVERT: C 40 SER cc_start: 0.6854 (OUTLIER) cc_final: 0.6179 (t) REVERT: C 44 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5329 (mm-30) REVERT: D 36 LEU cc_start: 0.8182 (tt) cc_final: 0.7671 (mp) REVERT: D 79 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8143 (mmmm) REVERT: D 93 LYS cc_start: 0.8366 (tttt) cc_final: 0.8005 (tptp) REVERT: E 25 MET cc_start: 0.7459 (ttm) cc_final: 0.6568 (tmm) REVERT: E 26 ARG cc_start: 0.7317 (mtt180) cc_final: 0.6926 (tpt-90) REVERT: E 56 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: E 63 ARG cc_start: 0.8296 (mmt180) cc_final: 0.7904 (mmt180) REVERT: E 72 LYS cc_start: 0.8708 (tttt) cc_final: 0.8438 (tptp) REVERT: F 19 THR cc_start: 0.7129 (OUTLIER) cc_final: 0.6823 (p) REVERT: F 20 GLU cc_start: 0.8034 (mp0) cc_final: 0.7766 (mp0) REVERT: F 26 ARG cc_start: 0.7518 (mtt180) cc_final: 0.6689 (ttm110) REVERT: F 38 ARG cc_start: 0.7939 (tpt90) cc_final: 0.7621 (tpt90) REVERT: F 48 GLU cc_start: 0.7225 (tt0) cc_final: 0.6508 (tm-30) REVERT: F 76 THR cc_start: 0.8214 (m) cc_final: 0.7859 (p) REVERT: F 78 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6968 (mm-30) REVERT: G 19 THR cc_start: 0.7480 (OUTLIER) cc_final: 0.6731 (p) REVERT: G 20 GLU cc_start: 0.8083 (mp0) cc_final: 0.7862 (mt-10) REVERT: G 38 ARG cc_start: 0.7893 (tpt90) cc_final: 0.7447 (tpt90) REVERT: G 44 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6109 (tm-30) REVERT: G 58 GLU cc_start: 0.7662 (pt0) cc_final: 0.7425 (pt0) REVERT: G 66 LEU cc_start: 0.8074 (mm) cc_final: 0.7807 (mp) REVERT: G 72 LYS cc_start: 0.8733 (tttt) cc_final: 0.8407 (mmtm) REVERT: H 48 GLU cc_start: 0.7248 (tt0) cc_final: 0.6953 (tm-30) REVERT: H 54 ARG cc_start: 0.8036 (ttm110) cc_final: 0.7805 (ttp-110) REVERT: H 70 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7493 (tm-30) REVERT: H 72 LYS cc_start: 0.8753 (tttt) cc_final: 0.8474 (tptp) REVERT: H 78 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7904 (tp30) REVERT: H 79 LYS cc_start: 0.8229 (mmtm) cc_final: 0.7966 (mptt) REVERT: H 93 LYS cc_start: 0.8105 (tttt) cc_final: 0.7871 (tttp) REVERT: H 95 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8033 (mm-40) REVERT: I 19 THR cc_start: 0.6740 (OUTLIER) cc_final: 0.6394 (p) REVERT: I 25 MET cc_start: 0.7028 (ttm) cc_final: 0.6210 (tmm) REVERT: I 44 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7084 (tp30) REVERT: I 70 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7560 (tm-30) REVERT: I 72 LYS cc_start: 0.8505 (tttt) cc_final: 0.7753 (tptp) REVERT: I 78 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8085 (tp30) REVERT: I 93 LYS cc_start: 0.7814 (tttt) cc_final: 0.7110 (mmtm) REVERT: I 95 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8331 (mm110) REVERT: J 20 GLU cc_start: 0.8029 (mp0) cc_final: 0.7703 (mp0) REVERT: J 38 ARG cc_start: 0.7646 (tpt90) cc_final: 0.7122 (tpt90) REVERT: J 44 GLU cc_start: 0.5607 (OUTLIER) cc_final: 0.5205 (tm-30) REVERT: J 46 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7440 (tm-30) REVERT: J 72 LYS cc_start: 0.8472 (tttt) cc_final: 0.7704 (mppt) REVERT: J 93 LYS cc_start: 0.7493 (tttt) cc_final: 0.6544 (mmtm) REVERT: K 20 GLU cc_start: 0.7694 (mp0) cc_final: 0.7330 (mp0) REVERT: K 24 ASP cc_start: 0.7395 (m-30) cc_final: 0.7109 (t0) REVERT: K 28 LYS cc_start: 0.7178 (mtpp) cc_final: 0.6922 (mtpp) REVERT: K 38 ARG cc_start: 0.7696 (tpt90) cc_final: 0.7487 (tpt90) REVERT: K 59 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6859 (mmt180) REVERT: K 72 LYS cc_start: 0.8274 (tttt) cc_final: 0.7872 (mmtm) REVERT: K 79 LYS cc_start: 0.8266 (mmtm) cc_final: 0.7910 (tptt) REVERT: K 87 ARG cc_start: 0.7571 (ttm-80) cc_final: 0.7333 (mtp85) REVERT: K 95 GLN cc_start: 0.8339 (mm-40) cc_final: 0.7647 (tp40) REVERT: L 18 ASP cc_start: 0.7435 (p0) cc_final: 0.6544 (p0) REVERT: L 19 THR cc_start: 0.6396 (OUTLIER) cc_final: 0.6189 (p) REVERT: L 20 GLU cc_start: 0.7514 (mp0) cc_final: 0.7175 (mp0) REVERT: L 30 GLN cc_start: 0.7961 (tt0) cc_final: 0.7700 (tm-30) REVERT: L 38 ARG cc_start: 0.7950 (tpt90) cc_final: 0.7520 (tpt90) REVERT: L 78 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: L 93 LYS cc_start: 0.7645 (tttt) cc_final: 0.7323 (tttp) REVERT: L 95 GLN cc_start: 0.8640 (mm-40) cc_final: 0.7928 (mm110) REVERT: M 18 ASP cc_start: 0.7618 (p0) cc_final: 0.7209 (p0) REVERT: M 19 THR cc_start: 0.6797 (OUTLIER) cc_final: 0.6438 (p) REVERT: M 20 GLU cc_start: 0.7586 (mp0) cc_final: 0.7354 (mp0) REVERT: M 30 GLN cc_start: 0.8080 (tt0) cc_final: 0.7837 (tm-30) REVERT: M 38 ARG cc_start: 0.7862 (tpt90) cc_final: 0.7462 (tpt90) REVERT: M 78 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7673 (mm-30) REVERT: N 20 GLU cc_start: 0.7741 (mp0) cc_final: 0.7426 (mp0) REVERT: N 24 ASP cc_start: 0.7235 (m-30) cc_final: 0.6821 (t0) REVERT: N 59 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7063 (mmm-85) REVERT: N 72 LYS cc_start: 0.8450 (tttt) cc_final: 0.8142 (mmtm) REVERT: N 79 LYS cc_start: 0.8486 (mmtm) cc_final: 0.8140 (tptt) REVERT: N 95 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7764 (tp40) REVERT: O 20 GLU cc_start: 0.8126 (mp0) cc_final: 0.7755 (mp0) REVERT: O 38 ARG cc_start: 0.7685 (tpt90) cc_final: 0.7177 (tpt90) REVERT: O 40 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.8081 (p) REVERT: O 44 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.5225 (tm-30) REVERT: O 46 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7282 (tm-30) REVERT: O 72 LYS cc_start: 0.8341 (tttt) cc_final: 0.7527 (mppt) REVERT: O 93 LYS cc_start: 0.7318 (tttt) cc_final: 0.6452 (mmtm) REVERT: P 25 MET cc_start: 0.6945 (ttm) cc_final: 0.6166 (tmm) REVERT: P 44 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7434 (tp30) REVERT: P 52 THR cc_start: 0.7542 (t) cc_final: 0.7323 (p) REVERT: P 70 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7555 (tm-30) REVERT: P 72 LYS cc_start: 0.8525 (tttt) cc_final: 0.7854 (tptp) REVERT: P 78 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8149 (tp30) REVERT: P 93 LYS cc_start: 0.8039 (tttt) cc_final: 0.7282 (mmtm) REVERT: P 95 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8419 (mm110) REVERT: Q 26 ARG cc_start: 0.7540 (mtt180) cc_final: 0.6307 (tpt-90) REVERT: Q 40 SER cc_start: 0.7973 (OUTLIER) cc_final: 0.7761 (t) REVERT: Q 48 GLU cc_start: 0.7392 (tt0) cc_final: 0.7153 (tm-30) REVERT: Q 72 LYS cc_start: 0.8746 (tttt) cc_final: 0.8448 (tptp) REVERT: Q 93 LYS cc_start: 0.8072 (tttt) cc_final: 0.7834 (tttp) REVERT: Q 95 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8137 (mm-40) REVERT: R 19 THR cc_start: 0.7648 (OUTLIER) cc_final: 0.7002 (p) REVERT: R 38 ARG cc_start: 0.7805 (tpt90) cc_final: 0.7391 (tpt90) REVERT: R 44 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5969 (tm-30) REVERT: R 58 GLU cc_start: 0.7554 (pt0) cc_final: 0.7161 (pt0) REVERT: S 19 THR cc_start: 0.6933 (OUTLIER) cc_final: 0.6525 (p) REVERT: S 26 ARG cc_start: 0.7308 (mtt180) cc_final: 0.6843 (ttm110) REVERT: S 38 ARG cc_start: 0.8060 (tpt90) cc_final: 0.7695 (tpt90) REVERT: S 40 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.7904 (t) REVERT: S 48 GLU cc_start: 0.7521 (tt0) cc_final: 0.6903 (tm-30) REVERT: S 59 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7660 (mmm-85) REVERT: S 66 LEU cc_start: 0.8271 (mm) cc_final: 0.7950 (mp) REVERT: S 72 LYS cc_start: 0.8670 (tttt) cc_final: 0.8443 (mppt) REVERT: S 76 THR cc_start: 0.8007 (m) cc_final: 0.7675 (p) REVERT: S 78 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6845 (mm-30) REVERT: S 93 LYS cc_start: 0.7903 (tttt) cc_final: 0.7699 (tptp) REVERT: S 95 GLN cc_start: 0.8303 (mm-40) cc_final: 0.8073 (mt0) REVERT: S 108 GLN cc_start: 0.6493 (tt0) cc_final: 0.6249 (pm20) REVERT: T 25 MET cc_start: 0.7458 (ttm) cc_final: 0.6523 (tmm) REVERT: T 26 ARG cc_start: 0.7222 (mtt180) cc_final: 0.6849 (tpt-90) REVERT: T 56 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: T 58 GLU cc_start: 0.6800 (pt0) cc_final: 0.6177 (pm20) REVERT: T 59 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7148 (tpp80) REVERT: T 92 LEU cc_start: 0.8388 (tt) cc_final: 0.8138 (tp) REVERT: U 25 MET cc_start: 0.7182 (ttm) cc_final: 0.6957 (tmm) REVERT: U 36 LEU cc_start: 0.7920 (tt) cc_final: 0.7631 (mp) REVERT: U 75 LEU cc_start: 0.7846 (tt) cc_final: 0.7629 (tt) REVERT: U 79 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8223 (mmmm) REVERT: U 93 LYS cc_start: 0.8431 (tttt) cc_final: 0.8107 (mptt) REVERT: V 20 GLU cc_start: 0.7842 (mp0) cc_final: 0.7626 (mp0) REVERT: V 24 ASP cc_start: 0.7013 (m-30) cc_final: 0.6600 (t0) REVERT: V 44 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.5100 (mm-30) outliers start: 154 outliers final: 20 residues processed: 608 average time/residue: 0.4483 time to fit residues: 350.8348 Evaluate side-chains 374 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 318 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 172 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 199 optimal weight: 0.0870 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16478 Z= 0.201 Angle : 0.642 6.962 22198 Z= 0.322 Chirality : 0.049 0.134 2684 Planarity : 0.004 0.060 2904 Dihedral : 5.199 19.111 2376 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: -5.30 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.07 (0.13), residues: 1342 loop : -3.99 (0.14), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS V 68 PHE 0.007 0.001 PHE R 88 TYR 0.006 0.001 TYR U 14 ARG 0.006 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.6387 (t70) cc_final: 0.6177 (t70) REVERT: A 72 LYS cc_start: 0.7873 (tmtt) cc_final: 0.7566 (tptp) REVERT: A 78 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7754 (mm-30) REVERT: A 91 GLN cc_start: 0.7090 (mp10) cc_final: 0.6184 (tm-30) REVERT: B 72 LYS cc_start: 0.8108 (tmtt) cc_final: 0.7741 (tptp) REVERT: B 91 GLN cc_start: 0.7288 (mp10) cc_final: 0.6414 (tm-30) REVERT: C 24 ASP cc_start: 0.6992 (m-30) cc_final: 0.6762 (t0) REVERT: C 38 ARG cc_start: 0.6484 (ttp80) cc_final: 0.5723 (tmm160) REVERT: C 58 GLU cc_start: 0.4279 (pm20) cc_final: 0.3978 (pm20) REVERT: D 93 LYS cc_start: 0.8238 (tttt) cc_final: 0.7801 (tptp) REVERT: E 20 GLU cc_start: 0.8325 (mp0) cc_final: 0.8094 (mp0) REVERT: E 25 MET cc_start: 0.7196 (ttm) cc_final: 0.6472 (tmm) REVERT: E 26 ARG cc_start: 0.7092 (mtt180) cc_final: 0.6727 (tpt-90) REVERT: E 70 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7027 (tm-30) REVERT: E 72 LYS cc_start: 0.8730 (tttt) cc_final: 0.8420 (tptp) REVERT: E 78 GLU cc_start: 0.8586 (tp30) cc_final: 0.8303 (tp30) REVERT: F 20 GLU cc_start: 0.7919 (mp0) cc_final: 0.7614 (mp0) REVERT: F 26 ARG cc_start: 0.7419 (mtt180) cc_final: 0.6593 (ttm110) REVERT: F 38 ARG cc_start: 0.8187 (tpt90) cc_final: 0.7671 (tpt90) REVERT: F 59 ARG cc_start: 0.7765 (mmt-90) cc_final: 0.7372 (mmm-85) REVERT: F 70 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7624 (mp0) REVERT: G 20 GLU cc_start: 0.8040 (mp0) cc_final: 0.7706 (mt-10) REVERT: G 38 ARG cc_start: 0.7882 (tpt90) cc_final: 0.7428 (tpt90) REVERT: H 18 ASP cc_start: 0.7575 (p0) cc_final: 0.7172 (p0) REVERT: H 24 ASP cc_start: 0.7071 (t0) cc_final: 0.6855 (t0) REVERT: H 25 MET cc_start: 0.7648 (tmm) cc_final: 0.7032 (tmm) REVERT: H 95 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8179 (mm110) REVERT: H 100 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7036 (mm-30) REVERT: I 25 MET cc_start: 0.6547 (ttm) cc_final: 0.5838 (tmm) REVERT: I 70 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7431 (tm-30) REVERT: I 72 LYS cc_start: 0.8228 (tttt) cc_final: 0.7843 (tptp) REVERT: I 84 LYS cc_start: 0.8209 (tptp) cc_final: 0.7997 (tptp) REVERT: I 93 LYS cc_start: 0.7584 (tttt) cc_final: 0.6846 (mmtm) REVERT: I 95 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8351 (mm110) REVERT: J 20 GLU cc_start: 0.8045 (mp0) cc_final: 0.7804 (mp0) REVERT: J 38 ARG cc_start: 0.7904 (tpt90) cc_final: 0.7382 (tpt90) REVERT: J 72 LYS cc_start: 0.8400 (tttt) cc_final: 0.7671 (mmtm) REVERT: J 93 LYS cc_start: 0.7540 (tttt) cc_final: 0.6584 (mmtm) REVERT: K 28 LYS cc_start: 0.7367 (mtpp) cc_final: 0.6847 (mtpp) REVERT: K 40 SER cc_start: 0.7007 (p) cc_final: 0.6249 (t) REVERT: K 58 GLU cc_start: 0.6717 (pt0) cc_final: 0.6184 (pt0) REVERT: K 72 LYS cc_start: 0.8124 (tttt) cc_final: 0.7767 (mmtm) REVERT: K 87 ARG cc_start: 0.7392 (ttm-80) cc_final: 0.7106 (mtp85) REVERT: K 95 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7998 (mm-40) REVERT: L 18 ASP cc_start: 0.7634 (p0) cc_final: 0.6867 (p0) REVERT: L 20 GLU cc_start: 0.7590 (mp0) cc_final: 0.7185 (mp0) REVERT: L 30 GLN cc_start: 0.8139 (tt0) cc_final: 0.7856 (tm-30) REVERT: L 38 ARG cc_start: 0.7925 (tpt90) cc_final: 0.7508 (tpt90) REVERT: L 78 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7534 (tp30) REVERT: L 95 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8107 (mm110) REVERT: M 18 ASP cc_start: 0.7458 (p0) cc_final: 0.7072 (p0) REVERT: M 25 MET cc_start: 0.6519 (ttt) cc_final: 0.6190 (mtp) REVERT: M 78 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7303 (tp30) REVERT: M 93 LYS cc_start: 0.7496 (tttt) cc_final: 0.6608 (mmtm) REVERT: M 95 GLN cc_start: 0.8584 (mm-40) cc_final: 0.7979 (mm110) REVERT: N 18 ASP cc_start: 0.5968 (p0) cc_final: 0.5653 (p0) REVERT: N 72 LYS cc_start: 0.8284 (tttt) cc_final: 0.7963 (mmtm) REVERT: N 93 LYS cc_start: 0.7652 (tttt) cc_final: 0.7393 (mtpt) REVERT: N 95 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8148 (mm-40) REVERT: O 20 GLU cc_start: 0.7888 (mp0) cc_final: 0.7589 (mp0) REVERT: O 26 ARG cc_start: 0.6898 (mtt180) cc_final: 0.6605 (mtt-85) REVERT: O 38 ARG cc_start: 0.7787 (tpt90) cc_final: 0.7297 (tpt90) REVERT: O 72 LYS cc_start: 0.8263 (tttt) cc_final: 0.7526 (mppt) REVERT: O 93 LYS cc_start: 0.7313 (tttt) cc_final: 0.6428 (mmtm) REVERT: P 25 MET cc_start: 0.6759 (ttm) cc_final: 0.6064 (tmm) REVERT: P 32 ARG cc_start: 0.7688 (ttt90) cc_final: 0.7131 (ttt-90) REVERT: P 48 GLU cc_start: 0.7071 (tt0) cc_final: 0.6828 (tm-30) REVERT: P 52 THR cc_start: 0.7699 (t) cc_final: 0.7363 (p) REVERT: P 70 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7421 (tm-30) REVERT: P 72 LYS cc_start: 0.8234 (tttt) cc_final: 0.7831 (tptp) REVERT: P 84 LYS cc_start: 0.8298 (tptp) cc_final: 0.8092 (tptp) REVERT: P 93 LYS cc_start: 0.7863 (tttt) cc_final: 0.7098 (mmtm) REVERT: Q 25 MET cc_start: 0.7689 (tmm) cc_final: 0.6960 (tmm) REVERT: Q 72 LYS cc_start: 0.8830 (tttt) cc_final: 0.8505 (tptp) REVERT: Q 100 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6897 (mm-30) REVERT: R 38 ARG cc_start: 0.7766 (tpt90) cc_final: 0.7328 (tpt90) REVERT: R 93 LYS cc_start: 0.8541 (tttt) cc_final: 0.8330 (tttp) REVERT: S 26 ARG cc_start: 0.7264 (mtt180) cc_final: 0.6667 (ttm110) REVERT: S 38 ARG cc_start: 0.8126 (tpt90) cc_final: 0.7563 (tpt90) REVERT: S 59 ARG cc_start: 0.7953 (mmt-90) cc_final: 0.7215 (mmm-85) REVERT: S 93 LYS cc_start: 0.7816 (tttt) cc_final: 0.7403 (tptp) REVERT: S 95 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8047 (mm110) REVERT: T 20 GLU cc_start: 0.8229 (mp0) cc_final: 0.7964 (mp0) REVERT: T 25 MET cc_start: 0.7097 (ttm) cc_final: 0.6273 (tmm) REVERT: T 26 ARG cc_start: 0.7187 (mtt180) cc_final: 0.6752 (tpt-90) REVERT: T 59 ARG cc_start: 0.7762 (mmt-90) cc_final: 0.7391 (tpp80) REVERT: T 72 LYS cc_start: 0.8430 (tmtt) cc_final: 0.7951 (tptp) REVERT: T 78 GLU cc_start: 0.8333 (tp30) cc_final: 0.7429 (tp30) REVERT: T 79 LYS cc_start: 0.9027 (mmtm) cc_final: 0.8825 (mmpt) REVERT: T 84 LYS cc_start: 0.8290 (mmpt) cc_final: 0.8070 (tptp) REVERT: U 18 ASP cc_start: 0.7212 (p0) cc_final: 0.6641 (p0) REVERT: U 25 MET cc_start: 0.7063 (ttm) cc_final: 0.6771 (tmm) REVERT: U 93 LYS cc_start: 0.8274 (tttt) cc_final: 0.7921 (mptt) REVERT: U 108 GLN cc_start: 0.6575 (pp30) cc_final: 0.6352 (pp30) REVERT: V 24 ASP cc_start: 0.7595 (m-30) cc_final: 0.6717 (t0) REVERT: V 38 ARG cc_start: 0.6483 (ttp80) cc_final: 0.6257 (ttp80) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.4710 time to fit residues: 240.1282 Evaluate side-chains 291 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 198 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 GLN F 68 HIS G 95 GLN H 68 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 HIS J 68 HIS O 68 HIS Q 68 HIS R 95 GLN S 68 HIS V 68 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 16478 Z= 0.606 Angle : 0.948 8.769 22198 Z= 0.509 Chirality : 0.056 0.191 2684 Planarity : 0.007 0.056 2904 Dihedral : 7.554 25.039 2376 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.14 % Favored : 81.86 % Rotamer: Outliers : 0.18 % Allowed : 7.62 % Favored : 92.21 % 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: -5.77 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.70 (0.12), residues: 1320 loop : -3.68 (0.17), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS L 68 PHE 0.041 0.004 PHE O 105 