Starting phenix.real_space_refine on Sun Feb 18 20:03:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mks_9137/02_2024/6mks_9137.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mks_9137/02_2024/6mks_9137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mks_9137/02_2024/6mks_9137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mks_9137/02_2024/6mks_9137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mks_9137/02_2024/6mks_9137.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mks_9137/02_2024/6mks_9137.pdb" } resolution = 3.4 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 217 5.16 5 C 14508 2.51 5 N 3906 2.21 5 O 4123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22754 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "B" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "C" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "D" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "E" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "F" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "G" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "H" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "I" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "J" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "K" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "L" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "M" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "N" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "O" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "P" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "Q" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "R" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "S" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "T" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "U" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "V" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "W" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "X" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "Y" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "Z" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "a" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "b" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "c" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "d" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "e" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Time building chain proxies: 11.63, per 1000 atoms: 0.51 Number of scatterers: 22754 At special positions: 0 Unit cell: (91.08, 91.08, 192.72, 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 217 16.00 O 4123 8.00 N 3906 7.00 C 14508 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: 9.65 Conformation dependent library (CDL) restraints added in 4.3 seconds 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5332 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 0 sheets defined 92.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 4.292A pdb=" N LYS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 16 through 30 Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 16 through 30 Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 7 through 15 Processing helix chain 'C' and resid 16 through 30 Processing helix chain 'C' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU C 44 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 61 Processing helix chain 'C' and resid 61 through 77 removed outlier: 4.286A pdb=" N SER C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 85 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 7 through 15 Processing helix chain 'D' and resid 16 through 30 Processing helix chain 'D' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU D 44 " --> pdb=" O ILE D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 61 Processing helix chain 'D' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 85 Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 7 through 15 Processing helix chain 'E' and resid 16 through 30 Processing helix chain 'E' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU E 44 " --> pdb=" O ILE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 61 Processing helix chain 'E' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 85 Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 7 through 15 Processing helix chain 'F' and resid 16 through 30 Processing helix chain 'F' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 61 Processing helix chain 'F' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER F 65 " --> pdb=" O LYS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 85 Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 7 through 15 Processing helix chain 'G' and resid 16 through 30 Processing helix chain 'G' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU G 44 " --> pdb=" O ILE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 61 Processing helix chain 'G' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER G 65 " --> pdb=" O LYS G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 85 Processing helix chain 'H' and resid 2 through 7 Processing helix chain 'H' and resid 7 through 15 Processing helix chain 'H' and resid 16 through 30 Processing helix chain 'H' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU H 44 " --> pdb=" O ILE H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 61 Processing helix chain 'H' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER H 65 " --> pdb=" O LYS H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 85 Processing helix chain 'I' and resid 2 through 7 Processing helix chain 'I' and resid 7 through 15 Processing helix chain 'I' and resid 16 through 30 Processing helix chain 'I' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU I 44 " --> pdb=" O ILE I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 61 Processing helix chain 'I' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 85 Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 7 through 15 Processing helix chain 'J' and resid 16 through 30 Processing helix chain 'J' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU J 44 " --> pdb=" O ILE J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 61 Processing helix chain 'J' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 85 Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 7 through 15 Processing helix chain 'K' and resid 16 through 30 Processing helix chain 'K' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU K 44 " --> pdb=" O ILE K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 61 Processing helix chain 'K' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER K 65 " --> pdb=" O LYS K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 85 Processing helix chain 'L' and resid 2 through 7 Processing helix chain 'L' and resid 7 through 15 Processing helix chain 'L' and resid 16 through 30 Processing helix chain 'L' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU L 44 " --> pdb=" O ILE L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 61 Processing helix chain 'L' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER L 65 " --> pdb=" O LYS L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'M' and resid 2 through 7 Processing helix chain 'M' and resid 7 through 15 Processing helix chain 'M' and resid 16 through 30 Processing helix chain 'M' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU M 44 " --> pdb=" O ILE M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 61 Processing helix chain 'M' and resid 61 through 77 removed outlier: 4.286A pdb=" N SER M 65 " --> pdb=" O LYS M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 85 Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 7 through 15 Processing helix chain 'N' and resid 16 through 30 Processing helix chain 'N' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU N 44 " --> pdb=" O ILE N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 61 Processing helix chain 'N' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER N 65 " --> pdb=" O LYS N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 85 Processing helix chain 'O' and resid 2 through 7 Processing helix chain 'O' and resid 7 through 15 Processing helix chain 'O' and resid 16 through 30 Processing helix chain 'O' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU O 44 " --> pdb=" O ILE O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 61 Processing helix chain 'O' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER O 65 " --> pdb=" O LYS O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 85 Processing helix chain 'P' and resid 2 through 7 Processing helix chain 'P' and resid 7 through 15 Processing helix chain 'P' and resid 16 through 30 Processing helix chain 'P' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU P 44 " --> pdb=" O ILE P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 61 Processing helix chain 'P' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER P 65 " --> pdb=" O LYS P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 85 Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 7 through 15 Processing helix chain 'Q' and resid 16 through 30 Processing helix chain 'Q' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU Q 44 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 61 Processing helix chain 'Q' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER Q 65 " --> pdb=" O LYS Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 85 Processing helix chain 'R' and resid 2 through 7 Processing helix chain 'R' and resid 7 through 15 Processing helix chain 'R' and resid 16 through 30 Processing helix chain 'R' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU R 44 " --> pdb=" O ILE R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 61 Processing helix chain 'R' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER R 65 " --> pdb=" O LYS R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 85 Processing helix chain 'S' and resid 2 through 7 Processing helix chain 'S' and resid 7 through 15 Processing helix chain 'S' and resid 16 through 30 Processing helix chain 'S' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU S 44 " --> pdb=" O ILE S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 46 through 61 Processing helix chain 'S' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER S 65 " --> pdb=" O LYS S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 85 Processing helix chain 'T' and resid 2 through 7 Processing helix chain 'T' and resid 7 through 15 Processing helix chain 'T' and resid 16 through 30 Processing helix chain 'T' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU T 44 " --> pdb=" O ILE T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 61 Processing helix chain 'T' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER T 65 " --> pdb=" O LYS T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 85 Processing helix chain 'U' and resid 2 through 7 Processing helix chain 'U' and resid 7 through 15 Processing helix chain 'U' and resid 16 through 30 Processing helix chain 'U' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU U 44 " --> pdb=" O ILE U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 61 Processing helix chain 'U' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER U 65 " --> pdb=" O LYS U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 85 Processing helix chain 'V' and resid 2 through 7 Processing helix chain 'V' and resid 7 through 15 Processing helix chain 'V' and resid 16 through 30 Processing helix chain 'V' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU V 44 " --> pdb=" O ILE V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 61 Processing helix chain 'V' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER V 65 " --> pdb=" O LYS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 85 Processing helix chain 'W' and resid 2 through 7 Processing helix chain 'W' and resid 7 through 15 Processing helix chain 'W' and resid 16 through 30 Processing helix chain 'W' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU W 44 " --> pdb=" O ILE W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 46 through 61 Processing helix chain 'W' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER W 65 " --> pdb=" O LYS W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 85 Processing helix chain 'X' and resid 2 through 7 Processing helix chain 'X' and resid 7 through 15 Processing helix chain 'X' and resid 16 through 30 Processing helix chain 'X' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 46 through 61 Processing helix chain 'X' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER X 65 " --> pdb=" O LYS X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 77 through 85 Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 7 through 15 Processing helix chain 'Y' and resid 16 through 30 Processing helix chain 'Y' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU Y 44 " --> pdb=" O ILE Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 61 Processing helix chain 'Y' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER Y 65 " --> pdb=" O LYS Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 85 Processing helix chain 'Z' and resid 2 through 7 Processing helix chain 'Z' and resid 7 through 15 Processing helix chain 'Z' and resid 16 through 30 Processing helix chain 'Z' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU Z 44 " --> pdb=" O ILE Z 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 61 Processing helix chain 'Z' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER Z 65 " --> pdb=" O LYS Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 77 through 85 Processing helix chain 'a' and resid 2 through 7 Processing helix chain 'a' and resid 7 through 15 Processing helix chain 'a' and resid 16 through 30 Processing helix chain 'a' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU a 44 " --> pdb=" O ILE a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 61 Processing helix chain 'a' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER a 65 " --> pdb=" O LYS a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 85 Processing helix chain 'b' and resid 2 through 7 Processing helix chain 'b' and resid 7 through 15 Processing helix chain 'b' and resid 16 through 30 Processing helix chain 'b' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU b 44 " --> pdb=" O ILE b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 46 through 61 Processing helix chain 'b' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER b 65 " --> pdb=" O LYS b 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 85 Processing helix chain 'c' and resid 2 through 7 Processing helix chain 'c' and resid 7 through 15 Processing helix chain 'c' and resid 16 through 30 Processing helix chain 'c' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU c 44 " --> pdb=" O ILE c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 61 Processing helix chain 'c' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER c 65 " --> pdb=" O LYS c 61 " (cutoff:3.500A) Processing helix chain 'c' and resid 77 through 85 Processing helix chain 'd' and resid 2 through 7 Processing helix chain 'd' and resid 7 through 15 Processing helix chain 'd' and resid 16 through 30 Processing helix chain 'd' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU d 44 " --> pdb=" O ILE d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 46 through 61 Processing helix chain 'd' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER d 65 " --> pdb=" O LYS d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 85 Processing helix chain 'e' and resid 2 through 7 Processing helix chain 'e' and resid 7 through 15 Processing helix chain 'e' and resid 16 through 30 Processing helix chain 'e' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU e 44 " --> pdb=" O ILE e 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 61 Processing helix chain 'e' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 77 through 85 1643 hydrogen bonds defined for protein. 