TYR 0.020 0.003 TYR J 14 ARG 0.019 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 315 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.0146 (mtp) cc_final: -0.0104 (ttt) REVERT: A 72 LYS cc_start: 0.8187 (tmtt) cc_final: 0.7730 (tmtt) REVERT: B 61 GLU cc_start: 0.5740 (mp0) cc_final: 0.4529 (tm-30) REVERT: B 72 LYS cc_start: 0.8247 (tmtt) cc_final: 0.7773 (tmtt) REVERT: C 24 ASP cc_start: 0.7500 (m-30) cc_final: 0.6824 (t0) REVERT: C 38 ARG cc_start: 0.6243 (ttp80) cc_final: 0.5894 (ttp80) REVERT: D 24 ASP cc_start: 0.6993 (t0) cc_final: 0.6739 (t0) REVERT: D 59 ARG cc_start: 0.7807 (mpt180) cc_final: 0.7358 (mpt90) REVERT: D 93 LYS cc_start: 0.8514 (tttt) cc_final: 0.7929 (mptt) REVERT: D 100 GLU cc_start: 0.8385 (mp0) cc_final: 0.8014 (mp0) REVERT: E 25 MET cc_start: 0.7849 (ttm) cc_final: 0.6751 (tmm) REVERT: E 72 LYS cc_start: 0.8900 (tttt) cc_final: 0.8326 (tptp) REVERT: E 79 LYS cc_start: 0.9154 (mmtm) cc_final: 0.8848 (mmpt) REVERT: E 93 LYS cc_start: 0.7817 (mmtt) cc_final: 0.7517 (mmtt) REVERT: F 38 ARG cc_start: 0.8329 (tpt90) cc_final: 0.7795 (tpt90) REVERT: F 59 ARG cc_start: 0.7564 (mmt-90) cc_final: 0.7106 (mmm-85) REVERT: F 63 ARG cc_start: 0.7690 (mmt180) cc_final: 0.7482 (mmt180) REVERT: F 70 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7643 (mp0) REVERT: G 20 GLU cc_start: 0.8312 (mp0) cc_final: 0.7792 (mt-10) REVERT: G 38 ARG cc_start: 0.8280 (tpt90) cc_final: 0.7708 (tpt90) REVERT: G 93 LYS cc_start: 0.8240 (tttt) cc_final: 0.7963 (tttp) REVERT: H 18 ASP cc_start: 0.7911 (p0) cc_final: 0.7229 (p0) REVERT: H 24 ASP cc_start: 0.7317 (t0) cc_final: 0.7052 (t0) REVERT: H 52 THR cc_start: 0.7684 (t) cc_final: 0.7482 (t) REVERT: H 95 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8146 (mp10) REVERT: I 79 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8217 (mmmt) REVERT: I 84 LYS cc_start: 0.8154 (tptp) cc_final: 0.7908 (tptp) REVERT: I 93 LYS cc_start: 0.7648 (tttt) cc_final: 0.7328 (tttp) REVERT: J 20 GLU cc_start: 0.8284 (mp0) cc_final: 0.7934 (mp0) REVERT: J 38 ARG cc_start: 0.8264 (tpt90) cc_final: 0.7546 (tpt90) REVERT: J 72 LYS cc_start: 0.8755 (tttt) cc_final: 0.8325 (ttmm) REVERT: J 78 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7375 (tm-30) REVERT: J 93 LYS cc_start: 0.7892 (tttt) cc_final: 0.6770 (mtmm) REVERT: K 72 LYS cc_start: 0.8649 (tttt) cc_final: 0.7948 (tmtt) REVERT: K 78 GLU cc_start: 0.7547 (tp30) cc_final: 0.6883 (tm-30) REVERT: K 93 LYS cc_start: 0.7716 (tttt) cc_final: 0.7463 (mtpp) REVERT: K 95 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7610 (tp-100) REVERT: K 100 GLU cc_start: 0.7143 (mp0) cc_final: 0.6932 (mp0) REVERT: L 18 ASP cc_start: 0.7245 (p0) cc_final: 0.6523 (p0) REVERT: L 78 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7797 (tp30) REVERT: L 93 LYS cc_start: 0.8080 (tttt) cc_final: 0.7060 (mmtm) REVERT: L 95 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8082 (mm-40) REVERT: M 18 ASP cc_start: 0.7430 (p0) cc_final: 0.6807 (p0) REVERT: M 25 MET cc_start: 0.6994 (ttt) cc_final: 0.6282 (mtp) REVERT: M 78 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7558 (tp30) REVERT: M 79 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7750 (mmtp) REVERT: M 93 LYS cc_start: 0.7818 (tttt) cc_final: 0.6799 (mmtm) REVERT: M 95 GLN cc_start: 0.8594 (mm-40) cc_final: 0.7662 (mm-40) REVERT: N 59 ARG cc_start: 0.7541 (mmt-90) cc_final: 0.6989 (mmt180) REVERT: N 72 LYS cc_start: 0.8793 (tttt) cc_final: 0.8175 (tmtt) REVERT: N 78 GLU cc_start: 0.7766 (tp30) cc_final: 0.7166 (tm-30) REVERT: N 93 LYS cc_start: 0.7929 (tttt) cc_final: 0.7667 (mtpp) REVERT: N 95 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7715 (tp-100) REVERT: O 20 GLU cc_start: 0.8346 (mp0) cc_final: 0.8081 (mp0) REVERT: O 38 ARG cc_start: 0.8250 (tpt90) cc_final: 0.7519 (tpt90) REVERT: O 72 LYS cc_start: 0.8586 (tttt) cc_final: 0.8206 (ttmm) REVERT: O 78 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7202 (tm-30) REVERT: O 93 LYS cc_start: 0.7588 (tttt) cc_final: 0.6860 (mtpp) REVERT: P 25 MET cc_start: 0.7309 (ttm) cc_final: 0.6158 (tmm) REVERT: P 32 ARG cc_start: 0.7878 (ttt90) cc_final: 0.6551 (ttt-90) REVERT: P 48 GLU cc_start: 0.7272 (tt0) cc_final: 0.6502 (tm-30) REVERT: P 79 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8199 (mmmt) REVERT: P 93 LYS cc_start: 0.7884 (tttt) cc_final: 0.7557 (tttp) REVERT: Q 18 ASP cc_start: 0.7967 (p0) cc_final: 0.7465 (p0) REVERT: Q 72 LYS cc_start: 0.8777 (tttt) cc_final: 0.8550 (tmtt) REVERT: Q 95 GLN cc_start: 0.8230 (mm110) cc_final: 0.7870 (mp10) REVERT: R 28 LYS cc_start: 0.6506 (mmtm) cc_final: 0.6292 (mptt) REVERT: R 38 ARG cc_start: 0.8130 (tpt90) cc_final: 0.7682 (tpt90) REVERT: R 93 LYS cc_start: 0.8395 (tttt) cc_final: 0.8097 (tttp) REVERT: S 30 GLN cc_start: 0.7583 (tm-30) cc_final: 0.7263 (tm-30) REVERT: S 38 ARG cc_start: 0.8358 (tpt90) cc_final: 0.7919 (tpt90) REVERT: S 59 ARG cc_start: 0.7590 (mmt-90) cc_final: 0.7192 (mmm-85) REVERT: S 79 LYS cc_start: 0.7991 (tptp) cc_final: 0.7691 (mmtm) REVERT: S 93 LYS cc_start: 0.8240 (tttt) cc_final: 0.7719 (tptp) REVERT: S 95 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8444 (mm110) REVERT: T 25 MET cc_start: 0.7744 (ttm) cc_final: 0.6561 (tmm) REVERT: T 72 LYS cc_start: 0.8638 (tmtt) cc_final: 0.8014 (tptp) REVERT: T 79 LYS cc_start: 0.9144 (mmtm) cc_final: 0.8833 (mmpt) REVERT: T 84 LYS cc_start: 0.8418 (mmpt) cc_final: 0.8091 (tptp) REVERT: T 93 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7608 (mmtt) REVERT: U 18 ASP cc_start: 0.7374 (p0) cc_final: 0.6911 (p0) REVERT: U 25 MET cc_start: 0.6841 (ttm) cc_final: 0.6518 (tmm) REVERT: U 59 ARG cc_start: 0.7956 (mpt180) cc_final: 0.7565 (mmt-90) REVERT: U 78 GLU cc_start: 0.8298 (tt0) cc_final: 0.7905 (tm-30) REVERT: U 93 LYS cc_start: 0.8476 (tttt) cc_final: 0.7990 (tptp) REVERT: V 24 ASP cc_start: 0.7712 (m-30) cc_final: 0.6745 (t0) REVERT: V 32 ARG cc_start: 0.7038 (tmt-80) cc_final: 0.6725 (tpt90) REVERT: V 38 ARG cc_start: 0.6210 (ttp80) cc_final: 0.5770 (ttp80) outliers start: 3 outliers final: 1 residues processed: 318 average time/residue: 0.4694 time to fit residues: 190.5168 Evaluate side-chains 269 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16478 Z= 0.160 Angle : 0.637 6.993 22198 Z= 0.315 Chirality : 0.050 0.159 2684 Planarity : 0.003 0.039 2904 Dihedral : 5.522 23.766 2376 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: -5.51 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.50 (0.12), residues: 1342 loop : -3.54 (0.16), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 68 PHE 0.010 0.001 PHE N 88 TYR 0.006 0.001 TYR L 14 ARG 0.005 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8004 (tmtt) cc_final: 0.7616 (tmtt) REVERT: A 91 GLN cc_start: 0.6840 (mp10) cc_final: 0.5757 (tm-30) REVERT: B 34 ASP cc_start: 0.6459 (t70) cc_final: 0.6178 (t70) REVERT: B 61 GLU cc_start: 0.5359 (mp0) cc_final: 0.4417 (tm-30) REVERT: B 72 LYS cc_start: 0.8068 (tmtt) cc_final: 0.7686 (tmtt) REVERT: C 24 ASP cc_start: 0.7530 (m-30) cc_final: 0.6812 (t0) REVERT: C 38 ARG cc_start: 0.6755 (tmm160) cc_final: 0.6100 (ttp80) REVERT: D 24 ASP cc_start: 0.6928 (t0) cc_final: 0.6699 (t0) REVERT: D 93 LYS cc_start: 0.8269 (tttt) cc_final: 0.7834 (mptt) REVERT: D 98 GLU cc_start: 0.8508 (tp30) cc_final: 0.8238 (tp30) REVERT: D 100 GLU cc_start: 0.8444 (mp0) cc_final: 0.8130 (mp0) REVERT: E 25 MET cc_start: 0.7355 (ttm) cc_final: 0.6562 (tmm) REVERT: E 72 LYS cc_start: 0.8902 (tttt) cc_final: 0.8407 (tptp) REVERT: E 79 LYS cc_start: 0.9008 (mmtm) cc_final: 0.8727 (mmpt) REVERT: E 93 LYS cc_start: 0.7687 (mmtt) cc_final: 0.7421 (mmtt) REVERT: E 100 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7912 (mt-10) REVERT: F 38 ARG cc_start: 0.8114 (tpt90) cc_final: 0.7576 (tpt90) REVERT: F 46 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7453 (tm-30) REVERT: F 70 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7478 (mp0) REVERT: G 20 GLU cc_start: 0.8225 (mp0) cc_final: 0.7887 (mt-10) REVERT: G 32 ARG cc_start: 0.7696 (ttt90) cc_final: 0.7402 (ttt90) REVERT: G 38 ARG cc_start: 0.8055 (tpt90) cc_final: 0.7545 (tpt90) REVERT: G 93 LYS cc_start: 0.8492 (tttt) cc_final: 0.7715 (mmtm) REVERT: H 18 ASP cc_start: 0.7924 (p0) cc_final: 0.7252 (p0) REVERT: H 24 ASP cc_start: 0.7163 (t0) cc_final: 0.6903 (t0) REVERT: H 95 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8165 (mp10) REVERT: H 105 PHE cc_start: 0.7857 (t80) cc_final: 0.7626 (t80) REVERT: I 25 MET cc_start: 0.6762 (ttm) cc_final: 0.5890 (tmm) REVERT: I 79 LYS cc_start: 0.8407 (mmtt) cc_final: 0.7906 (mmmt) REVERT: I 93 LYS cc_start: 0.7472 (tttt) cc_final: 0.6723 (mmtm) REVERT: J 38 ARG cc_start: 0.7859 (tpt90) cc_final: 0.7234 (tpt90) REVERT: J 72 LYS cc_start: 0.8373 (tttt) cc_final: 0.7838 (mptt) REVERT: J 93 LYS cc_start: 0.7742 (tttt) cc_final: 0.6729 (mmtm) REVERT: K 24 ASP cc_start: 0.7897 (t0) cc_final: 0.7629 (m-30) REVERT: K 59 ARG cc_start: 0.7408 (mmt-90) cc_final: 0.6981 (mmm-85) REVERT: K 72 LYS cc_start: 0.8298 (tttt) cc_final: 0.7766 (mmtm) REVERT: K 78 GLU cc_start: 0.7563 (tp30) cc_final: 0.6910 (tm-30) REVERT: K 95 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7918 (mm-40) REVERT: L 18 ASP cc_start: 0.7379 (p0) cc_final: 0.6685 (p0) REVERT: L 78 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7801 (tm-30) REVERT: M 18 ASP cc_start: 0.7543 (p0) cc_final: 0.6950 (p0) REVERT: M 38 ARG cc_start: 0.7898 (tpt90) cc_final: 0.7448 (tpt90) REVERT: M 56 GLU cc_start: 0.7243 (tp30) cc_final: 0.6949 (mm-30) REVERT: M 79 LYS cc_start: 0.8121 (mmtm) cc_final: 0.7865 (mtpt) REVERT: N 72 LYS cc_start: 0.8442 (tttt) cc_final: 0.7962 (mmtm) REVERT: N 93 LYS cc_start: 0.7929 (tttt) cc_final: 0.7702 (mtpt) REVERT: N 95 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8081 (mm-40) REVERT: O 25 MET cc_start: 0.7038 (ttt) cc_final: 0.6544 (ttt) REVERT: O 38 ARG cc_start: 0.7852 (tpt90) cc_final: 0.7178 (tpt90) REVERT: O 72 LYS cc_start: 0.8249 (tttt) cc_final: 0.7624 (mptt) REVERT: O 93 LYS cc_start: 0.7540 (tttt) cc_final: 0.6807 (mtpp) REVERT: P 32 ARG cc_start: 0.7740 (ttt90) cc_final: 0.6661 (ttt-90) REVERT: P 48 GLU cc_start: 0.7157 (tt0) cc_final: 0.6781 (tm-30) REVERT: P 79 LYS cc_start: 0.8472 (mmtt) cc_final: 0.7948 (mmmt) REVERT: P 93 LYS cc_start: 0.7732 (tttt) cc_final: 0.7445 (tttp) REVERT: Q 18 ASP cc_start: 0.7791 (p0) cc_final: 0.7437 (p0) REVERT: Q 95 GLN cc_start: 0.8225 (mm110) cc_final: 0.8007 (mm110) REVERT: Q 100 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7309 (mm-30) REVERT: R 38 ARG cc_start: 0.7935 (tpt90) cc_final: 0.7537 (tpt90) REVERT: R 93 LYS cc_start: 0.8592 (tttt) cc_final: 0.7783 (mmtm) REVERT: S 20 GLU cc_start: 0.8102 (mp0) cc_final: 0.7786 (mp0) REVERT: S 38 ARG cc_start: 0.8052 (tpt90) cc_final: 0.7489 (tpt90) REVERT: S 59 ARG cc_start: 0.7697 (mmt-90) cc_final: 0.7197 (mmm-85) REVERT: S 63 ARG cc_start: 0.7659 (mmt180) cc_final: 0.7197 (mpt180) REVERT: S 72 LYS cc_start: 0.8383 (tptt) cc_final: 0.7826 (tppt) REVERT: S 79 LYS cc_start: 0.8056 (tptp) cc_final: 0.7789 (mmtm) REVERT: S 93 LYS cc_start: 0.8072 (tttt) cc_final: 0.7558 (tptp) REVERT: S 95 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8209 (mm110) REVERT: T 20 GLU cc_start: 0.8273 (mp0) cc_final: 0.7977 (mp0) REVERT: T 25 MET cc_start: 0.7514 (ttm) cc_final: 0.6644 (tmm) REVERT: T 59 ARG cc_start: 0.8373 (mmt180) cc_final: 0.7979 (tpp-160) REVERT: T 72 LYS cc_start: 0.8663 (tmtt) cc_final: 0.7974 (tptp) REVERT: T 78 GLU cc_start: 0.8303 (tp30) cc_final: 0.7351 (tp30) REVERT: T 79 LYS cc_start: 0.9098 (mmtm) cc_final: 0.8772 (mmpt) REVERT: T 93 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7618 (mmtm) REVERT: U 18 ASP cc_start: 0.7147 (p0) cc_final: 0.6736 (p0) REVERT: U 36 LEU cc_start: 0.7954 (mt) cc_final: 0.7723 (mt) REVERT: U 74 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7075 (mt-10) REVERT: U 93 LYS cc_start: 0.8383 (tttt) cc_final: 0.7918 (mptt) REVERT: V 20 GLU cc_start: 0.7297 (mp0) cc_final: 0.7031 (tm-30) REVERT: V 24 ASP cc_start: 0.7652 (m-30) cc_final: 0.6701 (t0) REVERT: V 38 ARG cc_start: 0.6516 (tmm160) cc_final: 0.5973 (ttp80) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.4732 time to fit residues: 214.0449 Evaluate side-chains 271 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 158 optimal weight: 0.0980 chunk 87 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 108 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 HIS T 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16478 Z= 0.398 Angle : 0.747 7.159 22198 Z= 0.394 Chirality : 0.052 0.162 2684 Planarity : 0.005 0.046 2904 Dihedral : 6.513 23.639 2376 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.23 % Favored : 81.77 % Rotamer: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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: -5.59 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.77 (0.12), residues: 1364 loop : -3.11 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS J 68 PHE 0.016 0.002 PHE K 105 TYR 0.018 0.002 TYR O 14 ARG 0.006 0.001 ARG L 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.1949 (ttt) cc_final: 0.0609 (mtp) REVERT: A 72 LYS cc_start: 0.8110 (tmtt) cc_final: 0.7672 (tmtt) REVERT: B 72 LYS cc_start: 0.8127 (tmtt) cc_final: 0.7673 (tmtt) REVERT: C 24 ASP cc_start: 0.7635 (m-30) cc_final: 0.6659 (t0) REVERT: C 38 ARG cc_start: 0.6230 (tmm160) cc_final: 0.5776 (tmm160) REVERT: C 78 GLU cc_start: 0.5062 (pt0) cc_final: 0.4475 (mm-30) REVERT: D 24 ASP cc_start: 0.7183 (t0) cc_final: 0.6888 (t0) REVERT: D 59 ARG cc_start: 0.8041 (mpt180) cc_final: 0.7757 (mmt-90) REVERT: D 93 LYS cc_start: 0.8367 (tttt) cc_final: 0.7923 (tptp) REVERT: D 100 GLU cc_start: 0.8383 (mp0) cc_final: 0.8074 (mp0) REVERT: E 25 MET cc_start: 0.7631 (ttm) cc_final: 0.6593 (tmm) REVERT: E 72 LYS cc_start: 0.8892 (tttt) cc_final: 0.8359 (tptp) REVERT: E 79 LYS cc_start: 0.9119 (mmtm) cc_final: 0.8804 (mmpt) REVERT: E 93 LYS cc_start: 0.7773 (mmtt) cc_final: 0.7494 (mmtm) REVERT: F 18 ASP cc_start: 0.7710 (p0) cc_final: 0.7444 (m-30) REVERT: F 20 GLU cc_start: 0.8071 (mp0) cc_final: 0.7783 (mp0) REVERT: F 21 VAL cc_start: 0.8984 (m) cc_final: 0.8751 (p) REVERT: F 38 ARG cc_start: 0.8247 (tpt90) cc_final: 0.7678 (tpt90) REVERT: G 26 ARG cc_start: 0.6333 (mtt90) cc_final: 0.5976 (mtt90) REVERT: G 32 ARG cc_start: 0.7652 (ttt90) cc_final: 0.6969 (ttt90) REVERT: G 38 ARG cc_start: 0.8270 (tpt90) cc_final: 0.7673 (tpt90) REVERT: G 93 LYS cc_start: 0.8201 (tttt) cc_final: 0.7868 (tttp) REVERT: H 18 ASP cc_start: 0.8095 (p0) cc_final: 0.7443 (p0) REVERT: H 24 ASP cc_start: 0.7317 (t0) cc_final: 0.6998 (t0) REVERT: H 95 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8081 (mp10) REVERT: I 25 MET cc_start: 0.7038 (ttm) cc_final: 0.6001 (tmm) REVERT: I 61 GLU cc_start: 0.7003 (mp0) cc_final: 0.6776 (mp0) REVERT: I 79 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8030 (mmmt) REVERT: I 93 LYS cc_start: 0.7545 (tttt) cc_final: 0.6797 (mmtm) REVERT: I 95 GLN cc_start: 0.8746 (mm110) cc_final: 0.8383 (mm110) REVERT: I 109 SER cc_start: 0.8812 (t) cc_final: 0.8338 (t) REVERT: J 20 GLU cc_start: 0.8193 (mp0) cc_final: 0.7954 (mp0) REVERT: J 25 MET cc_start: 0.7688 (ttm) cc_final: 0.7013 (tmm) REVERT: J 38 ARG cc_start: 0.8149 (tpt90) cc_final: 0.7608 (tpt90) REVERT: J 72 LYS cc_start: 0.8518 (tttt) cc_final: 0.8102 (ttmm) REVERT: J 93 LYS cc_start: 0.7754 (tttt) cc_final: 0.6926 (mtpp) REVERT: K 59 ARG cc_start: 0.7412 (mmt-90) cc_final: 0.6920 (mmt180) REVERT: K 72 LYS cc_start: 0.8496 (tttt) cc_final: 0.7866 (tmtt) REVERT: K 74 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6474 (mp0) REVERT: K 78 GLU cc_start: 0.7452 (tp30) cc_final: 0.6674 (tm-30) REVERT: K 95 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7419 (tp-100) REVERT: L 18 ASP cc_start: 0.7481 (p0) cc_final: 0.6518 (p0) REVERT: L 78 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7899 (tm-30) REVERT: L 93 LYS cc_start: 0.7981 (tttt) cc_final: 0.7442 (mtpp) REVERT: M 18 ASP cc_start: 0.7476 (p0) cc_final: 0.6484 (p0) REVERT: M 38 ARG cc_start: 0.8109 (tpt90) cc_final: 0.7534 (tpt90) REVERT: M 93 LYS cc_start: 0.7744 (tttt) cc_final: 0.7012 (mtpp) REVERT: N 24 ASP cc_start: 0.7521 (m-30) cc_final: 0.6890 (t0) REVERT: N 25 MET cc_start: 0.7707 (ttm) cc_final: 0.7468 (ttm) REVERT: N 72 LYS cc_start: 0.8595 (tttt) cc_final: 0.7933 (mtmm) REVERT: N 78 GLU cc_start: 0.7682 (tp30) cc_final: 0.6780 (tm-30) REVERT: N 93 LYS cc_start: 0.7872 (tttt) cc_final: 0.7557 (mtpt) REVERT: N 95 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7620 (tp-100) REVERT: O 38 ARG cc_start: 0.8137 (tpt90) cc_final: 0.7710 (tpt90) REVERT: O 63 ARG cc_start: 0.6987 (mpt180) cc_final: 0.6677 (mmt-90) REVERT: O 72 LYS cc_start: 0.8320 (tttt) cc_final: 0.7845 (ttmm) REVERT: O 93 LYS cc_start: 0.7485 (tttt) cc_final: 