4929 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: 7.35 Time building geometry restraints manager: 10.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6507 1.33 - 1.45: 3463 1.45 - 1.57: 12784 1.57 - 1.69: 0 1.69 - 1.81: 341 Bond restraints: 23095 Sorted by residual: bond pdb=" CB VAL O 32 " pdb=" CG1 VAL O 32 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.44e+00 bond pdb=" CB VAL C 32 " pdb=" CG1 VAL C 32 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.41e+00 bond pdb=" CB VAL P 32 " pdb=" CG1 VAL P 32 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.41e+00 bond pdb=" CB VAL S 32 " pdb=" CG1 VAL S 32 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.40e+00 bond pdb=" CB VAL N 32 " pdb=" CG1 VAL N 32 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.38e+00 ... (remaining 23090 not shown) Histogram of bond angle deviations from ideal: 97.75 - 105.00: 186 105.00 - 112.25: 11005 112.25 - 119.49: 8778 119.49 - 126.74: 10782 126.74 - 133.99: 249 Bond angle restraints: 31000 Sorted by residual: angle pdb=" N GLY a 62 " pdb=" CA GLY a 62 " pdb=" C GLY a 62 " ideal model delta sigma weight residual 112.17 116.26 -4.09 1.40e+00 5.10e-01 8.51e+00 angle pdb=" N GLY A 62 " pdb=" CA GLY A 62 " pdb=" C GLY A 62 " ideal model delta sigma weight residual 112.17 116.24 -4.07 1.40e+00 5.10e-01 8.44e+00 angle pdb=" N GLY d 62 " pdb=" CA GLY d 62 " pdb=" C GLY d 62 " ideal model delta sigma weight residual 112.17 116.23 -4.06 1.40e+00 5.10e-01 8.42e+00 angle pdb=" N GLY Q 62 " pdb=" CA GLY Q 62 " pdb=" C GLY Q 62 " ideal model delta sigma weight residual 112.17 116.23 -4.06 1.40e+00 5.10e-01 8.40e+00 angle pdb=" N GLY D 62 " pdb=" CA GLY D 62 " pdb=" C GLY D 62 " ideal model delta sigma weight residual 112.17 116.23 -4.06 1.40e+00 5.10e-01 8.39e+00 ... (remaining 30995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.40: 13500 14.40 - 28.81: 433 28.81 - 43.21: 141 43.21 - 57.62: 0 57.62 - 72.02: 31 Dihedral angle restraints: 14105 sinusoidal: 5983 harmonic: 8122 Sorted by residual: dihedral pdb=" C GLU V 64 " pdb=" N GLU V 64 " pdb=" CA GLU V 64 " pdb=" CB GLU V 64 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" C GLU Y 64 " pdb=" N GLU Y 64 " pdb=" CA GLU Y 64 " pdb=" CB GLU Y 64 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" C GLU Z 64 " pdb=" N GLU Z 64 " pdb=" CA GLU Z 64 " pdb=" CB GLU Z 64 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 14102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2690 0.071 - 0.142: 689 0.142 - 0.212: 58 0.212 - 0.283: 4 0.283 - 0.354: 31 Chirality restraints: 3472 Sorted by residual: chirality pdb=" CA GLU Y 64 " pdb=" N GLU Y 64 " pdb=" C GLU Y 64 " pdb=" CB GLU Y 64 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA GLU V 64 " pdb=" N GLU V 64 " pdb=" C GLU V 64 " pdb=" CB GLU V 64 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA GLU O 64 " pdb=" N GLU O 64 " pdb=" C GLU O 64 " pdb=" CB GLU O 64 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 3469 not shown) Planarity restraints: 3937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 53 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.38e+00 pdb=" C GLY Q 53 " -0.020 2.00e-02 2.50e+03 pdb=" O GLY Q 53 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE Q 54 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY b 53 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C GLY b 53 " 0.020 2.00e-02 2.50e+03 pdb=" O GLY b 53 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE b 54 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY J 53 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C GLY J 53 " -0.020 2.00e-02 2.50e+03 pdb=" O GLY J 53 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE J 54 " 0.007 2.00e-02 2.50e+03 ... (remaining 3934 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 7884 2.87 - 3.38: 26030 3.38 - 3.89: 40131 3.89 - 4.39: 46241 4.39 - 4.90: 77147 Nonbonded interactions: 197433 Sorted by model distance: nonbonded pdb=" OD2 ASP d 26 " pdb=" NE1 TRP d 76 " model vdw 2.367 2.520 nonbonded pdb=" OD2 ASP P 26 " pdb=" NE1 TRP P 76 " model vdw 2.367 2.520 nonbonded pdb=" OD2 ASP W 26 " pdb=" NE1 TRP W 76 " model vdw 2.367 2.520 nonbonded pdb=" OD2 ASP X 26 " pdb=" NE1 TRP X 76 " model vdw 2.367 2.520 nonbonded pdb=" OD2 ASP T 26 " pdb=" NE1 TRP T 76 " model vdw 2.367 2.520 ... (remaining 197428 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 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: 0.020 Extract box with map and model: 2.020 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 59.450 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.240 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.012 0.084 23095 Z= 0.763 Angle : 1.000 6.341 31000 Z= 0.560 Chirality : 0.067 0.354 3472 Planarity : 0.004 0.012 3937 Dihedral : 9.700 72.020 8773 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -1.30 (0.15), residues: 2728 helix: -0.59 (0.09), residues: 2449 sheet: None (None), residues: 0 loop : -1.74 (0.47), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP I 30 HIS 0.002 0.001 HIS O 56 PHE 0.009 0.003 PHE N 3 TYR 0.006 0.002 TYR e 78 ARG 0.001 0.000 ARG M 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1755 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1755 time to evaluate : 2.946 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: A 35 ARG cc_start: 0.7352 (ttm110) cc_final: 0.7149 (ttm170) REVERT: A 66 CYS cc_start: 0.8627 (m) cc_final: 0.8309 (m) REVERT: A 76 TRP cc_start: 0.8492 (m100) cc_final: 0.7794 (m100) REVERT: B 6 ASP cc_start: 0.8289 (m-30) cc_final: 0.8057 (m-30) REVERT: B 17 MET cc_start: 0.8125 (tpp) cc_final: 0.7760 (tpt) REVERT: B 19 VAL cc_start: 0.9206 (t) cc_final: 0.8977 (t) REVERT: B 33 LEU cc_start: 0.9004 (mt) cc_final: 0.8672 (mt) REVERT: B 34 ASN cc_start: 0.7590 (t160) cc_final: 0.6870 (t0) REVERT: B 66 CYS cc_start: 0.8602 (m) cc_final: 0.8352 (m) REVERT: B 83 ASP cc_start: 0.8552 (t70) cc_final: 0.8312 (t0) REVERT: C 3 PHE cc_start: 0.8737 (t80) cc_final: 0.8497 (t80) REVERT: C 19 VAL cc_start: 0.9339 (t) cc_final: 0.9132 (t) REVERT: C 39 ASN cc_start: 0.7774 (m-40) cc_final: 0.7529 (m110) REVERT: C 60 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8146 (mtpp) REVERT: C 83 ASP cc_start: 0.8575 (t70) cc_final: 0.8355 (t70) REVERT: D 13 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8736 (mm-40) REVERT: D 35 ARG cc_start: 0.7260 (ttm110) cc_final: 0.6856 (tpp80) REVERT: D 39 ASN cc_start: 0.7737 (m-40) cc_final: 0.7305 (m110) REVERT: D 43 CYS cc_start: 0.7877 (p) cc_final: 0.7051 (p) REVERT: D 66 CYS cc_start: 0.8461 (m) cc_final: 0.8236 (m) REVERT: D 74 LYS cc_start: 0.8662 (tttt) cc_final: 0.8416 (ttpp) REVERT: D 76 TRP cc_start: 0.8347 (m100) cc_final: 0.8099 (m100) REVERT: D 87 GLN cc_start: 0.8363 (mm-40) cc_final: 0.7790 (mm110) REVERT: E 13 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8889 (mm110) REVERT: E 17 MET cc_start: 0.8091 (tpp) cc_final: 0.7822 (tpt) REVERT: E 40 ILE cc_start: 0.8708 (mt) cc_final: 0.8496 (pt) REVERT: E 82 GLN cc_start: 0.8825 (mm110) cc_final: 0.8613 (mm110) REVERT: F 19 VAL cc_start: 0.9248 (t) cc_final: 0.8873 (t) REVERT: F 34 ASN cc_start: 0.7392 (t160) cc_final: 0.7128 (t160) REVERT: F 40 ILE cc_start: 0.8870 (mt) cc_final: 0.8649 (pt) REVERT: F 66 CYS cc_start: 0.8736 (m) cc_final: 0.8385 (m) REVERT: F 82 GLN cc_start: 0.8569 (mm110) cc_final: 0.7968 (mm110) REVERT: G 18 THR cc_start: 0.8815 (p) cc_final: 0.8583 (p) REVERT: G 33 LEU cc_start: 0.9030 (mt) cc_final: 0.8803 (mt) REVERT: G 34 ASN cc_start: 0.7192 (t160) cc_final: 0.6204 (t0) REVERT: G 35 ARG cc_start: 0.7305 (ttm110) cc_final: 0.6622 (tpp80) REVERT: G 39 ASN cc_start: 0.7809 (m-40) cc_final: 0.7554 (m110) REVERT: G 48 GLN cc_start: 0.8393 (mp10) cc_final: 0.7722 (mp10) REVERT: G 83 ASP cc_start: 0.8527 (t70) cc_final: 0.8307 (t0) REVERT: H 3 PHE cc_start: 0.8631 (t80) cc_final: 0.8377 (t80) REVERT: H 17 MET cc_start: 0.8015 (tpp) cc_final: 0.7804 (tpt) REVERT: H 31 ASN cc_start: 0.9165 (m-40) cc_final: 0.8914 (m-40) REVERT: H 76 TRP cc_start: 0.8425 (m100) cc_final: 0.7876 (m100) REVERT: H 87 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7862 (mm110) REVERT: I 13 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8764 (mm-40) REVERT: I 17 MET cc_start: 0.8192 (tpp) cc_final: 0.7981 (tpt) REVERT: I 34 ASN cc_start: 0.7683 (t160) cc_final: 0.7064 (t160) REVERT: I 76 TRP cc_start: 0.8322 (m100) cc_final: 0.7599 (m100) REVERT: J 5 LYS cc_start: 0.8554 (tttm) cc_final: 0.8336 (tttt) REVERT: J 8 SER cc_start: 0.8929 (p) cc_final: 0.8690 (p) REVERT: J 12 ILE cc_start: 0.9483 (mt) cc_final: 0.9205 (mp) REVERT: J 17 MET cc_start: 0.8444 (tpp) cc_final: 0.8165 (tpp) REVERT: J 19 VAL cc_start: 0.9363 (t) cc_final: 0.9128 (t) REVERT: J 35 ARG cc_start: 0.7317 (ttm110) cc_final: 0.6793 (tpp80) REVERT: J 39 ASN cc_start: 0.8096 (m-40) cc_final: 0.7712 (m-40) REVERT: J 48 GLN cc_start: 0.8529 (mp10) cc_final: 0.8322 (mp10) REVERT: J 76 TRP cc_start: 0.8486 (m100) cc_final: 0.8046 (m100) REVERT: K 3 PHE cc_start: 0.8709 (t80) cc_final: 0.8398 (t80) REVERT: K 13 GLN cc_start: 0.9090 (mm-40) cc_final: 0.7750 (mm-40) REVERT: K 21 LYS cc_start: 0.8668 (mttt) cc_final: 0.8440 (mttp) REVERT: K 25 ASP cc_start: 0.8103 (m-30) cc_final: 0.7193 (m-30) REVERT: K 39 ASN cc_start: 0.8117 (m-40) cc_final: 0.7846 (m110) REVERT: K 60 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7921 (mtpt) REVERT: K 66 CYS cc_start: 0.8537 (m) cc_final: 0.8213 (m) REVERT: K 83 ASP cc_start: 0.8615 (t70) cc_final: 0.8101 (t0) REVERT: K 87 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7075 (mm110) REVERT: L 6 ASP cc_start: 0.8341 (m-30) cc_final: 0.8083 (m-30) REVERT: L 35 ARG cc_start: 0.7171 (ttm110) cc_final: 0.6886 (ttm-80) REVERT: L 66 CYS cc_start: 0.8336 (m) cc_final: 0.7957 (m) REVERT: L 87 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7645 (mm110) REVERT: M 13 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8075 (mm-40) REVERT: M 39 ASN cc_start: 0.8025 (m-40) cc_final: 0.7424 (m110) REVERT: M 77 ASN cc_start: 0.9238 (t0) cc_final: 0.9025 (t0) REVERT: N 39 ASN cc_start: 0.7782 (m-40) cc_final: 0.7452 (m110) REVERT: O 6 ASP cc_start: 0.8362 (m-30) cc_final: 0.8156 (m-30) REVERT: O 34 ASN cc_start: 0.7612 (t160) cc_final: 0.6626 (t0) REVERT: O 35 ARG cc_start: 0.7268 (ttm110) cc_final: 0.6819 (ttp-110) REVERT: O 39 ASN cc_start: 0.7849 (m-40) cc_final: 0.7531 (m110) REVERT: O 48 GLN cc_start: 0.8435 (mp10) cc_final: 0.7974 (mp10) REVERT: O 61 LYS cc_start: 0.8895 (mttm) cc_final: 0.8649 (mttm) REVERT: P 12 ILE cc_start: 0.9366 (mt) cc_final: 0.9077 (mm) REVERT: P 13 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8037 (mm110) REVERT: P 66 CYS cc_start: 0.8584 (m) cc_final: 0.8186 (m) REVERT: P 67 ASN cc_start: 0.8777 (m-40) cc_final: 0.8435 (m-40) REVERT: Q 82 GLN cc_start: 0.8454 (mm110) cc_final: 0.8215 (mm-40) REVERT: R 5 LYS cc_start: 0.8713 (tttm) cc_final: 0.8498 (tttt) REVERT: R 8 SER cc_start: 0.9050 (p) cc_final: 0.8809 (p) REVERT: R 13 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8741 (mm110) REVERT: R 32 VAL cc_start: 0.9186 (m) cc_final: 0.8944 (p) REVERT: R 35 ARG cc_start: 0.7257 (ttm110) cc_final: 0.6712 (tpp80) REVERT: R 39 ASN cc_start: 0.7893 (m-40) cc_final: 0.7046 (m-40) REVERT: R 61 LYS cc_start: 0.9090 (mttm) cc_final: 0.8438 (mttm) REVERT: R 70 LEU cc_start: 0.9300 (mt) cc_final: 0.9031 (mt) REVERT: R 77 ASN cc_start: 0.9263 (t0) cc_final: 0.8702 (t0) REVERT: S 3 PHE cc_start: 0.8259 (t80) cc_final: 0.7801 (t80) REVERT: S 19 VAL cc_start: 0.9229 (t) cc_final: 0.8945 (t) REVERT: S 39 ASN cc_start: 0.7746 (m-40) cc_final: 0.7490 (m110) REVERT: S 48 GLN cc_start: 0.8310 (mp10) cc_final: 0.8074 (mp10) REVERT: S 60 LYS cc_start: 0.8547 (mtmt) cc_final: 0.8290 (mtpt) REVERT: S 66 CYS cc_start: 0.8570 (m) cc_final: 0.8059 (m) REVERT: T 13 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8886 (mm110) REVERT: T 17 MET cc_start: 0.8062 (tpp) cc_final: 0.7829 (tpp) REVERT: T 34 ASN cc_start: 0.7742 (t160) cc_final: 0.7077 (t0) REVERT: T 35 ARG cc_start: 0.7317 (ttm110) cc_final: 0.6695 (ttm-80) REVERT: T 39 ASN cc_start: 0.7794 (m-40) cc_final: 0.7362 (m110) REVERT: T 82 GLN cc_start: 0.8502 (mm110) cc_final: 0.8276 (mm110) REVERT: T 83 ASP cc_start: 0.8645 (t70) cc_final: 0.8274 (t70) REVERT: U 25 ASP cc_start: 0.8325 (m-30) cc_final: 0.7892 (m-30) REVERT: U 26 ASP cc_start: 0.8090 (m-30) cc_final: 0.7883 (m-30) REVERT: U 35 ARG cc_start: 0.7247 (ttm110) cc_final: 0.6650 (ttm-80) REVERT: U 39 ASN cc_start: 0.7550 (m-40) cc_final: 0.7321 (m110) REVERT: U 49 ASP cc_start: 0.8515 (m-30) cc_final: 0.8286 (m-30) REVERT: V 35 ARG cc_start: 0.7359 (ttm110) cc_final: 0.6840 (ttm110) REVERT: V 39 ASN cc_start: 0.7947 (m-40) cc_final: 0.7611 (m-40) REVERT: V 66 CYS cc_start: 0.8665 (m) cc_final: 0.8362 (m) REVERT: V 87 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7437 (mm110) REVERT: W 4 ILE cc_start: 0.8915 (mt) cc_final: 0.8508 (mt) REVERT: W 6 ASP cc_start: 0.8376 (m-30) cc_final: 0.8116 (m-30) REVERT: W 12 ILE cc_start: 0.9419 (mt) cc_final: 0.9201 (mt) REVERT: W 17 MET cc_start: 0.7951 (tpp) cc_final: 0.7622 (tpt) REVERT: W 33 LEU cc_start: 0.9068 (mt) cc_final: 0.8826 (mt) REVERT: W 34 ASN cc_start: 0.7543 (t160) cc_final: 0.6678 (t0) REVERT: W 66 CYS cc_start: 0.8650 (m) cc_final: 0.8428 (t) REVERT: W 76 TRP cc_start: 0.8384 (m100) cc_final: 0.8069 (m100) REVERT: X 3 PHE cc_start: 0.8879 (t80) cc_final: 0.8651 (t80) REVERT: X 25 ASP cc_start: 0.8313 (m-30) cc_final: 0.7969 (m-30) REVERT: X 48 GLN cc_start: 0.8459 (mp10) cc_final: 0.8151 (mp10) REVERT: X 66 CYS cc_start: 0.8844 (m) cc_final: 0.8280 (m) REVERT: X 82 GLN cc_start: 0.8532 (mm110) cc_final: 0.8301 (mm110) REVERT: X 87 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7476 (mm-40) REVERT: Y 5 LYS cc_start: 0.8416 (tttm) cc_final: 0.8210 (tttt) REVERT: Y 13 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8787 (mm110) REVERT: Y 17 MET cc_start: 0.8083 (tpp) cc_final: 0.7830 (tpt) REVERT: Y 19 VAL cc_start: 0.9410 (t) cc_final: 0.9113 (t) REVERT: Y 25 ASP cc_start: 0.8163 (m-30) cc_final: 0.7760 (m-30) REVERT: Y 35 ARG cc_start: 0.7409 (ttm110) cc_final: 0.7120 (ttp-110) REVERT: Y 39 ASN cc_start: 0.7715 (m-40) cc_final: 0.7346 (m-40) REVERT: Y 55 ILE cc_start: 0.9135 (mt) cc_final: 0.8823 (tt) REVERT: Y 60 LYS cc_start: 0.8991 (mtmt) cc_final: 0.7724 (tptt) REVERT: Y 61 LYS cc_start: 0.8678 (mttm) cc_final: 0.8400 (mttt) REVERT: Y 66 CYS cc_start: 0.8484 (m) cc_final: 0.8025 (m) REVERT: Z 8 SER cc_start: 0.8825 (p) cc_final: 0.8576 (p) REVERT: Z 12 ILE cc_start: 0.9465 (mt) cc_final: 0.9091 (mp) REVERT: Z 17 MET cc_start: 0.7915 (tpp) cc_final: 0.7487 (tpt) REVERT: Z 34 ASN cc_start: 0.7797 (t160) cc_final: 0.7035 (t0) REVERT: Z 36 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6801 (mt-10) REVERT: Z 48 GLN cc_start: 0.8487 (mp10) cc_final: 0.8174 (mp10) REVERT: Z 66 CYS cc_start: 0.8490 (m) cc_final: 0.8131 (m) REVERT: Z 77 ASN cc_start: 0.8985 (t0) cc_final: 0.8457 (t0) REVERT: a 3 PHE cc_start: 0.8669 (t80) cc_final: 0.8395 (t80) REVERT: a 5 LYS cc_start: 0.8766 (tttm) cc_final: 0.8364 (tptt) REVERT: a 8 SER cc_start: 0.9250 (p) cc_final: 0.8908 (p) REVERT: a 9 ARG cc_start: 0.7886 (mtp180) cc_final: 0.7476 (mmt-90) REVERT: a 12 ILE cc_start: 0.9346 (mt) cc_final: 0.9009 (mp) REVERT: a 27 LEU cc_start: 0.8787 (mt) cc_final: 0.8489 (mt) REVERT: a 31 ASN cc_start: 0.9112 (m-40) cc_final: 0.8889 (m-40) REVERT: a 34 ASN cc_start: 0.7737 (t160) cc_final: 0.7168 (t0) REVERT: a 35 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7129 (ttm-80) REVERT: a 39 ASN cc_start: 0.8156 (m-40) cc_final: 0.7898 (m110) REVERT: a 83 ASP cc_start: 0.8536 (t70) cc_final: 0.8328 (t0) REVERT: a 87 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7303 (mm-40) REVERT: b 3 PHE cc_start: 0.8633 (t80) cc_final: 0.8432 (t80) REVERT: b 23 ILE cc_start: 0.8821 (mt) cc_final: 0.8616 (mt) REVERT: b 36 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6742 (mt-10) REVERT: b 39 ASN cc_start: 0.7840 (m-40) cc_final: 0.7515 (m110) REVERT: b 49 ASP cc_start: 0.8403 (m-30) cc_final: 0.8173 (m-30) REVERT: b 66 CYS cc_start: 0.8568 (m) cc_final: 0.8353 (m) REVERT: c 17 MET cc_start: 0.8383 (tpp) cc_final: 0.8153 (tpt) REVERT: c 19 VAL cc_start: 0.9349 (t) cc_final: 0.8973 (t) REVERT: c 35 ARG cc_start: 0.7495 (ttm110) cc_final: 0.7290 (tpp80) REVERT: c 39 ASN cc_start: 0.7626 (m-40) cc_final: 0.6958 (m110) REVERT: c 74 LYS cc_start: 0.8614 (tttt) cc_final: 0.8397 (ttpp) REVERT: c 82 GLN cc_start: 0.8925 (mm110) cc_final: 0.8489 (mm110) REVERT: c 87 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7050 (mm110) REVERT: d 3 PHE cc_start: 0.8733 (t80) cc_final: 0.8530 (t80) REVERT: d 13 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8501 (mm110) REVERT: d 33 LEU cc_start: 0.9052 (mt) cc_final: 0.8731 (mt) REVERT: d 40 ILE cc_start: 0.8699 (mt) cc_final: 0.8439 (pt) REVERT: d 66 CYS cc_start: 0.8666 (m) cc_final: 0.8421 (m) REVERT: d 82 GLN cc_start: 0.8888 (mm110) cc_final: 0.8672 (mm-40) REVERT: d 83 ASP cc_start: 0.8460 (t70) cc_final: 0.8239 (t0) REVERT: e 34 ASN cc_start: 0.7798 (t160) cc_final: 0.7392 (t0) REVERT: e 35 ARG cc_start: 0.7290 (ttm110) cc_final: 0.6651 (tpp80) REVERT: e 39 ASN cc_start: 0.7689 (m-40) cc_final: 0.6498 (m110) REVERT: e 70 LEU cc_start: 0.8976 (mt) cc_final: 0.8720 (mt) REVERT: e 74 LYS cc_start: 0.8709 (tttt) cc_final: 0.8457 (ttpp) REVERT: e 87 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8409 (mm-40) outliers start: 0 outliers final: 0 residues processed: 1755 average time/residue: 0.3712 time to fit residues: 972.6392 Evaluate side-chains 1502 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1502 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 2.9990 chunk 211 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 39 ASN A 67 ASN A 82 GLN B 13 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 67 ASN B 82 GLN C 31 ASN C 39 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN D 56 HIS D 82 GLN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 56 HIS E 67 ASN G 13 GLN G 39 ASN G 67 ASN G 82 GLN H 13 GLN H 56 HIS H 67 ASN H 82 GLN I 56 HIS I 82 GLN J 39 ASN J 56 HIS J 67 ASN J 82 GLN K 31 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 ASN K 56 HIS ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 56 HIS L 67 ASN L 82 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 ASN M 56 HIS ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 ASN N 56 HIS N 67 ASN N 82 GLN O 13 GLN ** O 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 ASN O 56 HIS O 67 ASN O 82 GLN ** P 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 56 HIS P 82 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 ASN R 56 HIS R 82 GLN ** S 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 HIS S 82 GLN T 39 ASN T 56 HIS U 39 ASN U 56 HIS U 67 ASN U 82 GLN ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 HIS V 82 GLN W 13 GLN W 56 HIS W 67 ASN W 82 GLN X 67 ASN ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 ASN Y 67 ASN Y 82 GLN Z 56 HIS Z 67 ASN Z 82 GLN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 34 ASN a 39 ASN a 82 GLN b 39 ASN b 56 HIS c 39 ASN ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN d 67 ASN e 34 ASN e 67 ASN Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23095 Z= 0.258 Angle : 0.565 5.520 31000 Z= 0.311 Chirality : 0.042 0.217 3472 Planarity : 0.004 0.037 3937 Dihedral : 4.027 15.567 2914 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 5.29 % Allowed : 14.26 % Favored : 80.45 % 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: 1.00 (0.15), residues: 2728 helix: 0.98 (0.10), residues: 2480 sheet: None (None), residues: 0 loop : -1.92 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP c 76 HIS 0.009 0.001 HIS G 56 PHE 0.022 0.002 PHE I 28 TYR 0.007 0.002 TYR M 78 ARG 0.006 0.001 ARG P 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1849 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1713 time to evaluate : 2.934 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: A 22 GLN cc_start: 0.8557 (mt0) cc_final: 0.8116 (mt0) REVERT: A 34 ASN cc_start: 0.8039 (t0) cc_final: 0.7132 (t0) REVERT: A 47 GLU cc_start: 0.7274 (tt0) cc_final: 0.6927 (tt0) REVERT: A 60 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8371 (mtpt) REVERT: A 66 CYS cc_start: 0.8703 (m) cc_final: 0.8304 (m) REVERT: A 71 LYS cc_start: 0.9294 (ttmt) cc_final: 0.9090 (ttpp) REVERT: B 35 ARG cc_start: 0.7760 (ttm110) cc_final: 0.7555 (ttp-110) REVERT: B 60 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8442 (mtmm) REVERT: B 66 CYS cc_start: 0.8413 (m) cc_final: 0.8196 (m) REVERT: B 74 LYS cc_start: 0.8949 (ttpp) cc_final: 0.8703 (ptmm) REVERT: B 83 ASP cc_start: 0.8642 (t70) cc_final: 0.8398 (t0) REVERT: C 2 ASN cc_start: 0.7621 (m-40) cc_final: 0.6972 (m-40) REVERT: C 12 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9035 (mp) REVERT: C 22 GLN cc_start: 0.8390 (mt0) cc_final: 0.8174 (mt0) REVERT: C 60 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8458 (mtpp) REVERT: C 78 TYR cc_start: 0.8909 (t80) cc_final: 0.8699 (t80) REVERT: C 83 ASP cc_start: 0.8552 (t70) cc_final: 0.8190 (t0) REVERT: D 13 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8759 (mm-40) REVERT: D 35 ARG cc_start: 0.7533 (ttm110) cc_final: 0.7253 (tpp80) REVERT: D 39 ASN cc_start: 0.8197 (m110) cc_final: 0.7594 (m-40) REVERT: D 60 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8409 (mtpp) REVERT: D 66 CYS cc_start: 0.8187 (m) cc_final: 0.7975 (m) REVERT: D 74 LYS cc_start: 0.8863 (tttt) cc_final: 0.8548 (ttpp) REVERT: D 77 ASN cc_start: 0.9165 (t0) cc_final: 0.8932 (t0) REVERT: D 78 TYR cc_start: 0.8723 (t80) cc_final: 0.8305 (t80) REVERT: E 1 MET cc_start: 0.6887 (tpp) cc_final: 0.6491 (tpt) REVERT: E 34 ASN cc_start: 0.7811 (t160) cc_final: 0.7600 (t160) REVERT: E 47 GLU cc_start: 0.7691 (tt0) cc_final: 0.7145 (tt0) REVERT: E 57 MET cc_start: 0.8092 (mtm) cc_final: 0.7711 (mtp) REVERT: E 60 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8277 (mtpp) REVERT: E 78 TYR cc_start: 0.8804 (t80) cc_final: 0.8452 (t80) REVERT: F 6 ASP cc_start: 0.8260 (m-30) cc_final: 0.7952 (p0) REVERT: F 36 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7147 (mt-10) REVERT: G 18 THR cc_start: 0.9230 (p) cc_final: 0.9002 (p) REVERT: G 35 ARG cc_start: 0.7625 (ttm110) cc_final: 0.7379 (ttp-110) REVERT: G 39 ASN cc_start: 0.8342 (m110) cc_final: 0.7793 (m110) REVERT: G 77 ASN cc_start: 0.9120 (t0) cc_final: 0.8904 (t0) REVERT: G 83 ASP cc_start: 0.8499 (t70) cc_final: 0.8210 (t0) REVERT: H 2 ASN cc_start: 0.7445 (m-40) cc_final: 0.7115 (m110) REVERT: H 6 ASP cc_start: 0.8116 (m-30) cc_final: 0.7911 (m-30) REVERT: H 7 ASN cc_start: 0.8874 (m-40) cc_final: 0.8477 (m110) REVERT: H 21 LYS cc_start: 0.8811 (mttt) cc_final: 0.8514 (mttp) REVERT: H 31 ASN cc_start: 0.9163 (m-40) cc_final: 0.8956 (m-40) REVERT: H 34 ASN cc_start: 0.7655 (t0) cc_final: 0.6688 (t0) REVERT: H 60 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8227 (mtpt) REVERT: H 75 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8770 (tm-30) REVERT: H 83 ASP cc_start: 0.8522 (t0) cc_final: 0.8263 (t0) REVERT: I 7 ASN cc_start: 0.8930 (m-40) cc_final: 0.8662 (m110) REVERT: I 8 SER cc_start: 0.9011 (p) cc_final: 0.8757 (m) REVERT: I 9 ARG cc_start: 0.8369 (mtp-110) cc_final: 0.8126 (mtp-110) REVERT: I 37 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7784 (mt-10) REVERT: I 49 ASP cc_start: 0.8584 (m-30) cc_final: 0.8380 (m-30) REVERT: J 2 ASN cc_start: 0.8351 (m-40) cc_final: 0.7967 (m-40) REVERT: J 34 ASN cc_start: 0.7877 (t0) cc_final: 0.6935 (t0) REVERT: J 35 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7465 (ttp-170) REVERT: J 39 ASN cc_start: 0.8524 (m110) cc_final: 0.8120 (m110) REVERT: J 60 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8247 (mttt) REVERT: J 71 LYS cc_start: 0.9280 (ttmt) cc_final: 0.9070 (ttmm) REVERT: J 77 ASN cc_start: 0.9195 (t0) cc_final: 0.8747 (t0) REVERT: K 21 LYS cc_start: 0.9012 (mttt) cc_final: 0.8604 (mttp) REVERT: K 25 ASP cc_start: 0.7987 (m-30) cc_final: 0.7437 (m-30) REVERT: K 60 LYS cc_start: 0.8442 (mtmt) cc_final: 0.7982 (mtpp) REVERT: K 66 CYS cc_start: 0.8539 (m) cc_final: 0.8338 (m) REVERT: K 78 TYR cc_start: 0.8941 (t80) cc_final: 0.8675 (t80) REVERT: K 83 ASP cc_start: 0.8707 (t70) cc_final: 0.8327 (t0) REVERT: L 21 LYS cc_start: 0.9318 (mttp) cc_final: 0.8925 (mttm) REVERT: L 24 THR cc_start: 0.9348 (m) cc_final: 0.9134 (p) REVERT: L 35 ARG cc_start: 0.7634 (ttm110) cc_final: 0.6935 (tpp80) REVERT: L 66 CYS cc_start: 0.8272 (m) cc_final: 0.7960 (m) REVERT: M 39 ASN cc_start: 0.8536 (m110) cc_final: 0.7999 (m-40) REVERT: N 20 ILE cc_start: 0.9166 (mt) cc_final: 0.8956 (mp) REVERT: N 66 CYS cc_start: 0.8559 (m) cc_final: 0.8141 (m) REVERT: N 78 TYR cc_start: 0.8877 (t80) cc_final: 0.8564 (t80) REVERT: N 82 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8096 (mm110) REVERT: N 89 LEU cc_start: 0.6744 (tp) cc_final: 0.6399 (tp) REVERT: O 2 ASN cc_start: 0.8012 (m-40) cc_final: 0.7432 (m-40) REVERT: O 35 ARG cc_start: 0.7516 (ttm110) cc_final: 0.7171 (tpp80) REVERT: O 39 ASN cc_start: 0.8436 (m110) cc_final: 0.8137 (m110) REVERT: O 44 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7594 (mm-30) REVERT: O 60 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8364 (mtpt) REVERT: O 75 GLU cc_start: 0.9240 (tm-30) cc_final: 0.9022 (tm-30) REVERT: P 60 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8665 (mtpt) REVERT: P 66 CYS cc_start: 0.8655 (m) cc_final: 0.8234 (m) REVERT: P 67 ASN cc_start: 0.8927 (m-40) cc_final: 0.8561 (m-40) REVERT: Q 7 ASN cc_start: 0.8619 (m-40) cc_final: 0.8040 (m110) REVERT: Q 34 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7489 (t0) REVERT: Q 60 LYS cc_start: 0.9050 (mtmt) cc_final: 0.8793 (mtpt) REVERT: Q 78 TYR cc_start: 0.8846 (t80) cc_final: 0.8630 (t80) REVERT: Q 82 GLN cc_start: 0.8535 (mm110) cc_final: 0.8324 (mm110) REVERT: R 1 MET cc_start: 0.7119 (tpp) cc_final: 0.6813 (tpp) REVERT: R 21 LYS cc_start: 0.9240 (mttt) cc_final: 0.8766 (mttt) REVERT: R 25 ASP cc_start: 0.8525 (m-30) cc_final: 0.8221 (m-30) REVERT: R 34 ASN cc_start: 0.7593 (t0) cc_final: 0.7244 (t0) REVERT: R 35 ARG cc_start: 0.7593 (ttm110) cc_final: 0.7383 (tpp80) REVERT: R 36 GLU cc_start: 0.7040 (mp0) cc_final: 0.6576 (mp0) REVERT: R 39 ASN cc_start: 0.8357 (m110) cc_final: 0.7931 (m-40) REVERT: R 47 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7076 (tt0) REVERT: R 52 ARG cc_start: 0.7696 (mtt90) cc_final: 0.7325 (mtt-85) REVERT: R 60 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8438 (mttt) REVERT: R 66 CYS cc_start: 0.8402 (m) cc_final: 0.8086 (m) REVERT: S 2 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7172 (m-40) REVERT: S 34 ASN cc_start: 0.8076 (t0) cc_final: 0.7195 (t0) REVERT: S 39 ASN cc_start: 0.8437 (m-40) cc_final: 0.8148 (m110) REVERT: S 56 HIS cc_start: 0.8204 (m90) cc_final: 0.7753 (m-70) REVERT: S 60 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8344 (mtpt) REVERT: S 66 CYS cc_start: 0.8577 (m) cc_final: 0.8234 (m) REVERT: S 78 TYR