0.6762 (mtpp) REVERT: P 32 ARG cc_start: 0.7763 (ttt90) cc_final: 0.6730 (ttt-90) REVERT: P 48 GLU cc_start: 0.7122 (tt0) cc_final: 0.6641 (tm-30) REVERT: P 79 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8109 (mmmt) REVERT: P 93 LYS cc_start: 0.7835 (tttt) cc_final: 0.6992 (mmtm) REVERT: Q 18 ASP cc_start: 0.7922 (p0) cc_final: 0.7296 (p0) REVERT: Q 95 GLN cc_start: 0.8221 (mm110) cc_final: 0.7976 (mm110) REVERT: Q 100 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7503 (mm-30) REVERT: R 26 ARG cc_start: 0.6585 (mtt90) cc_final: 0.6278 (mtt90) REVERT: R 38 ARG cc_start: 0.8039 (tpt90) cc_final: 0.7587 (tpt90) REVERT: R 93 LYS cc_start: 0.8322 (tttt) cc_final: 0.7977 (tttp) REVERT: S 38 ARG cc_start: 0.8267 (tpt90) cc_final: 0.7785 (tpt90) REVERT: S 59 ARG cc_start: 0.7481 (mmt-90) cc_final: 0.7192 (mmm-85) REVERT: S 72 LYS cc_start: 0.8396 (tptt) cc_final: 0.7822 (tppt) REVERT: S 79 LYS cc_start: 0.8226 (tptp) cc_final: 0.7994 (mmtm) REVERT: S 93 LYS cc_start: 0.8144 (tttt) cc_final: 0.7643 (tptp) REVERT: T 25 MET cc_start: 0.7852 (ttm) cc_final: 0.6600 (tmm) REVERT: T 72 LYS cc_start: 0.8570 (tmtt) cc_final: 0.7983 (tptp) REVERT: T 79 LYS cc_start: 0.9146 (mmtm) cc_final: 0.8744 (mmpt) REVERT: T 93 LYS cc_start: 0.8017 (mmtt) cc_final: 0.7473 (mmtm) REVERT: U 18 ASP cc_start: 0.7205 (p0) cc_final: 0.6722 (p0) REVERT: U 78 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7701 (tm-30) REVERT: U 93 LYS cc_start: 0.8402 (tttt) cc_final: 0.7941 (tptp) REVERT: V 24 ASP cc_start: 0.7706 (m-30) cc_final: 0.6633 (t0) REVERT: V 32 ARG cc_start: 0.7267 (tmt-80) cc_final: 0.6664 (tpt90) REVERT: V 38 ARG cc_start: 0.6171 (tmm160) cc_final: 0.5847 (tmm160) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.4880 time to fit residues: 195.5697 Evaluate side-chains 266 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.8980 chunk 191 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16478 Z= 0.275 Angle : 0.695 7.598 22198 Z= 0.353 Chirality : 0.051 0.164 2684 Planarity : 0.003 0.038 2904 Dihedral : 5.925 22.650 2376 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: -5.47 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.65 (0.13), residues: 1232 loop : -3.33 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 68 PHE 0.011 0.002 PHE H 105 TYR 0.012 0.002 TYR O 14 ARG 0.005 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8061 (tmtt) cc_final: 0.7601 (tmtt) REVERT: A 91 GLN cc_start: 0.7077 (mp10) cc_final: 0.6233 (tm-30) REVERT: B 72 LYS cc_start: 0.8077 (tmtt) cc_final: 0.7619 (tmtt) REVERT: B 91 GLN cc_start: 0.7118 (mp10) cc_final: 0.6463 (tm-30) REVERT: C 24 ASP cc_start: 0.7794 (m-30) cc_final: 0.6716 (t0) REVERT: C 38 ARG cc_start: 0.6343 (tmm160) cc_final: 0.5892 (tmm160) REVERT: C 78 GLU cc_start: 0.4921 (pt0) cc_final: 0.4604 (mm-30) REVERT: D 24 ASP cc_start: 0.7087 (t0) cc_final: 0.6805 (t0) REVERT: D 59 ARG cc_start: 0.8015 (mpt180) cc_final: 0.7760 (mmt-90) REVERT: D 93 LYS cc_start: 0.8315 (tttt) cc_final: 0.7894 (tptp) REVERT: D 100 GLU cc_start: 0.8461 (mp0) cc_final: 0.8058 (mp0) REVERT: E 25 MET cc_start: 0.7167 (ttm) cc_final: 0.6542 (tmm) REVERT: E 38 ARG cc_start: 0.7630 (tpm170) cc_final: 0.7429 (tpm170) REVERT: E 72 LYS cc_start: 0.8900 (tttt) cc_final: 0.8456 (tptp) REVERT: E 74 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7842 (mt-10) REVERT: E 79 LYS cc_start: 0.9087 (mmtm) cc_final: 0.8748 (mmpt) REVERT: E 93 LYS cc_start: 0.7765 (mmtt) cc_final: 0.7563 (mmtm) REVERT: F 20 GLU cc_start: 0.8105 (mp0) cc_final: 0.7905 (mp0) REVERT: F 21 VAL cc_start: 0.8971 (m) cc_final: 0.8745 (p) REVERT: F 38 ARG cc_start: 0.8193 (tpt90) cc_final: 0.7647 (tpt90) REVERT: F 46 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7399 (tm-30) REVERT: F 70 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7218 (mp0) REVERT: G 26 ARG cc_start: 0.6387 (mtt90) cc_final: 0.6058 (mtt90) REVERT: G 32 ARG cc_start: 0.7585 (ttt90) cc_final: 0.7106 (ttt90) REVERT: G 38 ARG cc_start: 0.8214 (tpt90) cc_final: 0.7596 (tpt90) REVERT: G 66 LEU cc_start: 0.8229 (mm) cc_final: 0.7670 (tp) REVERT: G 84 LYS cc_start: 0.7985 (tptp) cc_final: 0.7505 (pptt) REVERT: G 93 LYS cc_start: 0.8264 (tttt) cc_final: 0.7852 (tttp) REVERT: H 18 ASP cc_start: 0.8188 (p0) cc_final: 0.7545 (p0) REVERT: H 24 ASP cc_start: 0.7303 (t0) cc_final: 0.6979 (t0) REVERT: H 95 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8134 (mp10) REVERT: I 25 MET cc_start: 0.7039 (ttm) cc_final: 0.5973 (tmm) REVERT: I 79 LYS cc_start: 0.8510 (mmtt) cc_final: 0.7986 (mmmt) REVERT: I 93 LYS cc_start: 0.7736 (tttt) cc_final: 0.6945 (mmtm) REVERT: I 95 GLN cc_start: 0.8793 (mm110) cc_final: 0.8408 (mm110) REVERT: J 20 GLU cc_start: 0.8254 (mp0) cc_final: 0.7966 (mp0) REVERT: J 25 MET cc_start: 0.7623 (ttm) cc_final: 0.6951 (tmm) REVERT: J 38 ARG cc_start: 0.7988 (tpt90) cc_final: 0.7618 (tpt90) REVERT: J 72 LYS cc_start: 0.8473 (tttt) cc_final: 0.7980 (ttmm) REVERT: J 93 LYS cc_start: 0.7603 (tttt) cc_final: 0.6774 (mtpp) REVERT: K 59 ARG cc_start: 0.7383 (mmt-90) cc_final: 0.6965 (mmm-85) REVERT: K 72 LYS cc_start: 0.8414 (tttt) cc_final: 0.7710 (mtmm) REVERT: K 95 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7140 (tp-100) REVERT: L 18 ASP cc_start: 0.7477 (p0) cc_final: 0.6644 (p0) REVERT: L 78 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7811 (tm-30) REVERT: L 93 LYS cc_start: 0.7967 (tttt) cc_final: 0.7391 (mtpp) REVERT: M 18 ASP cc_start: 0.7461 (p0) cc_final: 0.6927 (p0) REVERT: M 78 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7571 (tp30) REVERT: M 93 LYS cc_start: 0.7742 (tttt) cc_final: 0.7203 (mtpp) REVERT: N 58 GLU cc_start: 0.6689 (pt0) cc_final: 0.6387 (tm-30) REVERT: N 72 LYS cc_start: 0.8559 (tttt) cc_final: 0.7962 (mtmm) REVERT: N 78 GLU cc_start: 0.7642 (tp30) cc_final: 0.6745 (tm-30) REVERT: N 93 LYS cc_start: 0.7761 (tttt) cc_final: 0.7491 (mtpt) REVERT: N 95 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7443 (tp40) REVERT: O 38 ARG cc_start: 0.8039 (tpt90) cc_final: 0.7607 (tpt90) REVERT: O 72 LYS cc_start: 0.8256 (tttt) cc_final: 0.7806 (ttmm) REVERT: O 93 LYS cc_start: 0.7431 (tttt) cc_final: 0.6718 (mtpp) REVERT: P 32 ARG cc_start: 0.7755 (ttt90) cc_final: 0.6823 (ttt-90) REVERT: P 48 GLU cc_start: 0.7081 (tt0) cc_final: 0.6549 (tm-30) REVERT: P 79 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8029 (mmmt) REVERT: P 93 LYS cc_start: 0.7983 (tttt) cc_final: 0.7130 (mmtm) REVERT: P 95 GLN cc_start: 0.8725 (mm110) cc_final: 0.8410 (mm110) REVERT: P 109 SER cc_start: 0.8833 (t) cc_final: 0.8351 (t) REVERT: Q 18 ASP cc_start: 0.7901 (p0) cc_final: 0.7301 (p0) REVERT: R 26 ARG cc_start: 0.6595 (mtt90) cc_final: 0.6319 (mtt90) REVERT: R 28 LYS cc_start: 0.6457 (mmtm) cc_final: 0.6210 (mptt) REVERT: R 38 ARG cc_start: 0.8078 (tpt90) cc_final: 0.7600 (tpt90) REVERT: R 66 LEU cc_start: 0.8330 (mm) cc_final: 0.7787 (tp) REVERT: R 84 LYS cc_start: 0.7785 (tptp) cc_final: 0.7438 (pptt) REVERT: R 93 LYS cc_start: 0.8457 (tttt) cc_final: 0.7608 (mmtm) REVERT: S 18 ASP cc_start: 0.7089 (p0) cc_final: 0.6795 (p0) REVERT: S 26 ARG cc_start: 0.7523 (mtt180) cc_final: 0.6876 (ttm110) REVERT: S 38 ARG cc_start: 0.8192 (tpt90) cc_final: 0.7647 (tpt90) REVERT: S 59 ARG cc_start: 0.7521 (mmt-90) cc_final: 0.7198 (mmm-85) REVERT: S 72 LYS cc_start: 0.8439 (tptt) cc_final: 0.7811 (tppt) REVERT: S 79 LYS cc_start: 0.8339 (tptp) cc_final: 0.8077 (mmtm) REVERT: S 93 LYS cc_start: 0.8041 (tttt) cc_final: 0.7522 (tptp) REVERT: T 25 MET cc_start: 0.7986 (ttm) cc_final: 0.6639 (tmm) REVERT: T 28 LYS cc_start: 0.8337 (tptt) cc_final: 0.7906 (ttpt) REVERT: T 59 ARG cc_start: 0.8202 (mmt180) cc_final: 0.7907 (mtt-85) REVERT: T 72 LYS cc_start: 0.8619 (tmtt) cc_final: 0.8025 (tptp) REVERT: T 78 GLU cc_start: 0.8275 (tp30) cc_final: 0.7350 (tp30) REVERT: T 79 LYS cc_start: 0.9141 (mmtm) cc_final: 0.8744 (mmpt) REVERT: T 93 LYS cc_start: 0.7969 (mptt) cc_final: 0.7704 (mmtm) REVERT: U 18 ASP cc_start: 0.7207 (p0) cc_final: 0.6760 (p0) REVERT: U 93 LYS cc_start: 0.8340 (tttt) cc_final: 0.7858 (tptp) REVERT: V 24 ASP cc_start: 0.7854 (m-30) cc_final: 0.6693 (t0) REVERT: V 38 ARG cc_start: 0.6305 (tmm160) cc_final: 0.5966 (tmm160) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.4629 time to fit residues: 196.1847 Evaluate side-chains 273 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 chunk 121 optimal weight: 0.2980 chunk 155 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.6508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16478 Z= 0.370 Angle : 0.752 7.600 22198 Z= 0.393 Chirality : 0.052 0.162 2684 Planarity : 0.004 0.036 2904 Dihedral : 6.419 23.401 2376 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 23.