cc_start: 0.8936 (t80) cc_final: 0.8626 (t80) REVERT: S 82 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8389 (mm110) REVERT: T 17 MET cc_start: 0.7996 (tpp) cc_final: 0.7731 (tpp) REVERT: T 21 LYS cc_start: 0.9173 (mttp) cc_final: 0.8761 (mttm) REVERT: T 35 ARG cc_start: 0.7749 (ttm110) cc_final: 0.7097 (ttp-110) REVERT: T 37 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7306 (mt-10) REVERT: T 39 ASN cc_start: 0.8279 (m110) cc_final: 0.7560 (m110) REVERT: T 58 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9075 (tp) REVERT: T 77 ASN cc_start: 0.9180 (t0) cc_final: 0.8805 (t0) REVERT: T 83 ASP cc_start: 0.8711 (t70) cc_final: 0.8494 (t70) REVERT: U 2 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7713 (m-40) REVERT: U 34 ASN cc_start: 0.8281 (t0) cc_final: 0.7247 (t0) REVERT: U 35 ARG cc_start: 0.7585 (ttm110) cc_final: 0.7215 (ttp-110) REVERT: U 39 ASN cc_start: 0.8202 (m110) cc_final: 0.7550 (m110) REVERT: U 47 GLU cc_start: 0.7615 (tt0) cc_final: 0.6990 (tt0) REVERT: U 49 ASP cc_start: 0.8585 (m-30) cc_final: 0.8331 (m-30) REVERT: U 60 LYS cc_start: 0.8603 (mtmt) cc_final: 0.8369 (mtpp) REVERT: V 34 ASN cc_start: 0.7992 (t0) cc_final: 0.7374 (t0) REVERT: V 39 ASN cc_start: 0.8431 (m-40) cc_final: 0.7906 (m110) REVERT: V 66 CYS cc_start: 0.8712 (m) cc_final: 0.8449 (m) REVERT: W 6 ASP cc_start: 0.8340 (m-30) cc_final: 0.8104 (m-30) REVERT: W 35 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7355 (ttp-110) REVERT: W 39 ASN cc_start: 0.8157 (m-40) cc_final: 0.7312 (m110) REVERT: W 47 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: W 60 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8360 (mtmm) REVERT: X 21 LYS cc_start: 0.9073 (mttp) cc_final: 0.8271 (mttp) REVERT: X 25 ASP cc_start: 0.8150 (m-30) cc_final: 0.7737 (m-30) REVERT: X 35 ARG cc_start: 0.7685 (ttm110) cc_final: 0.7451 (tpp80) REVERT: X 39 ASN cc_start: 0.8502 (m110) cc_final: 0.8166 (m-40) REVERT: X 66 CYS cc_start: 0.8810 (m) cc_final: 0.8176 (m) REVERT: X 82 GLN cc_start: 0.8541 (mm110) cc_final: 0.8204 (mm110) REVERT: X 87 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7490 (mm-40) REVERT: Y 7 ASN cc_start: 0.8783 (m-40) cc_final: 0.8387 (m-40) REVERT: Y 31 ASN cc_start: 0.9054 (m-40) cc_final: 0.8823 (m-40) REVERT: Y 60 LYS cc_start: 0.9119 (mtmt) cc_final: 0.7871 (tptt) REVERT: Y 66 CYS cc_start: 0.8352 (m) cc_final: 0.7960 (m) REVERT: Z 1 MET cc_start: 0.6165 (tpp) cc_final: 0.5708 (tpp) REVERT: Z 2 ASN cc_start: 0.8086 (m-40) cc_final: 0.7478 (m110) REVERT: Z 9 ARG cc_start: 0.7916 (mtp85) cc_final: 0.7714 (mtp85) REVERT: Z 18 THR cc_start: 0.9363 (m) cc_final: 0.9130 (p) REVERT: Z 37 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7852 (mt-10) REVERT: Z 44 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7723 (mm-30) REVERT: Z 60 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8296 (mtpt) REVERT: Z 61 LYS cc_start: 0.8397 (mttp) cc_final: 0.8181 (mttm) REVERT: Z 77 ASN cc_start: 0.8936 (t0) cc_final: 0.8210 (t0) REVERT: a 2 ASN cc_start: 0.7993 (m-40) cc_final: 0.7681 (m110) REVERT: a 5 LYS cc_start: 0.8694 (tttm) cc_final: 0.8314 (tptt) REVERT: a 9 ARG cc_start: 0.7945 (mtp180) cc_final: 0.7521 (mmt-90) REVERT: a 12 ILE cc_start: 0.9347 (mt) cc_final: 0.9114 (mt) REVERT: a 35 ARG cc_start: 0.7376 (ttm110) cc_final: 0.7067 (ttm110) REVERT: a 45 LYS cc_start: 0.8354 (ttpt) cc_final: 0.7735 (tttp) REVERT: a 60 LYS cc_start: 0.8980 (mtmt) cc_final: 0.7777 (tptm) REVERT: b 37 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7618 (mt-10) REVERT: b 39 ASN cc_start: 0.8153 (m110) cc_final: 0.7606 (m110) REVERT: b 58 ILE cc_start: 0.9034 (tp) cc_final: 0.8795 (tp) REVERT: b 74 LYS cc_start: 0.9146 (ttpt) cc_final: 0.8910 (ttmm) REVERT: b 77 ASN cc_start: 0.9064 (t0) cc_final: 0.8742 (t0) REVERT: b 87 GLN cc_start: 0.8107 (mm-40) cc_final: 0.7810 (mm110) REVERT: c 20 ILE cc_start: 0.9052 (mt) cc_final: 0.8818 (mp) REVERT: c 39 ASN cc_start: 0.8478 (m110) cc_final: 0.8049 (m110) REVERT: c 44 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7780 (mm-30) REVERT: c 48 GLN cc_start: 0.8442 (mp10) cc_final: 0.7731 (mp10) REVERT: c 58 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8986 (tp) REVERT: d 1 MET cc_start: 0.7382 (tpp) cc_final: 0.7024 (tpt) REVERT: d 2 ASN cc_start: 0.8112 (m-40) cc_final: 0.7906 (m-40) REVERT: d 3 PHE cc_start: 0.8879 (t80) cc_final: 0.8627 (t80) REVERT: d 13 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8770 (mm110) REVERT: d 34 ASN cc_start: 0.7612 (t160) cc_final: 0.7300 (t0) REVERT: d 60 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8362 (mtpp) REVERT: d 74 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8879 (ttpp) REVERT: d 82 GLN cc_start: 0.8989 (mm110) cc_final: 0.8773 (mm-40) REVERT: d 83 ASP cc_start: 0.8537 (t70) cc_final: 0.8275 (t0) REVERT: e 9 ARG cc_start: 0.6371 (tpt170) cc_final: 0.6030 (ttm-80) REVERT: e 13 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8738 (mm-40) REVERT: e 34 ASN cc_start: 0.8081 (t0) cc_final: 0.7659 (t0) REVERT: e 39 ASN cc_start: 0.8386 (m-40) cc_final: 0.8109 (m-40) REVERT: e 74 LYS cc_start: 0.8841 (tttt) cc_final: 0.8581 (ttpp) REVERT: e 77 ASN cc_start: 0.9129 (t0) cc_final: 0.8639 (t0) REVERT: e 82 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8398 (mm110) REVERT: e 87 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8065 (mm110) outliers start: 136 outliers final: 64 residues processed: 1744 average time/residue: 0.3690 time to fit residues: 957.5798 Evaluate side-chains 1619 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1546 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain Q residue 34 ASN Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain S residue 42 CYS Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain T residue 58 ILE Chi-restraints excluded: chain U residue 2 ASN Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 54 ILE Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 8 SER Chi-restraints excluded: chain Y residue 20 ILE Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 58 ILE Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 54 ILE Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 74 LYS Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 210 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 253 optimal weight: 6.9990 chunk 274 optimal weight: 10.0000 chunk 226 optimal weight: 0.9990 chunk 251 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 31 ASN B 34 ASN C 31 ASN D 82 GLN E 34 ASN E 82 GLN F 31 ASN F 39 ASN G 67 ASN H 67 ASN H 82 GLN I 13 GLN I 31 ASN I 77 ASN J 67 ASN K 34 ASN K 39 ASN L 34 ASN L 82 GLN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN P 39 ASN P 77 ASN Q 22 GLN ** Q 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN R 34 ASN S 22 GLN S 39 ASN T 22 GLN T 34 ASN T 82 GLN V 39 ASN V 82 GLN W 22 GLN W 67 ASN ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 ASN Y 67 ASN Z 82 GLN b 22 GLN b 82 GLN ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 82 GLN d 34 ASN d 67 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23095 Z= 0.181 Angle : 0.536 7.368 31000 Z= 0.293 Chirality : 0.040 0.177 3472 Planarity : 0.003 0.029 3937 Dihedral : 3.746 14.326 2914 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 5.95 % Allowed : 20.02 % Favored : 74.04 % 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: 1.57 (0.16), residues: 2728 helix: 1.35 (0.10), residues: 2511 sheet: None (None), residues: 0 loop : -2.11 (0.35), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 30 HIS 0.007 0.001 HIS S 56 PHE 0.018 0.001 PHE G 3 TYR 0.011 0.001 TYR E 78 ARG 0.007 0.001 ARG P 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1839 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1686 time to evaluate : 3.041 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 18 THR cc_start: 0.8892 (p) cc_final: 0.8455 (p) REVERT: A 34 ASN cc_start: 0.8024 (t0) cc_final: 0.7603 (t0) REVERT: A 37 GLU cc_start: 0.8588 (mp0) cc_final: 0.8369 (mp0) REVERT: A 47 GLU cc_start: 0.7023 (tt0) cc_final: 0.6570 (tt0) REVERT: A 60 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8289 (mtpt) REVERT: A 66 CYS cc_start: 0.8498 (m) cc_final: 0.8218 (m) REVERT: B 37 GLU cc_start: 0.7727 (mt-10) cc_final: 0.6850 (mt-10) REVERT: B 60 LYS cc_start: 0.8693 (mtmt) cc_final: 0.8435 (mtmm) REVERT: B 74 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8695 (ptmm) REVERT: B 77 ASN cc_start: 0.8977 (t0) cc_final: 0.8561 (t0) REVERT: B 78 TYR cc_start: 0.8678 (t80) cc_final: 0.7527 (t80) REVERT: B 82 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7451 (mp10) REVERT: B 83 ASP cc_start: 0.8651 (t70) cc_final: 0.8364 (t0) REVERT: C 2 ASN cc_start: 0.7852 (m-40) cc_final: 0.7424 (m-40) REVERT: C 34 ASN cc_start: 0.7807 (t0) cc_final: 0.6937 (t0) REVERT: C 60 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8400 (mtpp) REVERT: C 83 ASP cc_start: 0.8505 (t70) cc_final: 0.8147 (t0) REVERT: D 13 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8618 (mm-40) REVERT: D 36 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7258 (tt0) REVERT: D 60 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8351 (mtpp) REVERT: D 66 CYS cc_start: 0.8238 (m) cc_final: 0.7919 (m) REVERT: D 74 LYS cc_start: 0.8959 (tttt) cc_final: 0.8654 (ttpp) REVERT: E 9 ARG cc_start: 0.8605 (mtp-110) cc_final: 0.8229 (mtp-110) REVERT: E 20 ILE cc_start: 0.9255 (mt) cc_final: 0.8853 (mp) REVERT: E 34 ASN cc_start: 0.7834 (t0) cc_final: 0.6926 (t0) REVERT: E 57 MET cc_start: 0.8024 (mtm) cc_final: 0.7755 (mtp) REVERT: E 60 LYS cc_start: 0.8560 (mtmt) cc_final: 0.8313 (mtpp) REVERT: E 72 SER cc_start: 0.9043 (m) cc_final: 0.8813 (t) REVERT: E 78 TYR cc_start: 0.8625 (t80) cc_final: 0.8205 (t80) REVERT: F 9 ARG cc_start: 0.8401 (mtp-110) cc_final: 0.8181 (mtp-110) REVERT: F 19 VAL cc_start: 0.9368 (t) cc_final: 0.9151 (t) REVERT: F 34 ASN cc_start: 0.7519 (t0) cc_final: 0.6541 (t0) REVERT: F 39 ASN cc_start: 0.8495 (m-40) cc_final: 0.8178 (m-40) REVERT: G 1 MET cc_start: 0.6164 (tpp) cc_final: 0.5832 (tpp) REVERT: G 34 ASN cc_start: 0.7461 (t0) cc_final: 0.7158 (t0) REVERT: G 35 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7556 (ttp-110) REVERT: G 39 ASN cc_start: 0.8325 (m110) cc_final: 0.8081 (m110) REVERT: G 77 ASN cc_start: 0.8938 (t0) cc_final: 0.8562 (t0) REVERT: G 83 ASP cc_start: 0.8473 (t70) cc_final: 0.8195 (t0) REVERT: H 2 ASN cc_start: 0.7542 (m-40) cc_final: 0.7099 (m110) REVERT: H 7 ASN cc_start: 0.8880 (m-40) cc_final: 0.8498 (m110) REVERT: H 31 ASN cc_start: 0.9116 (m-40) cc_final: 0.8912 (m110) REVERT: H 35 ARG cc_start: 0.7664 (ttm170) cc_final: 0.7221 (tpp80) REVERT: H 36 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: H 56 HIS cc_start: 0.8040 (m90) cc_final: 0.7498 (m-70) REVERT: I 1 MET cc_start: 0.5279 (tpp) cc_final: 0.4634 (tpt) REVERT: I 7 ASN cc_start: 0.8933 (m-40) cc_final: 0.8628 (m110) REVERT: J 1 MET cc_start: 0.7074 (tpp) cc_final: 0.6620 (tpp) REVERT: J 2 ASN cc_start: 0.8250 (m-40) cc_final: 0.7898 (m-40) REVERT: J 35 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7523 (ttm110) REVERT: J 39 ASN cc_start: 0.8463 (m110) cc_final: 0.7798 (m110) REVERT: J 77 ASN cc_start: 0.9092 (t0) cc_final: 0.8774 (t0) REVERT: K 13 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8298 (mm110) REVERT: K 21 LYS cc_start: 0.9077 (mttt) cc_final: 0.8571 (mttp) REVERT: K 25 ASP cc_start: 0.7907 (m-30) cc_final: 0.7564 (m-30) REVERT: K 34 ASN cc_start: 0.7908 (t0) cc_final: 0.7383 (t0) REVERT: K 37 GLU cc_start: 0.8840 (mp0) cc_final: 0.8548 (mp0) REVERT: K 39 ASN cc_start: 0.8511 (m-40) cc_final: 0.8124 (m110) REVERT: K 60 LYS cc_start: 0.8324 (mtmt) cc_final: 0.7998 (mtpp) REVERT: K 78 TYR cc_start: 0.8810 (t80) cc_final: 0.8547 (t80) REVERT: K 83 ASP cc_start: 0.8627 (t70) cc_final: 0.8326 (t0) REVERT: L 1 MET cc_start: 0.5836 (tpp) cc_final: 0.5595 (tpt) REVERT: L 35 ARG cc_start: 0.7262 (ttm110) cc_final: 0.6919 (tpp80) REVERT: L 52 ARG cc_start: 0.7831 (mtt90) cc_final: 0.7623 (mtt-85) REVERT: L 66 CYS cc_start: 0.8259 (m) cc_final: 0.7924 (m) REVERT: L 77 ASN cc_start: 0.9005 (t0) cc_final: 0.8520 (t0) REVERT: M 1 MET cc_start: 0.5830 (tpp) cc_final: 0.5559 (tpp) REVERT: M 34 ASN cc_start: 0.8035 (t0) cc_final: 0.7615 (t0) REVERT: M 35 ARG cc_start: 0.7777 (tpp80) cc_final: 0.7513 (tpp-160) REVERT: M 39 ASN cc_start: 0.8724 (m110) cc_final: 0.8313 (m110) REVERT: M 44 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7936 (mm-30) REVERT: N 2 ASN cc_start: 0.8363 (m-40) cc_final: 0.7868 (m110) REVERT: N 34 ASN cc_start: 0.7643 (t0) cc_final: 0.6859 (t0) REVERT: N 39 ASN cc_start: 0.8286 (m110) cc_final: 0.7964 (m110) REVERT: N 41 ILE cc_start: 0.9145 (mt) cc_final: 0.8844 (tt) REVERT: N 78 TYR cc_start: 0.8802 (t80) cc_final: 0.8498 (t80) REVERT: N 89 LEU cc_start: 0.6530 (tp) cc_final: 0.6019 (tp) REVERT: O 1 MET cc_start: 0.6480 (tpp) cc_final: 0.6226 (tpp) REVERT: O 34 ASN cc_start: 0.7863 (t0) cc_final: 0.7660 (t0) REVERT: O 39 ASN cc_start: 0.8450 (m110) cc_final: 0.8149 (m-40) REVERT: O 44 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7514 (mm-30) REVERT: O 60 LYS cc_start: 0.9017 (mtmt) cc_final: 0.8614 (mttt) REVERT: P 13 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8365 (mm110) REVERT: P 34 ASN cc_start: 0.7736 (t0) cc_final: 0.7117 (t0) REVERT: P 41 ILE cc_start: 0.9230 (mm) cc_final: 0.8983 (mt) REVERT: P 48 GLN cc_start: 0.8534 (mp10) cc_final: 0.8083 (mp10) REVERT: P 60 LYS cc_start: 0.9003 (mtmt) cc_final: 0.8662 (mtpt) REVERT: P 67 ASN cc_start: 0.8837 (m-40) cc_final: 0.8402 (m-40) REVERT: Q 7 ASN cc_start: 0.8693 (m-40) cc_final: 0.8092 (m110) REVERT: Q 60 LYS cc_start: 0.9003 (mtmt) cc_final: 0.8788 (mtpt) REVERT: Q 82 GLN cc_start: 0.8407 (mm110) cc_final: 0.7875 (mm-40) REVERT: R 21 LYS cc_start: 0.9217 (mttt) cc_final: 0.8774 (mttt) REVERT: R 36 GLU cc_start: 0.6749 (mp0) cc_final: 0.6066 (mp0) REVERT: R 39 ASN cc_start: 0.8298 (m110) cc_final: 0.8085 (m110) REVERT: R 44 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7564 (mm-30) REVERT: R 60 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8403 (mttt) REVERT: R 77 ASN cc_start: 0.9113 (t0) cc_final: 0.8428 (t0) REVERT: S 2 ASN cc_start: 0.7657 (m-40) cc_final: 0.7196 (m110) REVERT: S 24 THR cc_start: 0.9234 (m) cc_final: 0.8994 (p) REVERT: S 34 ASN cc_start: 0.8075 (t0) cc_final: 0.7840 (t0) REVERT: S 35 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7636 (tpp80) REVERT: S 39 ASN cc_start: 0.8477 (m110) cc_final: 0.8091 (m110) REVERT: S 66 CYS cc_start: 0.8624 (m) cc_final: 0.8310 (m) REVERT: S 78 TYR cc_start: 0.8817 (t80) cc_final: 0.8490 (t80) REVERT: T 35 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7073 (ttp-110) REVERT: T 39 ASN cc_start: 0.8241 (m110) cc_final: 0.7508 (m110) REVERT: T 45 LYS cc_start: 0.7982 (tttm) cc_final: 0.7259 (tttm) REVERT: U 35 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7228 (ttp-110) REVERT: U 39 ASN cc_start: 0.8254 (m110) cc_final: 0.7591 (m110) REVERT: U 49 ASP cc_start: 0.8456 (m-30) cc_final: 0.8188 (m-30) REVERT: U 60 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8369 (mtpp) REVERT: U 72 SER cc_start: 0.9064 (m) cc_final: 0.8701 (t) REVERT: U 82 GLN cc_start: 0.8252 (mm-40) cc_final: 0.8029 (mm-40) REVERT: V 35 ARG cc_start: 0.7880 (ttm170) cc_final: 0.7518 (tpp80) REVERT: V 39 ASN cc_start: 0.8232 (m110) cc_final: 0.7852 (m-40) REVERT: V 60 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8409 (mtpp) REVERT: V 66 CYS cc_start: 0.8632 (m) cc_final: 0.8363 (m) REVERT: W 60 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8375 (mtmm) REVERT: X 17 MET cc_start: 0.8140 (tpp) cc_final: 0.7853 (tpp) REVERT: X 21 LYS cc_start: 0.8981 (mttp) cc_final: 0.8495 (mttp) REVERT: X 22 GLN cc_start: 0.8603 (mt0) cc_final: 0.8260 (mt0) REVERT: X 25 ASP cc_start: 0.8226 (m-30) cc_final: 0.7767 (m-30) REVERT: X 39 ASN cc_start: 0.8677 (m110) cc_final: 0.8311 (m110) REVERT: X 66 CYS cc_start: 0.8687 (m) cc_final: 0.8117 (m) REVERT: X 82 GLN cc_start: 0.8433 (mm110) cc_final: 0.8199 (mm110) REVERT: Y 7 ASN cc_start: 0.8744 (m-40) cc_final: 0.8204 (m-40) REVERT: Y 37 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: Y 39 ASN cc_start: 0.8026 (m110) cc_final: 0.7707 (m-40) REVERT: Y 43 CYS cc_start: 0.7980 (p) cc_final: 0.7537 (p) REVERT: Y 60 LYS cc_start: 0.9141 (mtmt) cc_final: 0.7879 (tptt) REVERT: Y 66 CYS cc_start: 0.8404 (m) cc_final: 0.8050 (m) REVERT: Z 1 MET cc_start: 0.5919 (tpp) cc_final: 0.5476 (tpp) REVERT: Z 34 ASN cc_start: 0.7578 (t0) cc_final: 0.7221 (t0) REVERT: Z 44 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7766 (mm-30) REVERT: Z 60 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8318 (mtpt) REVERT: Z 77 ASN cc_start: 0.8830 (t0) cc_final: 0.8258 (t0) REVERT: a 5 LYS cc_start: 0.8908 (tttm) cc_final: 0.8293 (tptt) REVERT: a 9 ARG cc_start: 0.7843 (mtp180) cc_final: 0.7447 (mmt-90) REVERT: a 34 ASN cc_start: 0.7388 (t0) cc_final: 0.6579 (t0) REVERT: a 39 ASN cc_start: 0.8539 (m110) cc_final: 0.8293 (m-40) REVERT: a 60 LYS cc_start: 0.9006 (mtmt) cc_final: 0.7689 (tptm) REVERT: b 39 ASN cc_start: 0.8186 (m110) cc_final: 0.7680 (m110) REVERT: b 52 ARG cc_start: 0.7882 (mtt90) cc_final: 0.7677 (mtt90) REVERT: b 74 LYS cc_start: 0.9100 (ttpt) cc_final: 0.8882 (ttmm) REVERT: b 77 ASN cc_start: 0.8996 (t0) cc_final: 0.8691 (t0) REVERT: b 82 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8171 (mm110) REVERT: c 1 MET cc_start: 0.6120 (tpp) cc_final: 0.5903 (tpp) REVERT: c 13 GLN cc_start: 0.8864 (mm110) cc_final: 0.8653 (mm110) REVERT: c 35 ARG cc_start: 0.7785 (tpp80) cc_final: 0.7149 (tpp-160) REVERT: c 37 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8288 (mp0) REVERT: c 39 ASN cc_start: 0.8586 (m110) cc_final: 0.7965 (m110) REVERT: c 44 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7846 (mm-30) REVERT: c 57 MET cc_start: 0.8358 (mtm) cc_final: 0.8154 (mtp) REVERT: c 58 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8753 (tp) REVERT: d 1 MET cc_start: 0.7050 (tpp) cc_final: 0.6750 (tpt) REVERT: d 2 ASN cc_start: 0.8142 (m-40) cc_final: 0.7876 (m-40) REVERT: d 13 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8582 (mm-40) REVERT: d 26 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8113 (t0) REVERT: d 60 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8284 (mtpp) REVERT: d 74 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8833 (ttpp) REVERT: d 82 GLN cc_start: 0.8950 (mm110) cc_final: 0.8652 (mm110) REVERT: d 83 ASP cc_start: 0.8537 (t70) cc_final: 0.8256 (t0) REVERT: e 13 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8611 (mm-40) REVERT: e 34 ASN cc_start: 0.8251 (t0) cc_final: 0.7791 (t0) REVERT: e 39 ASN cc_start: 0.8597 (m-40) cc_final: 0.8136 (m110) REVERT: e 74 LYS cc_start: 0.8865 (tttt) cc_final: 0.8610 (ttpp) REVERT: e 77 ASN cc_start: 0.9003 (t0) cc_final: 0.8573 (t0) REVERT: e 80 LEU cc_start: 0.9010 (tp) cc_final: 0.8792 (tp) outliers start: 153 outliers final: 77 residues processed: 1717 average time/residue: 0.4000 time to fit residues: 1036.0315 Evaluate side-chains 1635 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1552 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain O residue 8 SER Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain S residue 15 MET Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain T residue 2 ASN Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 26 ASP Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 37 GLU Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 58 ILE Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain d residue 54 ILE Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 74 LYS Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 250 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 254 optimal weight: 0.8980 chunk 269 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN B 13 GLN B 31 ASN B 39 ASN C 31 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN F 82 GLN G 13 GLN G 67 ASN G 82 GLN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 ASN I 82 GLN J 67 ASN J 82 GLN L 82 GLN M 22 GLN M 31 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN O 82 GLN P 77 ASN P 82 GLN ** Q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN T 13 GLN ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 ASN ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 82 GLN ** W 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 ASN ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 67 ASN Y 13 GLN Y 67 ASN Y 82 GLN Z 2 ASN Z 82 GLN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 GLN b 13 GLN b 22 GLN c 13 GLN ** c 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 ASN ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 82 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23095 Z= 0.246 Angle : 0.563 6.031 31000 Z= 0.309 Chirality : 0.041 0.195 3472 Planarity : 0.004 0.033 3937 Dihedral : 3.709 13.855 2914 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 6.80 % Allowed : 21.92 % Favored : 71.28 % 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: 1.45 (0.16), residues: 2728 helix: 1.34 (0.10), residues: 2480 sheet: None (None), residues: 0 loop : -2.58 (0.30), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 30 HIS 0.003 0.001 HIS R 56 PHE 0.025 0.001 PHE Y 81 TYR 0.017 0.002 TYR a 78 ARG 0.007 0.001 ARG O 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1819 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1644 time to evaluate : 2.672 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: symmetry clash REVERT: A 1 MET cc_start: 0.6745 (tpp) cc_final: 0.6218 (tpt) REVERT: A 18 THR cc_start: 0.8858 (p) cc_final: 0.8565 (p) REVERT: A 47 GLU cc_start: 0.7153 (tt0) cc_final: 0.6900 (tt0) REVERT: A 60 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8368 (mtpt) REVERT: A 66 CYS cc_start: 0.8528 (m) cc_final: 0.8306 (m) REVERT: B 60 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8489 (mtmm) REVERT: C 2 ASN cc_start: 0.7897 (m-40) cc_final: 0.7583 (m110) REVERT: C 34 ASN cc_start: 0.7817 (t0) cc_final: 0.7593 (t0) REVERT: C 48 GLN cc_start: 0.8502 (mp10) cc_final: 0.8253 (mp10) REVERT: C 60 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8428 (mtpp) REVERT: D 5 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8789 (tptm) REVERT: D 13 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8672 (mm-40) REVERT: D 35 ARG cc_start: 0.7781 (tpp80) cc_final: 0.7481 (tpp80) REVERT: D 39 ASN cc_start: 0.8116 (m110) cc_final: 0.7513 (m-40) REVERT: D 60 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8382 (mtpp) REVERT: D 74 LYS cc_start: 0.8997 (tttt) cc_final: 0.8680 (ttpp) REVERT: E 57 MET cc_start: 0.8130 (mtm) cc_final: 0.7711 (mtp) REVERT: E 60 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8310 (mtpp) REVERT: E 78 TYR cc_start: 0.8694 (t80) cc_final: 0.8261 (t80) REVERT: F 34 ASN cc_start: 0.7900 (t0) cc_final: 0.7357 (t0) REVERT: F 37 GLU cc_start: 0.9004 (mp0) cc_final: 0.8623 (mp0) REVERT: F 82 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8247 (mm110) REVERT: G 35 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7709 (ttp-110) REVERT: G 39 ASN cc_start: 0.8437 (m110) cc_final: 0.7821 (m110) REVERT: G 83 ASP cc_start: 0.8446 (t70) cc_final: 0.8107 (t0) REVERT: H 1 MET cc_start: 0.5857 (tpp) cc_final: 0.5578 (tpt) REVERT: H 7 ASN cc_start: 0.8914 (m-40) cc_final: 0.8543 (m110) REVERT: H 35 ARG cc_start: 0.7676 (ttm170) cc_final: 0.7344 (tpp80) REVERT: H 36 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: H 60 LYS cc_start: 0.8272 (mtpt) cc_final: 0.8051 (mtpt) REVERT: I 2 ASN cc_start: 0.8156 (m-40) cc_final: 0.7903 (m110) REVERT: I 14 ARG cc_start: 0.7430 (mtt180) cc_final: 0.7100 (mtp180) REVERT: J 1 MET cc_start: 0.7275 (tpp) cc_final: 0.6428 (tpt) REVERT: J 2 ASN cc_start: 0.8285 (m-40) cc_final: 0.7693 (m-40) REVERT: J 22 GLN cc_start: 0.8984 (mt0) cc_final: 0.8599 (mt0) REVERT: J 39 ASN cc_start: 0.8377 (m110) cc_final: 0.8170 (m110) REVERT: K 17 MET cc_start: 0.8346 (tpp) cc_final: 0.7846 (tpt) REVERT: K 21 LYS cc_start: 0.9052 (mttt) cc_final: 0.8400 (mttp) REVERT: K 25 ASP cc_start: 0.8116 (m-30) cc_final: 0.7591 (m-30) REVERT: K 45 LYS cc_start: 0.8305 (tttm) cc_final: 0.8071 (tmtt) REVERT: K 60 LYS cc_start: 0.8348 (mtmt) cc_final: 0.8138 (mtpp) REVERT: K 77 ASN cc_start: 0.9153 (t0) cc_final: 0.8657 (t0) REVERT: K 83 ASP cc_start: 0.8633 (t70) cc_final: 0.8104 (t0) REVERT: L 1 MET cc_start: 0.5980 (tpp) cc_final: 0.5540 (tpt) REVERT: L 35 ARG cc_start: 0.7415 (ttm110) cc_final: 0.7069 (tpp80) REVERT: L 66 CYS cc_start: 0.8235 (m) cc_final: 0.7905 (m) REVERT: M 1 MET cc_start: 0.6223 (tpp) cc_final: 0.5849 (tpt) REVERT: M 9 ARG cc_start: 0.8487 (mtp-110) cc_final: 0.8266 (mtp-110) REVERT: M 35 ARG cc_start: 0.7813 (tpp80) cc_final: 0.7598 (tpp80) REVERT: M 39 ASN cc_start: 0.8592 (m110) cc_final: 0.7857 (m-40) REVERT: M 44 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7984 (mm-30) REVERT: M 71 LYS cc_start: 0.9271 (ptmt) cc_final: 0.8981 (ptmt) REVERT: M 82 GLN cc_start: 0.8685 (mm110) cc_final: 0.8293 (mm110) REVERT: N 39 ASN cc_start: 0.8446 (m-40) cc_final: 0.8005 (m-40) REVERT: N 78 TYR cc_start: 0.8918 (t80) cc_final: 0.8625 (t80) REVERT: N 89 LEU cc_start: 0.7206 (tp) cc_final: 0.6972 (tp) REVERT: O 1 MET cc_start: 0.6672 (tpp) cc_final: 0.6449 (tpp) REVERT: O 39 ASN cc_start: 0.8501 (m110) cc_final: 0.7689 (m110) REVERT: O 44 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7700 (mm-30) REVERT: O 52 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7184 (mtt-85) REVERT: O 60 LYS cc_start: 0.9033 (mtmt) cc_final: 0.8580 (mttt) REVERT: O 78 TYR cc_start: 0.8827 (t80) cc_final: 0.8500 (t80) REVERT: O 82 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8130 (mp10) REVERT: P 13 GLN cc_start: 0.8477 (mm-40) cc_final: 0.7830 (mm-40) REVERT: P 34 ASN cc_start: 0.8158 (t0) cc_final: 0.7856 (t0) REVERT: P 37 GLU cc_start: 0.8744 (mp0) cc_final: 0.8513 (mp0) REVERT: P 48 GLN cc_start: 0.8670 (mp10) cc_final: 0.8423 (mp10) REVERT: P 60 LYS cc_start: 0.9012 (mtmt) cc_final: 0.8654 (mtpt) REVERT: P 67 ASN cc_start: 0.8896 (m-40) cc_final: 0.8471 (m-40) REVERT: Q 7 ASN cc_start: 0.8748 (m-40) cc_final: 0.8120 (m110) REVERT: Q 34 ASN cc_start: 0.8230 (t0) cc_final: 0.7466 (t0) REVERT: Q 60 LYS cc_start: 0.8965 (mtmt) cc_final: 0.8734 (mtpt) REVERT: R 9 ARG cc_start: 0.8596 (mtp-110) cc_final: 0.8382 (mtp-110) REVERT: R 36 GLU cc_start: 0.6755 (mp0) cc_final: 0.6071 (mp0) REVERT: R 44 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7602 (mm-30) REVERT: R 48 GLN cc_start: 0.8584 (mp10) cc_final: 0.8383 (mp10) REVERT: R 60 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8431 (mttt) REVERT: S 2 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7318 (m-40) REVERT: S 20 ILE cc_start: 0.9164 (mt) cc_final: 0.8950 (mp) REVERT: S 24 THR cc_start: 0.9151 (m) cc_final: 0.8935 (p) REVERT: S 35 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7595 (tpp80) REVERT: S 39 ASN cc_start: 0.8565 (m110) cc_final: 0.8246 (m110) REVERT: S 66 CYS cc_start: 0.8498 (m) cc_final: 0.8243 (m) REVERT: T 1 MET cc_start: 0.6467 (tpp) cc_final: 0.5984 (tpt) REVERT: T 35 ARG cc_start: 0.7727 (ttm110) cc_final: 0.7314 (ttp-110) REVERT: T 39 ASN cc_start: 0.8209 (m110) cc_final: 0.7506 (m110) REVERT: T 45 LYS cc_start: 0.8089 (tttm) cc_final: 0.7391 (tttm) REVERT: U 35 ARG cc_start: 0.7536 (ttm110) cc_final: 0.7047 (ttp-110) REVERT: U 39 ASN cc_start: 0.8371 (m110) cc_final: 0.7700 (m110) REVERT: U 49 ASP cc_start: 0.8576 (m-30) cc_final: 0.8327 (m-30) REVERT: U 60 LYS cc_start: 0.8509 (mtmt) cc_final: 0.8191 (mtpp) REVERT: U 72 SER cc_start: 0.9032 (m) cc_final: 0.8802 (t) REVERT: U 82 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7936 (mm110) REVERT: V 35 ARG cc_start: 0.7994 (ttm170) cc_final: 0.7592 (tpp80) REVERT: V 39 ASN cc_start: 0.8340 (m110) cc_final: 0.8023 (m110) REVERT: V 47 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7013 (tt0) REVERT: V 57 MET cc_start: 0.8251 (mtm) cc_final: 0.8041 (mtp) REVERT: V 60 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8405 (mtpp) REVERT: V 66 CYS cc_start: 0.8536 (m) cc_final: 0.8280 (m) REVERT: W 2 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7762 (m-40) REVERT: W 34 ASN cc_start: 0.7936 (t0) cc_final: 0.7546 (t0) REVERT: W 41 ILE cc_start: 0.9013 (mm) cc_final: 0.8797 (mt) REVERT: W 47 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: W 60 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8446 (mtmm) REVERT: W 78 TYR cc_start: 0.8665 (t80) cc_final: 0.8241 (t80) REVERT: W 82 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8220 (mp10) REVERT: X 17 MET cc_start: 0.8322 (tpp) cc_final: 0.8106 (tpp) REVERT: X 21 LYS cc_start: 0.9079 (mttp) cc_final: 0.8443 (mttp) REVERT: X 22 GLN cc_start: 0.8678 (mt0) cc_final: 