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.86 % Favored : 82.14 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: -5.70 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.84 (0.13), residues: 1232 loop : -3.44 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS J 68 PHE 0.016 0.002 PHE H 105 TYR 0.019 0.002 TYR O 14 ARG 0.005 0.001 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8079 (tmtt) cc_final: 0.7613 (tmtt) REVERT: B 72 LYS cc_start: 0.8114 (tmtt) cc_final: 0.7642 (tmtt) REVERT: C 24 ASP cc_start: 0.7870 (m-30) cc_final: 0.6760 (t0) REVERT: C 38 ARG cc_start: 0.6360 (tmm160) cc_final: 0.5921 (tmm160) REVERT: C 78 GLU cc_start: 0.4738 (pt0) cc_final: 0.4476 (mm-30) REVERT: D 24 ASP cc_start: 0.7124 (t0) cc_final: 0.6798 (t0) REVERT: D 93 LYS cc_start: 0.8407 (tttt) cc_final: 0.7947 (tptp) REVERT: D 100 GLU cc_start: 0.8346 (mp0) cc_final: 0.7854 (mp0) REVERT: E 25 MET cc_start: 0.7529 (ttm) cc_final: 0.6545 (tmm) REVERT: E 72 LYS cc_start: 0.8881 (tttt) cc_final: 0.8373 (tptp) REVERT: E 78 GLU cc_start: 0.8376 (tp30) cc_final: 0.7638 (tp30) REVERT: E 79 LYS cc_start: 0.9089 (mmtm) cc_final: 0.8615 (mmpt) REVERT: F 20 GLU cc_start: 0.8285 (mp0) cc_final: 0.8010 (mp0) REVERT: F 26 ARG cc_start: 0.7297 (mtt180) cc_final: 0.6814 (ttm110) REVERT: F 38 ARG cc_start: 0.8240 (tpt90) cc_final: 0.7724 (tpt90) REVERT: G 32 ARG cc_start: 0.7517 (ttt90) cc_final: 0.6986 (ttt90) REVERT: G 38 ARG cc_start: 0.8221 (tpt90) cc_final: 0.7615 (tpt90) REVERT: G 93 LYS cc_start: 0.8229 (tttt) cc_final: 0.7877 (tttp) REVERT: H 18 ASP cc_start: 0.8207 (p0) cc_final: 0.7659 (p0) REVERT: H 24 ASP cc_start: 0.7314 (t0) cc_final: 0.6958 (t0) REVERT: H 95 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8075 (mp10) REVERT: I 25 MET cc_start: 0.7119 (ttm) cc_final: 0.6029 (tmm) REVERT: I 61 GLU cc_start: 0.7017 (mp0) cc_final: 0.6799 (mp0) REVERT: I 79 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8300 (mmmt) REVERT: I 93 LYS cc_start: 0.7627 (tttt) cc_final: 0.6871 (mmtm) REVERT: I 95 GLN cc_start: 0.8756 (mm110) cc_final: 0.8399 (mm110) REVERT: J 20 GLU cc_start: 0.8429 (mp0) cc_final: 0.8024 (mp0) REVERT: J 38 ARG cc_start: 0.8083 (tpt90) cc_final: 0.7709 (tpt90) REVERT: J 72 LYS cc_start: 0.8556 (tttt) cc_final: 0.8070 (ttmm) REVERT: J 78 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7246 (tm-30) REVERT: J 93 LYS cc_start: 0.7696 (tttt) cc_final: 0.6880 (mtpp) REVERT: K 59 ARG cc_start: 0.7531 (mmt-90) cc_final: 0.6908 (mmt90) REVERT: K 72 LYS cc_start: 0.8514 (tttt) cc_final: 0.7921 (tmtt) REVERT: K 78 GLU cc_start: 0.7428 (tp30) cc_final: 0.6723 (tm-30) REVERT: K 95 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7394 (tp-100) REVERT: L 18 ASP cc_start: 0.7432 (p0) cc_final: 0.6704 (p0) REVERT: L 78 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7924 (tm-30) REVERT: L 93 LYS cc_start: 0.8006 (tttt) cc_final: 0.7437 (mtpp) REVERT: M 18 ASP cc_start: 0.7436 (p0) cc_final: 0.6918 (p0) REVERT: M 38 ARG cc_start: 0.8195 (tpt90) cc_final: 0.7428 (tpt90) REVERT: M 93 LYS cc_start: 0.7788 (tttt) cc_final: 0.7236 (mtpp) REVERT: N 58 GLU cc_start: 0.6781 (pt0) cc_final: 0.6463 (tm-30) REVERT: N 72 LYS cc_start: 0.8588 (tttt) cc_final: 0.7962 (mtmm) REVERT: N 78 GLU cc_start: 0.7375 (tp30) cc_final: 0.6682 (tm-30) REVERT: N 93 LYS cc_start: 0.7811 (tttt) cc_final: 0.7518 (mtpt) REVERT: N 95 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7600 (tp-100) REVERT: O 38 ARG cc_start: 0.8137 (tpt90) cc_final: 0.7695 (tpt90) REVERT: O 72 LYS cc_start: 0.8357 (tttt) cc_final: 0.7851 (ttmm) REVERT: O 78 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7100 (tm-30) REVERT: O 93 LYS cc_start: 0.7482 (tttt) cc_final: 0.6737 (mtpp) REVERT: P 32 ARG cc_start: 0.7771 (ttt90) cc_final: 0.6919 (ttt-90) REVERT: P 48 GLU cc_start: 0.6967 (tt0) cc_final: 0.6381 (tm-30) REVERT: P 79 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8174 (mmmt) REVERT: P 93 LYS cc_start: 0.7987 (tttt) cc_final: 0.7117 (mmtm) REVERT: P 95 GLN cc_start: 0.8767 (mm110) cc_final: 0.8472 (mm110) REVERT: Q 18 ASP cc_start: 0.8040 (p0) cc_final: 0.7362 (p0) REVERT: R 28 LYS cc_start: 0.6625 (mmtm) cc_final: 0.6294 (mptt) REVERT: R 38 ARG cc_start: 0.8086 (tpt90) cc_final: 0.7598 (tpt90) REVERT: R 84 LYS cc_start: 0.7933 (tptp) cc_final: 0.7496 (pptt) REVERT: R 93 LYS cc_start: 0.8417 (tttt) cc_final: 0.8054 (tttp) REVERT: S 26 ARG cc_start: 0.7256 (mtt180) cc_final: 0.6727 (ttm110) REVERT: S 38 ARG cc_start: 0.8216 (tpt90) cc_final: 0.7677 (tpt90) REVERT: S 59 ARG cc_start: 0.7466 (mmt-90) cc_final: 0.7139 (mmm-85) REVERT: S 72 LYS cc_start: 0.8475 (tptt) cc_final: 0.7848 (tppt) REVERT: S 93 LYS cc_start: 0.8053 (tttt) cc_final: 0.7537 (tptp) REVERT: T 25 MET cc_start: 0.8014 (ttm) cc_final: 0.6592 (tmm) REVERT: T 28 LYS cc_start: 0.8448 (tptt) cc_final: 0.7873 (tmmt) REVERT: T 72 LYS cc_start: 0.8589 (tmtt) cc_final: 0.8043 (tptp) REVERT: T 79 LYS cc_start: 0.9174 (mmtm) cc_final: 0.8775 (mmpt) REVERT: U 18 ASP cc_start: 0.7380 (p0) cc_final: 0.6781 (p0) REVERT: U 93 LYS cc_start: 0.8442 (tttt) cc_final: 0.7913 (tptp) REVERT: V 24 ASP cc_start: 0.7691 (m-30) cc_final: 0.6569 (t0) REVERT: V 28 LYS cc_start: 0.6483 (mmmm) cc_final: 0.5770 (mmmm) REVERT: V 32 ARG cc_start: 0.7437 (tmt-80) cc_final: 0.6924 (tpt90) REVERT: V 38 ARG cc_start: 0.6254 (tmm160) cc_final: 0.5910 (tmm160) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.4798 time to fit residues: 196.7714 Evaluate side-chains 279 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 6.9990 chunk 84 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 192 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16478 Z= 0.154 Angle : 0.670 7.997 22198 Z= 0.323 Chirality : 0.051 0.161 2684 Planarity : 0.002 0.031 2904 Dihedral : 4.984 20.545 2376 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: -5.25 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.48 (0.14), residues: 1232 loop : -3.24 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 68 PHE 0.009 0.001 PHE B 88 TYR 0.004 0.001 TYR E 14 ARG 0.003 0.000 ARG C 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7681 (tmtt) REVERT: A 91 GLN cc_start: 0.6857 (mp10) cc_final: 0.6007 (tm-30) REVERT: B 72 LYS cc_start: 0.8050 (tmtt) cc_final: 0.7611 (tmtt) REVERT: B 91 GLN cc_start: 0.7106 (mp10) cc_final: 0.6274 (tm-30) REVERT: C 24 ASP cc_start: 0.7747 (m-30) cc_final: 0.6617 (t0) REVERT: C 32 ARG cc_start: 0.7243 (tpt90) cc_final: 0.6858 (tpt90) REVERT: C 38 ARG cc_start: 0.6464 (tmm160) cc_final: 0.6210 (tmm160) REVERT: C 78 GLU cc_start: 0.5118 (pt0) cc_final: 0.4755 (mm-30) REVERT: D 24 ASP cc_start: 0.6966 (t0) cc_final: 0.6653 (t0) REVERT: D 93 LYS cc_start: 0.8261 (tttt) cc_final: 0.7790 (mptt) REVERT: D 100 GLU cc_start: 0.8285 (mp0) cc_final: 0.7868 (mp0) REVERT: E 25 MET cc_start: 0.6922 (ttm) cc_final: 0.6318 (tmm) REVERT: E 72 LYS cc_start: 0.8862 (tttt) cc_final: 0.8380 (tptp) REVERT: E 78 GLU cc_start: 0.8237 (tp30) cc_final: 0.7364 (tp30) REVERT: E 79 LYS cc_start: 0.8965 (mmtm) cc_final: 0.8602 (mmpt) REVERT: F 20 GLU cc_start: 0.8251 (mp0) cc_final: 0.8033 (mp0) REVERT: F 26 ARG cc_start: 0.7453 (mtt180) cc_final: 0.6763 (ttm110) REVERT: F 38 ARG cc_start: 0.8113 (tpt90) cc_final: 0.7535 (tpt90) REVERT: G 32 ARG cc_start: 0.7624 (ttt90) cc_final: 0.7401 (ttt90) REVERT: G 38 ARG cc_start: 0.8056 (tpt90) cc_final: 0.7571 (tpt90) REVERT: G 66 LEU cc_start: 0.8121 (mm) cc_final: 0.7785 (mp) REVERT: G 84 LYS cc_start: 0.7837 (tptp) cc_final: 0.7427 (pptt) REVERT: G 93 LYS cc_start: 0.8286 (tttt) cc_final: 0.7901 (tttp) REVERT: H 18 ASP cc_start: 0.8113 (p0) cc_final: 0.7606 (p0) REVERT: H 24 ASP cc_start: 0.7268 (t0) cc_final: 0.6906 (t0) REVERT: H 91 GLN cc_start: 0.7028 (mp10) cc_final: 0.6722 (mp10) REVERT: I 79 LYS cc_start: 0.8450 (mmtt) cc_final: 0.8031 (mmmt) REVERT: I 93 LYS cc_start: 0.7663 (tttt) cc_final: 0.6924 (mmtm) REVERT: I 95 GLN cc_start: 0.8722 (mm110) cc_final: 0.8506 (mm110) REVERT: J 38 ARG cc_start: 0.7847 (tpt90) cc_final: 0.7411 (tpt90) REVERT: J 72 LYS cc_start: 0.8393 (tttt) cc_final: 0.7854 (mptt) REVERT: J 93 LYS cc_start: 0.7428 (tttt) cc_final: 0.6679 (mtpp) REVERT: K 24 ASP cc_start: 0.8114 (t0) cc_final: 0.7743 (m-30) REVERT: K 58 GLU cc_start: 0.6593 (pt0) cc_final: 0.5547 (pm20) REVERT: K 59 ARG cc_start: 0.7572 (mmt-90) cc_final: 0.7017 (mmm-85) REVERT: K 72 LYS cc_start: 0.8334 (tttt) cc_final: 0.7880 (mptt) REVERT: K 78 GLU cc_start: 0.7377 (tp30) cc_final: 0.6453 (tm-30) REVERT: K 95 GLN cc_start: 0.8078 (mm-40) cc_final: 0.6887 (tp40) REVERT: L 18 ASP cc_start: 0.7749 (p0) cc_final: 0.6953 (p0) REVERT: L 100 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7263 (mt-10) REVERT: M 18 ASP cc_start: 0.7573 (p0) cc_final: 0.7314 (p0) REVERT: M 25 MET cc_start: 0.6555 (ttt) cc_final: 0.6046 (mtp) REVERT: M 78 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7781 (mm-30) REVERT: N 72 LYS cc_start: 0.8338 (tttt) cc_final: 0.8003 (mptt) REVERT: N 78 GLU cc_start: 0.7482 (tp30) cc_final: 0.6523 (tm-30) REVERT: N 93 LYS cc_start: 0.7806 (tttt) cc_final: 0.7503 (mtpt) REVERT: N 95 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7037 (tp40) REVERT: O 38 ARG cc_start: 0.7907 (tpt90) cc_final: 0.7418 (tpt90) REVERT: O 72 LYS cc_start: 0.8273 (tttt) cc_final: 0.7684 (mptt) REVERT: O 93 LYS cc_start: 0.7278 (tttt) cc_final: 0.6605 (mtpp) REVERT: P 48 GLU cc_start: 0.6964 (tt0) cc_final: 0.6719 (tm-30) REVERT: P 79 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8077 (mmmt) REVERT: P 93 LYS cc_start: 0.7915 (tttt) cc_final: 0.7142 (mmtm) REVERT: Q 18 ASP cc_start: 0.7796 (p0) cc_final: 0.7380 (p0) REVERT: Q 72 LYS cc_start: 0.8139 (mppt) cc_final: 0.7774 (mppt) REVERT: R 28 LYS cc_start: 0.6530 (mmtm) cc_final: 0.6228 (mptt) REVERT: R 38 ARG cc_start: 0.7951 (tpt90) cc_final: 0.7394 (tpt90) REVERT: R 84 LYS cc_start: 0.7874 (tptp) cc_final: 0.7440 (pptt) REVERT: R 93 LYS cc_start: 0.8501 (tttt) cc_final: 0.8088 (tttp) REVERT: S 38 ARG cc_start: 0.8151 (tpt90) cc_final: 0.7557 (tpt90) REVERT: S 59 ARG cc_start: 0.7527 (mmt-90) cc_final: 0.7197 (mmm-85) REVERT: S 63 ARG cc_start: 0.7945 (mmt90) cc_final: 0.7587 (mpt180) REVERT: S 72 LYS cc_start: 0.8506 (tptt) cc_final: 0.7779 (tppt) REVERT: S 93 LYS cc_start: 0.7978 (tttt) cc_final: 0.7444 (tptp) REVERT: T 20 GLU cc_start: 0.8326 (mp0) cc_final: 0.8023 (mp0) REVERT: T 25 MET cc_start: 0.7871 (ttm) cc_final: 0.6575 (tmm) REVERT: T 59 ARG cc_start: 0.8369 (mtt-85) cc_final: 0.7831 (tpp-160) REVERT: T 72 LYS cc_start: 0.8581 (tmtt) cc_final: 0.8025 (tptp) REVERT: T 79 LYS cc_start: 0.9080 (mmtm) cc_final: 0.8754 (mmmt) REVERT: U 18 ASP cc_start: 0.7288 (p0) cc_final: 0.6971 (p0) REVERT: U 78 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7690 (tt0) REVERT: U 93 LYS cc_start: 0.8315 (tttt) cc_final: 0.7803 (mptt) REVERT: V 28 LYS cc_start: 0.6661 (mmmm) cc_final: 0.6169 (mmmm) REVERT: V 32 ARG cc_start: 0.7353 (tmt-80) cc_final: 0.6775 (tpt90) REVERT: V 38 ARG cc_start: 0.6477 (tmm160) cc_final: 0.6263 (tmm160) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.4864 time to fit residues: 213.3768 Evaluate side-chains 284 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 129 optimal weight: 0.4980 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.6843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16478 Z= 0.421 Angle : 0.805 8.261 22198 Z= 0.421 Chirality : 0.052 0.163 2684 Planarity : 0.005 0.051 2904 Dihedral : 6.370 23.849 2376 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.06 % Favored : 79.94 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -5.76 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.92 (0.12), residues: 1364 loop : -3.12 (0.18), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS J 68 PHE 0.019 0.003 PHE H 105 TYR 0.023 0.002 TYR J 14 ARG 0.007 0.001 ARG H 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8093 (tmtt) cc_final: 0.7638 (tmtt) REVERT: B 72 LYS cc_start: 0.8120 (tmtt) cc_final: 0.7659 (tmtt) REVERT: C 24 ASP cc_start: 0.7907 (m-30) cc_final: 0.6738 (t0) REVERT: C 38 ARG cc_start: 0.6280 (tmm160) cc_final: 0.6078 (tmm160) REVERT: D 24 ASP cc_start: 0.7073 (t0) cc_final: 0.6745 (t0) REVERT: D 32 ARG cc_start: 0.7898 (ttt-90) cc_final: 0.7688 (ttt90) REVERT: D 93 LYS cc_start: 0.8401 (tttt) cc_final: 0.7971 (tptp) REVERT: D 100 GLU cc_start: 0.8139 (mp0) cc_final: 0.7670 (mp0) REVERT: E 25 MET cc_start: 0.7804 (ttm) cc_final: 0.6531 (tmm) REVERT: E 26 ARG cc_start: 0.7315 (tpt170) cc_final: 0.6603 (ptp90) REVERT: E 66 LEU cc_start: 0.8836 (tp) cc_final: 0.8623 (tp) REVERT: E 72 LYS cc_start: 0.8837 (tttt) cc_final: 0.8350 (tptp) REVERT: E 78 GLU cc_start: 0.8393 (tp30) cc_final: 0.7697 (tp30) REVERT: E 79 LYS cc_start: 0.9103 (mmtm) cc_final: 0.8647 (mmpt) REVERT: F 20 GLU cc_start: 0.8290 (mp0) cc_final: 0.7826 (mp0) REVERT: F 26 ARG cc_start: 0.7423 (mtt180) cc_final: 0.6895 (ttm110) REVERT: F 38 ARG cc_start: 0.8245 (tpt90) cc_final: 0.7722 (tpt90) REVERT: G 32 ARG cc_start: 0.7586 (ttt90) cc_final: 0.6996 (ttt90) REVERT: G 38 ARG cc_start: 0.8233 (tpt90) cc_final: 0.7619 (tpt90) REVERT: G 66 LEU cc_start: 0.8384 (mm) cc_final: 0.8059 (mp) REVERT: G 93 LYS cc_start: 0.8216 (tttt) cc_final: 0.7891 (tttp) REVERT: H 18 ASP cc_start: 0.8427 (p0) cc_final: 0.8020 (p0) REVERT: H 24 ASP cc_start: 0.7401 (t0) cc_final: 0.6995 (t0) REVERT: I 79 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8085 (mmmt) REVERT: I 93 LYS cc_start: 0.7723 (tttt) cc_final: 0.7408 (tttp) REVERT: I 95 GLN cc_start: 0.8706 (mm110) cc_final: 0.8339 (mm110) REVERT: J 38 ARG cc_start: 0.8110 (tpt90) cc_final: 0.7714 (tpt90) REVERT: J 44 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7907 (mt-10) REVERT: J 72 LYS cc_start: 0.8582 (tttt) cc_final: 0.8099 (ttmm) REVERT: J 78 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7276 (tm-30) REVERT: J 93 LYS cc_start: 0.7744 (tttt) cc_final: 0.6910 (mtpp) REVERT: K 58 GLU cc_start: 0.6025 (pt0) cc_final: 0.5246 (pm20) REVERT: K 59 ARG cc_start: 0.7581 (mmt-90) cc_final: 0.6869 (mmt90) REVERT: K 72 LYS cc_start: 0.8533 (tttt) cc_final: 0.7889 (tmtt) REVERT: K 78 GLU cc_start: 0.7402 (tp30) cc_final: 0.6545 (tm-30) REVERT: K 95 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7357 (tp-100) REVERT: L 18 ASP cc_start: 0.7685 (p0) cc_final: 0.7037 (p0) REVERT: L 93 LYS cc_start: 0.8056 (tttt) cc_final: 0.7037 (mmtm) REVERT: M 18 ASP cc_start: 0.7469 (p0) cc_final: 0.7063 (p0) REVERT: M 25 MET cc_start: 0.7142 (ttt) cc_final: 0.6275 (mtp) REVERT: M 78 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7773 (tm-30) REVERT: M 93 LYS cc_start: 0.7787 (tttt) cc_final: 0.7332 (mtpp) REVERT: N 72 LYS cc_start: 0.8601 (tttt) cc_final: 0.8067 (tmtt) REVERT: N 78 GLU cc_start: 0.7438 (tp30) cc_final: 0.6647 (tm-30) REVERT: N 93 LYS cc_start: 0.7965 (tttt) cc_final: 0.7594 (mtpt) REVERT: N 95 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7618 (tp-100) REVERT: O 38 ARG cc_start: 0.8152 (tpt90) cc_final: 0.7705 (tpt90) REVERT: O 44 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8011 (mt-10) REVERT: O 72 LYS cc_start: 0.8354 (tttt) cc_final: 0.7849 (ttmm) REVERT: O 78 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7100 (tm-30) REVERT: O 93 LYS cc_start: 0.7495 (tttt) cc_final: 0.6740 (mtpp) REVERT: P 48 GLU cc_start: 0.6994 (tt0) cc_final: 0.6617 (tm-30) REVERT: P 79 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8161 (mmmt) REVERT: P 93 LYS cc_start: 0.8020 (tttt) cc_final: 0.7681 (tttp) REVERT: Q 18 ASP cc_start: 0.8077 (p0) cc_final: 0.7416 (p0) REVERT: R 28 LYS cc_start: 0.6736 (mmtm) cc_final: 0.6417 (mptt) REVERT: R 38 ARG cc_start: 0.8151 (tpt90) cc_final: 0.7668 (tpt90) REVERT: R 84 LYS cc_start: 0.8000 (tptp) cc_final: 0.7540 (pptt) REVERT: R 93 LYS cc_start: 0.8450 (tttt) cc_final: 0.8061 (tttp) REVERT: S 26 ARG cc_start: 0.7289 (mtt180) cc_final: 0.6751 (ttm110) REVERT: S 38 ARG cc_start: 0.8250 (tpt90) cc_final: 0.7673 (tpt90) REVERT: S 59 ARG cc_start: 0.7453 (mmt-90) cc_final: 0.7165 (mmm-85) REVERT: S 72 LYS cc_start: 0.8512 (tptt) cc_final: 0.7840 (tppt) REVERT: S 79 LYS cc_start: 0.8374 (mmtm) cc_final: 0.8149 (mmtm) REVERT: S 93 LYS cc_start: 0.8025 (tttt) cc_final: 0.7511 (tptp) REVERT: T 24 ASP cc_start: 0.8065 (t70) cc_final: 0.7864 (t0) REVERT: T 25 MET cc_start: 0.7969 (ttm) cc_final: 0.6486 (tmm) REVERT: T 26 ARG cc_start: 0.7408 (tpt170) cc_final: 0.6788 (ptp90) REVERT: T 28 LYS cc_start: 0.8505 (tptt) cc_final: 0.7963 (ttpt) REVERT: T 72 LYS cc_start: 0.8527 (tmtt) cc_final: 0.7976 (tptp) REVERT: T 79 LYS cc_start: 0.9101 (mmtm) cc_final: 0.8706 (mmpt) REVERT: U 18 ASP cc_start: 0.7317 (p0) cc_final: 0.7029 (p0) REVERT: U 24 ASP cc_start: 0.7078 (m-30) cc_final: 0.6619 (t0) REVERT: U 93 LYS cc_start: 0.8505 (tttt) cc_final: 0.7972 (tptp) REVERT: U 100 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7949 (mt-10) REVERT: V 24 ASP cc_start: 0.7583 (m-30) cc_final: 0.6511 (t0) REVERT: V 28 LYS cc_start: 0.6500 (mmmm) cc_final: 0.5988 (mmmm) REVERT: V 32 ARG cc_start: 0.7394 (tmt-80) cc_final: 0.6825 (tpt90) REVERT: V 38 ARG cc_start: 0.6274 (tmm160) cc_final: 0.5701 (ttp80) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.4757 time to fit residues: 185.7676 Evaluate side-chains 263 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 219 optimal weight: 30.0000 chunk 201 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.6866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16478 Z= 0.263 Angle : 0.729 8.243 22198 Z= 0.366 Chirality : 0.051 0.162 2684 Planarity : 0.003 0.035 2904 Dihedral : 5.808 22.299 2376 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -5.55 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.76 (0.12), residues: 1342 loop : -3.09 (0.18), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 68 PHE 0.009 0.002 PHE T 105 TYR 0.012 0.001 TYR O 14 ARG 0.006 0.000 ARG P 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8017 (tmtt) cc_final: 0.7587 (tmtt) REVERT: A 91 GLN cc_start: 0.6881 (mp10) cc_final: 0.6446 (tm-30) REVERT: B 72 LYS cc_start: 0.8059 (tmtt) cc_final: 0.7589 (tmtt) REVERT: B 91 GLN cc_start: 0.7091 (mp10) cc_final: 0.6544 (tm-30) REVERT: C 24 ASP cc_start: 0.7887 (m-30) cc_final: 0.6700 (t0) REVERT: C 38 ARG cc_start: 0.6362 (tmm160) cc_final: 0.6142 (tmm160) REVERT: D 24 ASP cc_start: 0.7079 (t0) cc_final: 0.6722 (t0) REVERT: D 32 ARG cc_start: 0.7907 (ttt-90) cc_final: 0.7670 (ttt90) REVERT: D 78 GLU cc_start: 0.7980 (tt0) cc_final: 0.7708 (tm-30) REVERT: D 93 LYS cc_start: 0.8339 (tttt) cc_final: 0.7855 (mptt) REVERT: D 100 GLU cc_start: 0.8129 (mp0) cc_final: 0.7730 (mp0) REVERT: E 25 MET cc_start: 0.7651 (ttm) cc_final: 0.6488 (tmm) REVERT: E 26 ARG cc_start: 0.7261 (tpt170) cc_final: 0.6494 (ptp90) REVERT: E 66 LEU cc_start: 0.8787 (tp) cc_final: 0.8568 (tp) REVERT: E 72 LYS cc_start: 0.8829 (tttt) cc_final: 0.8335 (tptp) REVERT: E 78 GLU cc_start: 0.8325 (tp30) cc_final: 0.7558 (tp30) REVERT: E 79 LYS cc_start: 0.9078 (mmtm) cc_final: 0.8594 (mmpt) REVERT: E 93 LYS cc_start: 0.7675 (mptt) cc_final: 0.7394 (mmtm) REVERT: F 20 GLU cc_start: 0.8118 (mp0) cc_final: 0.7720 (mp0) REVERT: F 26 ARG cc_start: 0.7315 (mtt180) cc_final: 0.6831 (ttm110) REVERT: F 38 ARG cc_start: 0.8204 (tpt90) cc_final: 0.7666 (tpt90) REVERT: F 46 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7372 (tm-30) REVERT: G 32 ARG cc_start: 0.7609 (ttt90) cc_final: 0.6993 (ttt90) REVERT: G 38 ARG cc_start: 0.8123 (tpt90) cc_final: 0.7519 (tpt90) REVERT: G 66 LEU cc_start: 0.8245 (mm) cc_final: 0.7854 (mp) REVERT: G 79 LYS cc_start: 0.8725 (tmmt) cc_final: 0.8311 (tmmt) REVERT: G 84 LYS cc_start: 0.8267 (tptp) cc_final: 0.7863 (pptt) REVERT: G 85 THR cc_start: 0.6681 (t) cc_final: 0.5643 (t) REVERT: G 93 LYS cc_start: 0.8266 (tttt) cc_final: 0.7910 (tttp) REVERT: H 18 ASP cc_start: 0.8368 (p0) cc_final: 0.7857 (p0) REVERT: H 24 ASP cc_start: 0.7387 (t0) cc_final: 0.7026 (t0) REVERT: I 79 LYS cc_start: 0.8471 (mmtt) cc_final: 0.7922 (mmmt) REVERT: I 93 LYS cc_start: 0.7727 (tttt) cc_final: 0.6970 (mmtm) REVERT: I 95 GLN cc_start: 0.8752 (mm110) cc_final: 0.8417 (mm110) REVERT: J 38 ARG cc_start: 0.8036 (tpt90) cc_final: 0.7644 (tpt90) REVERT: J 44 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7835 (mt-10) REVERT: J 72 LYS cc_start: 0.8480 (tttt) cc_final: 0.7996 (ttmm) REVERT: J 78 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7256 (tm-30) REVERT: J 93 LYS cc_start: 0.7657 (tttt) cc_final: 0.6873 (mtpp) REVERT: K 58 GLU cc_start: 0.6020 (pt0) cc_final: 0.5380 (pm20) REVERT: K 59 ARG cc_start: 0.7423 (mmt-90) cc_final: 0.6886 (mmm-85) REVERT: K 72 LYS cc_start: 0.8408 (tttt) cc_final: 0.7796 (mtmm) REVERT: K 78 GLU cc_start: 0.7429 (tp30) cc_final: 0.6954 (tp30) REVERT: K 95 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7092 (tp-100) REVERT: L 18 ASP cc_start: 0.7767 (p0) cc_final: 0.7066 (p0) REVERT: M 18 ASP cc_start: 0.7504 (p0) cc_final: 0.7171 (p0) REVERT: M 25 MET cc_start: 0.6989 (ttt) cc_final: 0.6160 (mtp) REVERT: M 78 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7707 (tm-30) REVERT: M 93 LYS cc_start: 0.7690 (tttt) cc_final: 0.7233 (mtpp) REVERT: N 72 LYS cc_start: 0.8400 (tttt) cc_final: 0.7905 (mtmm) REVERT: N 78 GLU cc_start: 0.7482 (tp30) cc_final: 0.6538 (tm-30) REVERT: N 93 LYS cc_start: 0.7846 (tttt) cc_final: 0.7555 (mtpt) REVERT: N 95 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7308 (tp-100) REVERT: O 38 ARG cc_start: 0.8038 (tpt90) cc_final: 0.7592 (tpt90) REVERT: O 44 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7788 (mt-10) REVERT: O 72 LYS cc_start: 0.8277 (tttt) cc_final: 0.7778 (ttmm) REVERT: O 78 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7106 (tm-30) REVERT: O 93 LYS cc_start: 0.7433 (tttt) cc_final: 0.6726 (mtpp) REVERT: P 48 GLU cc_start: 0.7071 (tt0) cc_final: 0.6719 (tm-30) REVERT: P 79 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8291 (mmmt) REVERT: P 93 LYS cc_start: 0.7975 (tttt) cc_final: 0.7143 (mmtm) REVERT: Q 18 ASP cc_start: 0.8052 (p0) cc_final: 0.7392 (p0) REVERT: R 28 LYS cc_start: 0.6670 (mmtm) cc_final: 0.6315 (mptt) REVERT: R 38 ARG cc_start: 0.8098 (tpt90) cc_final: 0.7596 (tpt90) REVERT: R 84 LYS cc_start: 0.7899 (tptp) cc_final: 0.7442 (pptt) REVERT: R 93 LYS cc_start: 0.8454 (tttt) cc_final: 0.8060 (tttp) REVERT: S 26 ARG cc_start: 0.7503 (mtt180) cc_final: 0.6569 (ttm110) REVERT: S 38 ARG cc_start: 0.8181 (tpt90) cc_final: 0.7640 (tpt90) REVERT: S 59 ARG cc_start: 0.7452 (mmt-90) cc_final: 0.7203 (mmm-85) REVERT: S 72 LYS cc_start: 0.8479 (tptt) cc_final: 0.7792 (tppt) REVERT: S 79 LYS cc_start: 0.8275 (mmtm) cc_final: 0.8030 (mmtm) REVERT: S 93 LYS cc_start: 0.8016 (tttt) cc_final: 0.7545 (tptp) REVERT: T 20 GLU cc_start: 0.8501 (mp0) cc_final: 0.8149 (mp0) REVERT: T 25 MET cc_start: 0.7934 (ttm) cc_final: 0.6554 (tmm) REVERT: T 28 LYS cc_start: 0.8427 (tptt) cc_final: 0.8013 (ttpt) REVERT: T 59 ARG cc_start: 0.8331 (mtt-85) cc_final: 0.7823 (tpp-160) REVERT: T 72 LYS cc_start: 0.8557 (tmtt) cc_final: 0.8029 (tptp) REVERT: T 79 LYS cc_start: 0.9195 (mmtm) cc_final: 0.8899 (mmmt) REVERT: T 93 LYS cc_start: 0.7899 (mptt) cc_final: 0.7614 (mmtm) REVERT: U 18 ASP cc_start: 0.7257 (p0) cc_final: 0.7021 (p0) REVERT: U 24 ASP cc_start: 0.6824 (m-30) cc_final: 0.6457 (t0) REVERT: U 59 ARG cc_start: 0.7690 (mpt90) cc_final: 0.7142 (mmt-90) REVERT: U 93 LYS cc_start: 0.8519 (tttt) cc_final: 0.7968 (tptp) REVERT: V 28 LYS cc_start: 0.6546 (mmmm) cc_final: 0.6097 (mmmm) REVERT: V 32 ARG cc_start: 0.7337 (tmt-80) cc_final: 0.6737 (tpt90) REVERT: V 88 PHE cc_start: 0.4531 (t80) cc_final: 0.4307 (t80) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.4836 time to fit residues: 193.0862 Evaluate side-chains 275 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** 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 = 0.4847 r_free = 0.4847 target = 0.109319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.081426 restraints weight = 33073.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.082683 restraints weight = 24251.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.083719 restraints weight = 19118.622| |-----------------------------------------------------------------------------| r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.7122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16478 Z= 0.398 Angle : 0.809 8.228 22198 Z= 0.420 Chirality : 0.053 0.158 2684 Planarity : 0.005 0.037 2904 Dihedral : 6.473 23.611 2376 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.79 % Favored : 80.21 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -5.81 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -4.13 (0.12), residues: 1276 loop : -3.04 (0.17), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS O 68 PHE 0.018 0.002 PHE H 105 TYR 0.020 0.002 TYR J 14 ARG 0.006 0.001 ARG P 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4096.90 seconds wall clock time: 73 minutes 53.76 seconds (4433.76 seconds total)