0.8312 (mt0) REVERT: X 25 ASP cc_start: 0.8248 (m-30) cc_final: 0.7617 (m-30) REVERT: X 34 ASN cc_start: 0.8039 (t0) cc_final: 0.7511 (t0) REVERT: X 37 GLU cc_start: 0.8837 (mp0) cc_final: 0.8511 (mp0) REVERT: X 66 CYS cc_start: 0.8624 (m) cc_final: 0.8080 (m) REVERT: X 82 GLN cc_start: 0.8708 (mm110) cc_final: 0.8327 (mp10) REVERT: Y 1 MET cc_start: 0.6911 (tpp) cc_final: 0.6114 (tpt) REVERT: Y 7 ASN cc_start: 0.8799 (m-40) cc_final: 0.8180 (m110) REVERT: Y 60 LYS cc_start: 0.9122 (mtmt) cc_final: 0.7914 (tptt) REVERT: Y 78 TYR cc_start: 0.8789 (t80) cc_final: 0.8399 (t80) REVERT: Y 82 GLN cc_start: 0.8485 (mm-40) cc_final: 0.7939 (mp10) REVERT: Z 44 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7809 (mm-30) REVERT: Z 60 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8463 (mtpt) REVERT: a 5 LYS cc_start: 0.8719 (tttm) cc_final: 0.8418 (tptt) REVERT: a 9 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7476 (mmt-90) REVERT: a 39 ASN cc_start: 0.8828 (m110) cc_final: 0.8580 (m-40) REVERT: a 60 LYS cc_start: 0.8999 (mtmt) cc_final: 0.7626 (tptm) REVERT: b 1 MET cc_start: 0.6634 (tpp) cc_final: 0.6330 (tpt) REVERT: b 17 MET cc_start: 0.8025 (tpt) cc_final: 0.7728 (tpt) REVERT: b 20 ILE cc_start: 0.9253 (mp) cc_final: 0.8997 (mp) REVERT: b 39 ASN cc_start: 0.8329 (m110) cc_final: 0.7764 (m110) REVERT: b 74 LYS cc_start: 0.9110 (ttpt) cc_final: 0.8899 (ttmm) REVERT: b 82 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8327 (mm110) REVERT: c 35 ARG cc_start: 0.7860 (tpp80) cc_final: 0.7444 (tpp-160) REVERT: c 39 ASN cc_start: 0.8439 (m110) cc_final: 0.7685 (m110) REVERT: c 58 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8977 (tp) REVERT: c 82 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8302 (mm110) REVERT: d 26 ASP cc_start: 0.8621 (t70) cc_final: 0.8293 (t70) REVERT: d 37 GLU cc_start: 0.8769 (mp0) cc_final: 0.8522 (mp0) REVERT: d 39 ASN cc_start: 0.8530 (m110) cc_final: 0.8266 (m110) REVERT: d 60 LYS cc_start: 0.8607 (mtmt) cc_final: 0.8208 (mtpt) REVERT: d 74 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8844 (ttpp) REVERT: d 82 GLN cc_start: 0.8979 (mm110) cc_final: 0.8756 (mm110) REVERT: e 13 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8517 (mm-40) REVERT: e 26 ASP cc_start: 0.8474 (t70) cc_final: 0.7809 (t0) REVERT: e 34 ASN cc_start: 0.8517 (t0) cc_final: 0.8116 (t0) REVERT: e 39 ASN cc_start: 0.8489 (m-40) cc_final: 0.7882 (m110) REVERT: e 74 LYS cc_start: 0.8886 (tttt) cc_final: 0.8594 (ttpp) outliers start: 175 outliers final: 110 residues processed: 1683 average time/residue: 0.3712 time to fit residues: 933.5639 Evaluate side-chains 1691 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1573 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 15 MET Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 15 MET Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain S residue 15 MET Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain T residue 2 ASN Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 26 ASP Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 2 ASN Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 71 LYS Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 36 GLU Chi-restraints excluded: chain Y residue 37 GLU Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 58 ILE Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain d residue 54 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 74 LYS Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 224 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 230 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 242 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 ASN B 82 GLN C 31 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN E 67 ASN E 82 GLN F 2 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN H 2 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN I 82 GLN J 67 ASN K 34 ASN K 82 GLN L 82 GLN M 31 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN O 13 GLN P 2 ASN P 82 GLN Q 34 ASN Q 82 GLN ** R 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 34 ASN W 39 ASN W 67 ASN ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 GLN Y 67 ASN Z 2 ASN Z 82 GLN Z 87 GLN a 2 ASN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 22 GLN ** c 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 13 GLN d 34 ASN d 67 ASN e 22 GLN e 39 ASN e 82 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23095 Z= 0.326 Angle : 0.615 6.234 31000 Z= 0.338 Chirality : 0.043 0.204 3472 Planarity : 0.004 0.047 3937 Dihedral : 3.903 15.753 2914 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 7.23 % Allowed : 23.28 % Favored : 69.49 % 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: 1.15 (0.16), residues: 2728 helix: 1.15 (0.10), residues: 2480 sheet: None (None), residues: 0 loop : -2.72 (0.28), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 30 HIS 0.006 0.001 HIS Z 56 PHE 0.020 0.001 PHE C 3 TYR 0.018 0.002 TYR F 78 ARG 0.008 0.001 ARG d 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1822 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1636 time to evaluate : 2.891 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: A 1 MET cc_start: 0.6803 (tpp) cc_final: 0.6340 (tpt) REVERT: A 60 LYS cc_start: 0.8828 (mtpt) cc_final: 0.8353 (mtpt) REVERT: A 66 CYS cc_start: 0.8487 (m) cc_final: 0.8274 (m) REVERT: B 71 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8720 (ttpp) REVERT: B 81 PHE cc_start: 0.9229 (t80) cc_final: 0.8733 (t80) REVERT: C 2 ASN cc_start: 0.7635 (m-40) cc_final: 0.7372 (m-40) REVERT: C 31 ASN cc_start: 0.8999 (m-40) cc_final: 0.8662 (m110) REVERT: C 60 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8428 (mtpp) REVERT: D 1 MET cc_start: 0.6330 (tpp) cc_final: 0.6013 (tpt) REVERT: D 13 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8644 (mm-40) REVERT: D 35 ARG cc_start: 0.7932 (tpp80) cc_final: 0.7565 (tpp80) REVERT: D 39 ASN cc_start: 0.8243 (m110) cc_final: 0.7776 (m110) REVERT: D 45 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8200 (ttpt) REVERT: D 74 LYS cc_start: 0.8998 (tttt) cc_final: 0.8660 (ttpp) REVERT: E 9 ARG cc_start: 0.8678 (mtp-110) cc_final: 0.8325 (mtp-110) REVERT: E 35 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7263 (tpp80) REVERT: E 39 ASN cc_start: 0.8454 (m110) cc_final: 0.7685 (m110) REVERT: E 57 MET cc_start: 0.8196 (mtm) cc_final: 0.7845 (mtp) REVERT: E 60 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8278 (mtpp) REVERT: E 78 TYR cc_start: 0.8824 (t80) cc_final: 0.8479 (t80) REVERT: F 34 ASN cc_start: 0.8086 (t0) cc_final: 0.7090 (t0) REVERT: F 37 GLU cc_start: 0.8990 (mp0) cc_final: 0.8355 (mp0) REVERT: G 35 ARG cc_start: 0.7856 (ttm110) cc_final: 0.7370 (ttm110) REVERT: G 39 ASN cc_start: 0.8417 (m110) cc_final: 0.7879 (m110) REVERT: G 66 CYS cc_start: 0.8283 (t) cc_final: 0.8050 (t) REVERT: G 67 ASN cc_start: 0.8742 (m-40) cc_final: 0.8508 (m110) REVERT: H 34 ASN cc_start: 0.7979 (t0) cc_final: 0.7702 (t0) REVERT: H 35 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7490 (tpp80) REVERT: H 36 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: H 45 LYS cc_start: 0.8332 (pttt) cc_final: 0.8097 (ptmt) REVERT: I 2 ASN cc_start: 0.8191 (m-40) cc_final: 0.7572 (m110) REVERT: I 6 ASP cc_start: 0.8100 (m-30) cc_final: 0.7873 (m-30) REVERT: I 14 ARG cc_start: 0.7401 (mtt180) cc_final: 0.7113 (mtp180) REVERT: J 1 MET cc_start: 0.7466 (tpp) cc_final: 0.6843 (tpt) REVERT: J 2 ASN cc_start: 0.8295 (m-40) cc_final: 0.7967 (m-40) REVERT: J 22 GLN cc_start: 0.8913 (mt0) cc_final: 0.8640 (mt0) REVERT: J 60 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8366 (mttt) REVERT: K 17 MET cc_start: 0.8276 (tpp) cc_final: 0.7843 (tpt) REVERT: K 21 LYS cc_start: 0.8935 (mttt) cc_final: 0.8482 (mttp) REVERT: K 25 ASP cc_start: 0.8224 (m-30) cc_final: 0.7646 (m-30) REVERT: K 34 ASN cc_start: 0.7931 (t0) cc_final: 0.7191 (t0) REVERT: K 37 GLU cc_start: 0.8853 (mp0) cc_final: 0.8006 (mp0) REVERT: K 60 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8203 (mtpp) REVERT: K 83 ASP cc_start: 0.8692 (t70) cc_final: 0.8306 (t0) REVERT: L 66 CYS cc_start: 0.8095 (m) cc_final: 0.7796 (m) REVERT: M 1 MET cc_start: 0.6700 (tpp) cc_final: 0.6299 (tpt) REVERT: M 35 ARG cc_start: 0.7914 (tpp80) cc_final: 0.7333 (tpp80) REVERT: M 39 ASN cc_start: 0.8461 (m110) cc_final: 0.7778 (m110) REVERT: M 71 LYS cc_start: 0.9273 (ptmt) cc_final: 0.8983 (ptmt) REVERT: N 1 MET cc_start: 0.6124 (tpt) cc_final: 0.5407 (tpt) REVERT: O 9 ARG cc_start: 0.8576 (mtp-110) cc_final: 0.8221 (mtp-110) REVERT: O 35 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7375 (tpp80) REVERT: O 39 ASN cc_start: 0.8605 (m110) cc_final: 0.7140 (m110) REVERT: O 44 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7737 (mm-30) REVERT: O 45 LYS cc_start: 0.8637 (pttt) cc_final: 0.8235 (pttt) REVERT: O 52 ARG cc_start: 0.7732 (mtm-85) cc_final: 0.7299 (mtt-85) REVERT: O 60 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8223 (mttt) REVERT: P 2 ASN cc_start: 0.7799 (m-40) cc_final: 0.7338 (t0) REVERT: P 35 ARG cc_start: 0.7739 (tpp80) cc_final: 0.7275 (tpp80) REVERT: P 48 GLN cc_start: 0.8716 (mp10) cc_final: 0.8486 (mp10) REVERT: P 60 LYS cc_start: 0.8991 (mtmt) cc_final: 0.8668 (mtpt) REVERT: Q 14 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7638 (mtp180) REVERT: R 60 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8452 (mttt) REVERT: R 74 LYS cc_start: 0.9006 (ttpp) cc_final: 0.8676 (mtpp) REVERT: S 1 MET cc_start: 0.5664 (tpt) cc_final: 0.5195 (tpt) REVERT: S 2 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7771 (m-40) REVERT: S 5 LYS cc_start: 0.9257 (tptm) cc_final: 0.8731 (tptm) REVERT: S 66 CYS cc_start: 0.8588 (m) cc_final: 0.8301 (m) REVERT: S 78 TYR cc_start: 0.8897 (t80) cc_final: 0.8696 (t80) REVERT: S 82 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8542 (mm110) REVERT: T 1 MET cc_start: 0.6540 (tpp) cc_final: 0.6071 (tpt) REVERT: T 45 LYS cc_start: 0.8214 (tttm) cc_final: 0.7593 (tttm) REVERT: U 1 MET cc_start: 0.5753 (tpt) cc_final: 0.4984 (tpt) REVERT: U 2 ASN cc_start: 0.8586 (m110) cc_final: 0.8242 (m110) REVERT: U 35 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7263 (ttm110) REVERT: U 39 ASN cc_start: 0.8415 (m110) cc_final: 0.7772 (m110) REVERT: U 49 ASP cc_start: 0.8529 (m-30) cc_final: 0.8286 (m-30) REVERT: U 60 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8155 (mtpp) REVERT: U 74 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8753 (ptmm) REVERT: U 82 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8088 (mm110) REVERT: V 3 PHE cc_start: 0.9196 (t80) cc_final: 0.8948 (t80) REVERT: V 35 ARG cc_start: 0.7964 (ttm170) cc_final: 0.7445 (tpp80) REVERT: V 39 ASN cc_start: 0.8492 (m110) cc_final: 0.8038 (m110) REVERT: V 47 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: V 56 HIS cc_start: 0.8261 (m-70) cc_final: 0.7387 (m-70) REVERT: V 66 CYS cc_start: 0.8483 (m) cc_final: 0.8209 (m) REVERT: W 47 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: W 60 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8398 (mtmm) REVERT: X 17 MET cc_start: 0.8409 (tpp) cc_final: 0.8197 (tpp) REVERT: X 21 LYS cc_start: 0.9022 (mttp) cc_final: 0.8420 (mttp) REVERT: X 25 ASP cc_start: 0.8125 (m-30) cc_final: 0.7556 (m-30) REVERT: X 66 CYS cc_start: 0.8704 (m) cc_final: 0.8121 (m) REVERT: X 82 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8341 (mp10) REVERT: Y 1 MET cc_start: 0.6773 (tpp) cc_final: 0.6299 (tpt) REVERT: Y 7 ASN cc_start: 0.8825 (m-40) cc_final: 0.8210 (m-40) REVERT: Y 60 LYS cc_start: 0.9035 (mtmt) cc_final: 0.7905 (tptt) REVERT: Z 44 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7899 (mm-30) REVERT: Z 60 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8462 (mtpt) REVERT: Z 74 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8706 (ttpp) REVERT: a 1 MET cc_start: 0.6599 (tpp) cc_final: 0.5810 (tpt) REVERT: a 5 LYS cc_start: 0.8794 (tttm) cc_final: 0.8433 (tptt) REVERT: a 9 ARG cc_start: 0.7892 (mtp180) cc_final: 0.7475 (mmt-90) REVERT: a 60 LYS cc_start: 0.9031 (mtmt) cc_final: 0.7587 (tptm) REVERT: b 17 MET cc_start: 0.8108 (tpt) cc_final: 0.7745 (tpt) REVERT: b 20 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8979 (mp) REVERT: b 39 ASN cc_start: 0.8391 (m110) cc_final: 0.7826 (m110) REVERT: c 9 ARG cc_start: 0.5003 (mmt-90) cc_final: 0.4512 (mtt-85) REVERT: c 20 ILE cc_start: 0.9241 (mp) cc_final: 0.9014 (mp) REVERT: c 34 ASN cc_start: 0.7895 (t0) cc_final: 0.7614 (t0) REVERT: c 39 ASN cc_start: 0.8291 (m110) cc_final: 0.7973 (t0) REVERT: c 58 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9030 (tp) REVERT: d 26 ASP cc_start: 0.8646 (t70) cc_final: 0.8290 (t70) REVERT: d 37 GLU cc_start: 0.8879 (mp0) cc_final: 0.8276 (mp0) REVERT: d 60 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8099 (mtpt) REVERT: d 74 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8842 (ttpp) REVERT: e 13 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8449 (mm-40) REVERT: e 26 ASP cc_start: 0.8491 (t0) cc_final: 0.7902 (t0) REVERT: e 34 ASN cc_start: 0.8655 (t0) cc_final: 0.8452 (t0) REVERT: e 39 ASN cc_start: 0.8347 (m110) cc_final: 0.7847 (m110) REVERT: e 74 LYS cc_start: 0.8902 (tttt) cc_final: 0.8599 (ttpp) outliers start: 186 outliers final: 138 residues processed: 1676 average time/residue: 0.3745 time to fit residues: 940.1920 Evaluate side-chains 1716 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1570 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 15 MET Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 36 GLU Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain W residue 2 ASN Chi-restraints excluded: chain W residue 26 ASP Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 71 LYS Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 36 GLU Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain c residue 2 ASN Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 74 LYS Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Chi-restraints excluded: chain e residue 71 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 90 optimal weight: 20.0000 chunk 242 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 158 optimal weight: 0.3980 chunk 66 optimal weight: 6.9990 chunk 269 optimal weight: 0.8980 chunk 224 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN E 67 ASN E 82 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN H 82 GLN J 67 ASN K 82 GLN L 82 GLN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 2 ASN O 13 GLN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 34 ASN ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 ASN W 87 GLN ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 67 ASN Y 13 GLN ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 ASN Y 82 GLN Z 2 ASN a 2 ASN b 22 GLN b 67 ASN ** b 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 13 GLN ** c 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN d 67 ASN ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23095 Z= 0.241 Angle : 0.599 6.814 31000 Z= 0.326 Chirality : 0.042 0.206 3472 Planarity : 0.004 0.041 3937 Dihedral : 3.911 13.376 2914 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 6.65 % Allowed : 26.20 % Favored : 67.16 % 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: 1.08 (0.16), residues: 2728 helix: 1.11 (0.10), residues: 2480 sheet: None (None), residues: 0 loop : -2.84 (0.26), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 30 HIS 0.004 0.001 HIS R 56 PHE 0.024 0.001 PHE X 81 TYR 0.012 0.002 TYR N 78 ARG 0.008 0.001 ARG d 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1838 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1667 time to evaluate : 2.902 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: A 1 MET cc_start: 0.6779 (tpp) cc_final: 0.6380 (tpt) REVERT: A 47 GLU cc_start: 0.6851 (tt0) cc_final: 0.6620 (tt0) REVERT: A 60 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8383 (mtpt) REVERT: B 2 ASN cc_start: 0.8365 (m-40) cc_final: 0.8148 (m-40) REVERT: B 45 LYS cc_start: 0.8305 (tttt) cc_final: 0.8013 (tttt) REVERT: C 2 ASN cc_start: 0.7684 (m-40) cc_final: 0.7377 (m-40) REVERT: C 31 ASN cc_start: 0.8902 (m-40) cc_final: 0.8515 (m110) REVERT: C 35 ARG cc_start: 0.7753 (tpp80) cc_final: 0.7271 (tpp80) REVERT: C 60 LYS cc_start: 0.8757 (mtmt) cc_final: 0.8404 (mttt) REVERT: D 13 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8612 (mm-40) REVERT: D 39 ASN cc_start: 0.8168 (m110) cc_final: 0.7825 (t0) REVERT: D 60 LYS cc_start: 0.8679 (mtmm) cc_final: 0.8286 (mtpp) REVERT: D 74 LYS cc_start: 0.9009 (tttt) cc_final: 0.8677 (ttpp) REVERT: E 9 ARG cc_start: 0.8677 (mtp-110) cc_final: 0.8410 (mtp-110) REVERT: E 39 ASN cc_start: 0.8387 (m110) cc_final: 0.7725 (m110) REVERT: E 57 MET cc_start: 0.8293 (mtm) cc_final: 0.7891 (mtp) REVERT: E 60 LYS cc_start: 0.8529 (mtmt) cc_final: 0.8237 (mtpp) REVERT: E 78 TYR cc_start: 0.8728 (t80) cc_final: 0.8488 (t80) REVERT: F 34 ASN cc_start: 0.8068 (t0) cc_final: 0.6823 (t0) REVERT: F 37 GLU cc_start: 0.8886 (mp0) cc_final: 0.8339 (mp0) REVERT: G 35 ARG cc_start: 0.7843 (ttm110) cc_final: 0.7489 (ttp-110) REVERT: G 39 ASN cc_start: 0.8468 (m110) cc_final: 0.7900 (m110) REVERT: G 67 ASN cc_start: 0.8885 (m-40) cc_final: 0.8610 (m110) REVERT: H 34 ASN cc_start: 0.7976 (t0) cc_final: 0.7697 (t0) REVERT: H 35 ARG cc_start: 0.7877 (ttm170) cc_final: 0.7395 (tpp80) REVERT: H 36 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: H 37 GLU cc_start: 0.8425 (mp0) cc_final: 0.8192 (mp0) REVERT: H 78 TYR cc_start: 0.8939 (t80) cc_final: 0.8403 (t80) REVERT: H 82 GLN cc_start: 0.8717 (mm-40) cc_final: 0.7938 (mp10) REVERT: I 2 ASN cc_start: 0.8152 (m-40) cc_final: 0.7633 (m110) REVERT: I 6 ASP cc_start: 0.8110 (m-30) cc_final: 0.7888 (m-30) REVERT: I 14 ARG cc_start: 0.7345 (mtt180) cc_final: 0.7045 (mtp180) REVERT: J 1 MET cc_start: 0.7440 (tpp) cc_final: 0.6838 (tpt) REVERT: J 2 ASN cc_start: 0.8324 (m-40) cc_final: 0.7919 (m-40) REVERT: J 22 GLN cc_start: 0.8914 (mt0) cc_final: 0.8630 (mt0) REVERT: J 36 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: J 43 CYS cc_start: 0.7676 (p) cc_final: 0.7159 (p) REVERT: J 65 SER cc_start: 0.9117 (m) cc_final: 0.8894 (m) REVERT: K 17 MET cc_start: 0.8215 (tpp) cc_final: 0.7788 (tpt) REVERT: K 21 LYS cc_start: 0.8872 (mttt) cc_final: 0.8503 (mttp) REVERT: K 25 ASP cc_start: 0.8175 (m-30) cc_final: 0.7632 (m-30) REVERT: K 60 LYS cc_start: 0.8567 (mtmt) cc_final: 0.8103 (mtpp) REVERT: K 83 ASP cc_start: 0.8635 (t70) cc_final: 0.8203 (t0) REVERT: L 37 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7413 (mp0) REVERT: L 66 CYS cc_start: 0.8239 (m) cc_final: 0.7894 (m) REVERT: M 1 MET cc_start: 0.6583 (tpp) cc_final: 0.6233 (tpt) REVERT: M 35 ARG cc_start: 0.7964 (tpp80) cc_final: 0.7426 (tpp80) REVERT: M 39 ASN cc_start: 0.8263 (m110) cc_final: 0.7533 (m110) REVERT: M 58 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8824 (tp) REVERT: M 71 LYS cc_start: 0.9301 (ptmt) cc_final: 0.8936 (ptmt) REVERT: N 1 MET cc_start: 0.6076 (tpt) cc_final: 0.5326 (tpt) REVERT: N 2 ASN cc_start: 0.8759 (m110) cc_final: 0.8512 (m-40) REVERT: O 9 ARG cc_start: 0.8574 (mtp-110) cc_final: 0.8310 (mtp-110) REVERT: O 35 ARG cc_start: 0.7941 (tpp80) cc_final: 0.7249 (tpp80) REVERT: O 39 ASN cc_start: 0.8515 (m110) cc_final: 0.7229 (m110) REVERT: O 44 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7738 (mm-30) REVERT: O 52 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7357 (mtt-85) REVERT: O 60 LYS cc_start: 0.9006 (mtmt) cc_final: 0.8695 (mtmm) REVERT: P 60 LYS cc_start: 0.8963 (mtmt) cc_final: 0.8600 (mtpt) REVERT: P 71 LYS cc_start: 0.9457 (ttmt) cc_final: 0.9172 (ttpp) REVERT: Q 14 ARG cc_start: 0.8005 (mtp180) cc_final: 0.7707 (mtp180) REVERT: Q 15 MET cc_start: 0.7815 (ttm) cc_final: 0.7611 (ttp) REVERT: R 44 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7658 (mm-30) REVERT: R 60 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8315 (mttt) REVERT: S 2 ASN cc_start: 0.8027 (m-40) cc_final: 0.7655 (m-40) REVERT: S 66 CYS cc_start: 0.8608 (m) cc_final: 0.8261 (m) REVERT: S 78 TYR cc_start: 0.8866 (t80) cc_final: 0.8634 (t80) REVERT: T 1 MET cc_start: 0.6644 (tpp) cc_final: 0.6286 (tpt) REVERT: T 34 ASN cc_start: 0.8698 (p0) cc_final: 0.8357 (p0) REVERT: T 78 TYR cc_start: 0.8446 (t80) cc_final: 0.8220 (t80) REVERT: U 1 MET cc_start: 0.6016 (tpt) cc_final: 0.5503 (tpt) REVERT: U 2 ASN cc_start: 0.8605 (m110) cc_final: 0.8351 (m-40) REVERT: U 35 ARG cc_start: 0.7733 (ttm110) cc_final: 0.6974 (tpp80) REVERT: U 39 ASN cc_start: 0.8351 (m110) cc_final: 0.7514 (m110) REVERT: U 44 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7677 (mm-30) REVERT: U 49 ASP cc_start: 0.8456 (m-30) cc_final: 0.7890 (m-30) REVERT: U 60 LYS cc_start: 0.8523 (mtmt) cc_final: 0.8255 (mtpp) REVERT: U 74 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8752 (ptmm) REVERT: U 89 LEU cc_start: 0.7873 (tp) cc_final: 0.7605 (tp) REVERT: V 35 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7483 (tpp80) REVERT: V 39 ASN cc_start: 0.8414 (m110) cc_final: 0.8027 (m110) REVERT: V 66 CYS cc_start: 0.8422 (m) cc_final: 0.8099 (m) REVERT: W 60 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8359 (mtmm) REVERT: X 17 MET cc_start: 0.8338 (tpp) cc_final: 0.8108 (tpp) REVERT: X 21 LYS cc_start: 0.9089 (mttp) cc_final: 0.8480 (mttp) REVERT: X 22 GLN cc_start: 0.8706 (mt0) cc_final: 0.8391 (mt0) REVERT: X 25 ASP cc_start: 0.8103 (m-30) cc_final: 0.7548 (m-30) REVERT: X 66 CYS cc_start: 0.8655 (m) cc_final: 0.8051 (m) REVERT: X 82 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8420 (mp10) REVERT: Y 7 ASN cc_start: 0.8749 (m-40) cc_final: 0.8085 (m-40) REVERT: Y 8 SER cc_start: 0.8709 (m) cc_final: 0.8339 (m) REVERT: Y 60 LYS cc_start: 0.9076 (mtmt) cc_final: 0.8023 (tmtt) REVERT: Y 78 TYR cc_start: 0.8997 (t80) cc_final: 0.8666 (t80) REVERT: Y 82 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8061 (mp10) REVERT: Z 1 MET cc_start: 0.6060 (tpp) cc_final: 0.5634 (tpt) REVERT: Z 2 ASN cc_start: 0.8523 (m-40) cc_final: 0.8303 (m110) REVERT: Z 60 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8677 (mtpt) REVERT: Z 74 LYS cc_start: 0.9102 (ttpt) cc_final: 0.8817 (ttpp) REVERT: Z 82 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8205 (mp10) REVERT: a 1 MET cc_start: 0.6583 (tpp) cc_final: 0.6309 (tpt) REVERT: a 5 LYS cc_start: 0.8793 (tttm) cc_final: 0.8516 (tptt) REVERT: a 9 ARG cc_start: 0.7902 (mtp180) cc_final: 0.7522 (mmt-90) REVERT: a 60 LYS cc_start: 0.9014 (mtmt) cc_final: 0.7541 (tptm) REVERT: b 1 MET cc_start: 0.6216 (tpt) cc_final: 0.5854 (tpt) REVERT: b 20 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.8977 (mp) REVERT: b 39 ASN cc_start: 0.8392 (m110) cc_final: 0.7753 (m110) REVERT: b 74 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8814 (ptmm) REVERT: c 9 ARG cc_start: 0.4915 (mmt-90) cc_final: 0.4395 (mtt-85) REVERT: c 20 ILE cc_start: 0.9275 (mp) cc_final: 0.9012 (mp) REVERT: c 58 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.8954 (tp) REVERT: c 82 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8201 (mm110) REVERT: c 87 GLN cc_start: 0.7603 (mm-40) cc_final: 0.7310 (mm110) REVERT: d 13 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8621 (mm110) REVERT: d 26 ASP cc_start: 0.8702 (t70) cc_final: 0.8390 (t70) REVERT: d 37 GLU cc_start: 0.8738 (mp0) cc_final: 0.8249 (mp0) REVERT: d 39 ASN cc_start: 0.8743 (m-40) cc_final: 0.8402 (m110) REVERT: d 60 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8080 (mtpp) REVERT: d 74 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8844 (ttpp) REVERT: d 78 TYR cc_start: 0.8889 (t80) cc_final: 0.8527 (t80) REVERT: e 9 ARG cc_start: 0.6017 (tpt170) cc_final: 0.5793 (ttt90) REVERT: e 13 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8468 (mm-40) REVERT: e 26 ASP cc_start: 0.8611 (t0) cc_final: 0.8013 (t0) REVERT: e 34 ASN cc_start: 0.8632 (t0) cc_final: 0.8285 (t0) REVERT: e 45 LYS cc_start: 0.8388 (ttpt) cc_final: 0.8102 (tmtt) REVERT: e 74 LYS cc_start: 0.8965 (tttt) cc_final: 0.8677 (ttpp) REVERT: e 82 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8438 (mm110) REVERT: e 87 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7562 (mp10) outliers start: 171 outliers final: 128 residues processed: 1705 average time/residue: 0.3979 time to fit residues: 1016.1311 Evaluate side-chains 1730 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1594 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain S residue 15 MET Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain W residue 2 ASN Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 71 LYS Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain c residue 2 ASN Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 13 GLN Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 15 MET Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 74 LYS Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 260 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 268 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN D 2 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN E 67 ASN E 82 GLN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 ASN ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN K 34 ASN K 82 GLN L 82 GLN M 31 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN P 82 GLN ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN U 82 GLN ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 ASN W 67 ASN X 67 ASN Y 67 ASN Z 13 GLN Z 22 GLN a 2 ASN b 67 ASN ** b 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 ASN d 82 GLN ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23095 Z= 0.272 Angle : 0.638 6.222 31000 Z= 0.350 Chirality : 0.043 0.225 3472 Planarity : 0.004 0.033 3937 Dihedral : 3.991 15.071 2914 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 6.41 % Allowed : 28.29 % Favored : 65.29 % 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: 0.92 (0.16), residues: 2728 helix: 1.00 (0.10), residues: 2480 sheet: None (None), residues: 0 loop : -2.80 (0.25), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 30 HIS 0.005 0.001 HIS Z 56 PHE 0.023 0.001 PHE C 3 TYR 0.017 0.002 TYR N 78 ARG 0.009 0.001 ARG R 9 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1810 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1645 time to evaluate : 2.848 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: A 60 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8354 (mtpt) REVERT: B 2 ASN cc_start: 0.8398 (m-40) cc_final: 0.8181 (m-40) REVERT: B 34 ASN cc_start: 0.8451 (p0) cc_final: 0.8188 (p0) REVERT: B 45 LYS cc_start: 0.8368 (tttt) cc_final: 0.8092 (tttt) REVERT: B 60 LYS cc_start: 0.8465 (mttt) cc_final: 0.8195 (mttp) REVERT: C 2 ASN cc_start: 0.7694 (m-40) cc_final: 0.7466 (m110) REVERT: C 31 ASN cc_start: 0.8880 (m-40) cc_final: 0.8480 (m110) REVERT: C 47 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7099 (tt0) REVERT: C 60 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8373 (mttt) REVERT: D 13 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8611 (mm-40) REVERT: D 39 ASN cc_start: 0.8360 (m110) cc_final: 0.7690 (m-40) REVERT: D 60 LYS cc_start: 0.8712 (mtmm) cc_final: 0.8334 (mtpp) REVERT: D 74 LYS cc_start: 0.8994 (tttt) cc_final: 0.8642 (ttpp) REVERT: D 78 TYR cc_start: 0.8649 (t80) cc_final: 0.7726 (t80) REVERT: D 82 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8070 (mp10) REVERT: E 9 ARG cc_start: 0.8692 (mtp-110) cc_final: 0.8448 (mtp-110) REVERT: E 39 ASN cc_start: 0.8391 (m110) cc_final: 0.7689 (m110) REVERT: E 57 MET cc_start: 0.8334 (mtm) cc_final: 0.7917 (mtp) REVERT: E 60 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8255 (mtpp) REVERT: E 74 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8679 (ttmm) REVERT: E 78 TYR cc_start: 0.8725 (t80) cc_final: 0.8376 (t80) REVERT: F 34 ASN cc_start: 0.7879 (t0) cc_final: 0.6920 (t0) REVERT: F 37 GLU cc_start: 0.8909 (mp0) cc_final: 0.8505 (mp0) REVERT: G 67 ASN cc_start: 0.8875 (m-40) cc_final: 0.8627 (m110) REVERT: H 35 ARG cc_start: 0.7891 (ttm170) cc_final: 0.7473 (tpp80) REVERT: H 36 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: H 44 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7899 (mm-30) REVERT: H 82 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8252 (mp10) REVERT: I 2 ASN cc_start: 0.8174 (m-40) cc_final: 0.7594 (m-40) REVERT: I 14 ARG cc_start: 0.7447 (mtt180) cc_final: 0.7030 (mtp180) REVERT: J 2 ASN cc_start: 0.8364 (m-40) cc_final: 0.7987 (m-40) REVERT: K 17 MET cc_start: 0.8207 (tpp) cc_final: 0.7806 (tpt) REVERT: K 21 LYS cc_start: 0.8889 (mttt) cc_final: 0.8501 (mttp) REVERT: K 25 ASP cc_start: 0.8174 (m-30) cc_final: 0.7662 (m-30) REVERT: K 34 ASN cc_start: 0.8034 (t0) cc_final: 0.7332 (t0) REVERT: K 35 ARG cc_start: 0.7664 (tpp80) cc_final: 0.7444 (tpp80) REVERT: K 37 GLU cc_start: 0.8859 (mp0) cc_final: 0.8207 (mp0) REVERT: K 60 LYS cc_start: 0.8573 (mtmt) cc_final: 0.8344 (mtpt) REVERT: K 83 ASP cc_start: 0.8639 (t70) cc_final: 0.8152 (t0) REVERT: L 36 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: L 37 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: L 66 CYS cc_start: 0.8175 (m) cc_final: 0.7823 (m) REVERT: M 1 MET cc_start: 0.6771 (tpp) cc_final: 0.6455 (tpt) REVERT: M 35 ARG cc_start: 0.8026 (tpp80) cc_final: 0.7773 (tpp-160) REVERT: M 39 ASN cc_start: 0.8296 (m110) cc_final: 0.7298 (m110) REVERT: M 43 CYS cc_start: 0.7746 (p) cc_final: 0.6721 (p) REVERT: M 58 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8844 (tp) REVERT: M 71 LYS cc_start: 0.9284 (ptmt) cc_final: 0.8964 (ptmt) REVERT: O 9 ARG cc_start: 0.8587 (mtp-110) cc_final: 0.8330 (mtp-110) REVERT: O 44 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7651 (mm-30) REVERT: O 52 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7357 (mtt-85) REVERT: P 1 MET cc_start: 0.5442 (tmm) cc_final: 0.4999 (ppp) REVERT: P 60 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8663 (mtpt) REVERT: P 71 LYS cc_start: 0.9476 (ttmt) cc_final: 0.9188 (ttpp) REVERT: Q 14 ARG cc_start: 0.8107 (mtp180) cc_final: 0.7782 (mtp180) REVERT: Q 71 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8929 (ttpp) REVERT: R 60 LYS cc_start: 0.8948 (mtmt) cc_final: 0.8584 (mttt) REVERT: R 82 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7937 (mm-40) REVERT: S 2 ASN cc_start: 0.7826 (m-40) cc_final: 0.7533 (m-40) REVERT: S 66 CYS cc_start: 0.8597 (m) cc_final: 0.8196 (m) REVERT: S 78 TYR cc_start: 0.8858 (t80) cc_final: 0.8625 (t80) REVERT: T 1 MET cc_start: 0.6871 (tpp) cc_final: 0.6423 (tpt) REVERT: U 35 ARG cc_start: 0.7692 (ttm110) cc_final: 0.6894 (tpp80) REVERT: U 39 ASN cc_start: 0.8287 (m110) cc_final: 0.7580 (m110) REVERT: U 49 ASP cc_start: 0.8505 (m-30) cc_final: 0.8024 (m-30) REVERT: U 60 LYS cc_start: 0.8482 (mtmt) cc_final: 0.8247 (mtpp) REVERT: U 74 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8734 (ptmm) REVERT: V 47 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6890 (tt0) REVERT: V 56 HIS cc_start: 0.8055 (m-70) cc_final: 0.7476 (m-70) REVERT: V 66 CYS cc_start: 0.8451 (m) cc_final: 0.8129 (m) REVERT: W 60 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8304 (mtmm) REVERT: X 14 ARG cc_start: 0.7655 (mtt180) cc_final: 0.6127 (tpt170) REVERT: X 21 LYS cc_start: 0.9099 (mttp) cc_final: 0.8462 (mttp) REVERT: X 22 GLN cc_start: 0.8648 (mt0) cc_final: 0.8331 (mt0) REVERT: X 25 ASP cc_start: 0.8131 (m-30) cc_final: 0.7537 (m-30) REVERT: X 66 CYS cc_start: 0.8692 (m) cc_final: 0.8052 (m) REVERT: X 78 TYR cc_start: 0.9028 (t80) cc_final: 0.8629 (t80) REVERT: Y 7 ASN cc_start: 0.8746 (m-40) cc_final: 0.8136 (m-40) REVERT: Y 8 SER cc_start: 0.8682 (m) cc_final: 0.8339 (m) REVERT: Y 60 LYS cc_start: 0.9083 (mtmt) cc_final: 0.8017 (tmtt) REVERT: Y 82 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8367 (mp10) REVERT: Z 1 MET cc_start: 0.6191 (tpp) cc_final: 0.5809 (tpt) REVERT: Z 60 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8544 (mtpt) REVERT: Z 74 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8785 (ttpp) REVERT: a 5 LYS cc_start: 0.8814 (tttm) cc_final: 0.8529 (tptt) REVERT: a 9 ARG cc_start: 0.7919 (mtp180) cc_final: 0.7458 (mmt-90) REVERT: a 60 LYS cc_start: 0.9000 (mtmt) cc_final: 0.7525 (tptm) REVERT: b 1 MET cc_start: 0.6272 (tpt) cc_final: 0.6010 (tpt) REVERT: b 20 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8981 (mp) REVERT: b 26 ASP cc_start: 0.8077 (t70) cc_final: 0.7725 (t0) REVERT: b 39 ASN cc_start: 0.8306 (m110) cc_final: 0.7716 (m110) REVERT: b 74 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8820 (ptmm) REVERT: c 9 ARG cc_start: 0.5163 (mmt-90) cc_final: 0.4671 (mtt-85) REVERT: c 20 ILE cc_start: 0.9273 (mp) cc_final: 0.8975 (mp) REVERT: c 35 ARG cc_start: 0.7972 (tpp80) cc_final: 0.7716 (tpp80) REVERT: c 58 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9068 (tp) REVERT: c 68 LEU cc_start: 0.9294 (mt) cc_final: 0.9093 (mp) REVERT: c 82 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8421 (mm110) REVERT: d 13 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8713 (mm110) REVERT: d 26 ASP cc_start: 0.8675 (t70) cc_final: 0.8319 (t70) REVERT: d 37 GLU cc_start: 0.8729 (mp0) cc_final: 0.8232 (mp0) REVERT: d 39 ASN cc_start: 0.8934 (m-40) cc_final: 0.8732 (m110) REVERT: d 60 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8142 (mtpt) REVERT: d 74 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8859 (ttpp) REVERT: d 78 TYR cc_start: 0.8897 (t80) cc_final: 0.8640 (t80) REVERT: e 13 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8465 (mm-40) REVERT: e 26 ASP cc_start: 0.8603 (t0) cc_final: 0.8006 (t0) REVERT: e 34 ASN cc_start: 0.8615 (t0) cc_final: 0.8284 (t0) REVERT: e 87 GLN cc_start: 0.8381 (mm-40) cc_final: 0.7647 (mp10) outliers start: 165 outliers final: 136 residues processed: 1691 average time/residue: 0.3855 time to fit residues: 977.4633 Evaluate side-chains 1749 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1601 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain O residue 15 MET Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain P residue 36 GLU Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain S residue 15 MET Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain W residue 2 ASN Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 71 LYS Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 26 ASP Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain c residue 13 GLN Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 15 MET Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 74 LYS Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 166 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 170 optimal weight: 20.0000 chunk 183 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 2 ASN D 22 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN E 82 GLN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 ASN I 67 ASN J 67 ASN K 82 GLN L 67 ASN L 82 GLN M 22 GLN M 31 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN O 39 ASN O 67 ASN ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN V 39 ASN ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 ASN X 67 ASN X 82 GLN Y 13 GLN Y 67 ASN Z 82 GLN a 2 ASN b 67 ASN b 82 GLN c 87 GLN d 67 ASN ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 23095 Z= 0.349 Angle : 0.682 6.768 31000 Z= 0.375 Chirality : 0.046 0.233 3472 Planarity : 0.004 0.038 3937 Dihedral : 4.148 19.634 2914 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 6.84 % Allowed : 28.29 % Favored : 64.87 % 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: 0.68 (0.16), residues: 2728 helix: 0.83 (0.10), residues: 2480 sheet: None (None), residues: 0 loop : -2.78 (0.25), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP V 30 HIS 0.006 0.001 HIS Z 56 PHE 0.019 0.001 PHE a 3 TYR 0.014 0.002 TYR M 78 ARG 0.010 0.001 ARG d 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1809 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1633 time to evaluate : 2.835 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: A 34 ASN cc_start: 0.8181 (t0) cc_final: 0.7192 (t0) REVERT: A 37 GLU cc_start: 0.8881 (mp0) cc_final: 0.8341 (mp0) REVERT: A 60 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8199 (mtpt) REVERT: B 2 ASN cc_start: 0.8495 (m-40) cc_final: 0.8266 (m-40) REVERT: B 34 ASN cc_start: 0.8470 (p0) cc_final: 0.8034 (p0) REVERT: B 45 LYS cc_start: 0.8470 (tttt) cc_final: 0.8124 (tttt) REVERT: B 60 LYS cc_start: 0.8508 (mttt) cc_final: 0.8211 (mttp) REVERT: C 31 ASN cc_start: 0.8898 (m-40) cc_final: 0.8562 (m110) REVERT: C 47 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: C 56 HIS cc_start: 0.8242 (m-70) cc_final: 0.7956 (m-70) REVERT: C 60 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8057 (mttt) REVERT: D 13 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8618 (mm-40) REVERT: D 38 VAL cc_start: 0.9185 (t) cc_final: 0.8980 (t) REVERT: D 39 ASN cc_start: 0.8212 (m110) cc_final: 0.7915 (t0) REVERT: D 74 LYS cc_start: 0.9027 (tttt) cc_final: 0.8650 (ttpp) REVERT: D 78 TYR cc_start: 0.8722 (t80) cc_final: 0.8404 (t80) REVERT: E 39 ASN cc_start: 0.8435 (m110) cc_final: 0.7749 (m110) REVERT: E 57 MET cc_start: 0.8332 (mtm) cc_final: 0.8008 (mtp) REVERT: E 60 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8228 (mtpp) REVERT: E 74 LYS cc_start: 0.9035 (mtpp) cc_final: 0.8686 (ttmm) REVERT: E 78 TYR cc_start: 0.8805 (t80) cc_final: 0.8390 (t80) REVERT: F 34 ASN cc_start: 0.8079 (t0) cc_final: 0.7181 (t0) REVERT: F 37 GLU cc_start: 0.8924 (mp0) cc_final: 0.8531 (mp0) REVERT: G 35 ARG cc_start: 0.7639 (ttp-110) cc_final: 0.7285 (tpp80) REVERT: G 37 GLU cc_start: 0.8616 (pm20) cc_final: 0.8381 (pm20) REVERT: G 39 ASN cc_start: 0.8497 (m110) cc_final: 0.7553 (m110) REVERT: H 35 ARG cc_start: 0.7937 (ttm170) cc_final: 0.7589 (tpp80) REVERT: H 36 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: H 44 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8015 (mm-30) REVERT: I 14 ARG cc_start: 0.7540 (mtt180) cc_final: 0.7076 (mtp180) REVERT: I 66 CYS cc_start: 0.8430 (t) cc_final: 0.8100 (m) REVERT: J 39 ASN cc_start: 0.8631 (m-40) cc_final: 0.8112 (m110) REVERT: J 82 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8530 (mm-40) REVERT: J 87 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7571 (mm-40) REVERT: K 17 MET cc_start: 0.8247 (tpp) cc_final: 0.7908 (tpp) REVERT: K 21 LYS cc_start: 0.8932 (mttt) cc_final: 0.8517 (mttp) REVERT: K 25 ASP cc_start: 0.8213 (m-30) cc_final: 0.7674 (m-30) REVERT: K 60 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8303 (mtpt) REVERT: K 83 ASP cc_start: 0.8601 (t70) cc_final: 0.8171 (t0) REVERT: L 9 ARG cc_start: 0.8802 (mtp-110) cc_final: 0.8581 (mtp-110) REVERT: L 36 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: L 66 CYS cc_start: 0.8014 (m) cc_final: 0.7695 (m) REVERT: L 74 LYS cc_start: 0.9006 (ttmm) cc_final: 0.8730 (ttpp) REVERT: M 35 ARG cc_start: 0.7971 (tpp80) cc_final: 0.7448 (tpp80) REVERT: M 39 ASN cc_start: 0.8515 (m110) cc_final: 0.7317 (m110) REVERT: M 44 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7952 (mm-30) REVERT: M 71 LYS cc_start: 0.9289 (ptmt) cc_final: 0.8977 (ptmt) REVERT: N 47 GLU cc_start: 0.7530 (tt0) cc_final: 0.7314 (tt0) REVERT: O 1 MET cc_start: 0.6478 (tpp) cc_final: 0.6078 (tpt) REVERT: O 9 ARG cc_start: 0.8595 (mtp-110) cc_final: 0.8361 (mtp-110) REVERT: O 35 ARG cc_start: 0.7665 (tpp80) cc_final: 0.7244 (tpp80) REVERT: O 39 ASN cc_start: 0.8631 (m110) cc_final: 0.8030 (m110) REVERT: O 44 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7907 (mm-30) REVERT: O 52 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7414 (mtt-85) REVERT: O 60 LYS cc_start: 0.8449 (mtpt) cc_final: 0.7863 (mtpt) REVERT: P 60 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8655 (mtpt) REVERT: P 71 LYS cc_start: 0.9497 (ttmt) cc_final: 0.9208 (ttpp) REVERT: Q 14 ARG cc_start: 0.8252 (mtp180) cc_final: 0.7869 (mtp180) REVERT: R 9 ARG cc_start: 0.8660 (mtp-110) cc_final: 0.8439 (mtp-110) REVERT: R 60 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8423 (mttt) REVERT: S 66 CYS cc_start: 0.8596 (m) cc_final: 0.8215 (m) REVERT: T 1 MET cc_start: 0.6876 (tpp) cc_final: 0.6446 (tpt) REVERT: U 35 ARG cc_start: 0.7666 (ttm110) cc_final: 0.7217 (ttm110) REVERT: U 39 ASN cc_start: 0.8330 (m110) cc_final: 0.7647 (m110) REVERT: U 49 ASP cc_start: 0.8265 (m-30) cc_final: 0.7943 (m-30) REVERT: U 60 LYS cc_start: 0.8473 (mtmt) cc_final: 0.8226 (mtpp) REVERT: U 74 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8749 (ptmm) REVERT: V 35 ARG cc_start: 0.7840 (tpp80) cc_final: 0.7382 (tpp80) REVERT: V 39 ASN cc_start: 0.8274 (m-40) cc_final: 0.7823 (m110) REVERT: V 47 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6885 (tt0) REVERT: V 66 CYS cc_start: 0.8426 (m) cc_final: 0.8061 (m) REVERT: W 47 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: W 60 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8329 (mtmm) REVERT: X 14 ARG cc_start: 0.7786 (mtt180) cc_final: 0.6287 (tpt170) REVERT: X 21 LYS cc_start: 0.9103 (mttp) cc_final: 0.8460 (mttp) REVERT: X 25 ASP cc_start: 0.8115 (m-30) cc_final: 0.7525 (m-30) REVERT: X 66 CYS cc_start: 0.8695 (m) cc_final: 0.8046 (m) REVERT: X 82 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8392 (mp10) REVERT: Y 7 ASN cc_start: 0.8786 (m-40) cc_final: 0.8271 (m-40) REVERT: Y 8 SER cc_start: 0.8682 (m) cc_final: 0.8436 (m) REVERT: Y 60 LYS cc_start: 0.9015 (mtmt) cc_final: 0.7964 (tmtt) REVERT: Y 82 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8365 (mp10) REVERT: Z 1 MET cc_start: 0.6406 (tpp) cc_final: 0.6061 (tpt) REVERT: Z 36 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: Z 43 CYS cc_start: 0.7849 (p) cc_final: 0.7290 (p) REVERT: Z 74 LYS cc_start: 0.9089 (ttpt) cc_final: 0.8806 (ttpp) REVERT: a 5 LYS cc_start: 0.8919 (tttm) cc_final: 0.8522 (tptt) REVERT: a 9 ARG cc_start: 0.7904 (mtp180) cc_final: 0.7385 (mmt-90) REVERT: a 60 LYS cc_start: 0.9011 (mtmt) cc_final: 0.7521 (tptm) REVERT: b 1 MET cc_start: 0.5982 (tpt) cc_final: 0.5740 (tpt) REVERT: b 17 MET cc_start: 0.8144 (tpt) cc_final: 0.7791 (tpt) REVERT: b 20 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8967 (mp) REVERT: b 39 ASN cc_start: 0.8195 (m110) cc_final: 0.7609 (m110) REVERT: b 71 LYS cc_start: 0.9413 (ptmt) cc_final: 0.9206 (ptmt) REVERT: b 74 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8777 (ptmm) REVERT: b 78 TYR cc_start: 0.9072 (t80) cc_final: 0.8724 (t80) REVERT: c 9 ARG cc_start: 0.4807 (mmt-90) cc_final: 0.4321 (mtt-85) REVERT: c 20 ILE cc_start: 0.9284 (mp) cc_final: 0.8941 (mp) REVERT: c 36 GLU cc_start: 0.7374 (tt0) cc_final: 0.7171 (pt0) REVERT: c 37 GLU cc_start: 0.8755 (pm20) cc_final: 0.8301 (pm20) REVERT: c 58 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9087 (tp) REVERT: c 82 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8417 (mm110) REVERT: d 13 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8750 (mm110) REVERT: d 26 ASP cc_start: 0.8674 (t70) cc_final: 0.8327 (t70) REVERT: d 60 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8151 (mtpt) REVERT: d 74 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8839 (ttpp) REVERT: d 78 TYR cc_start: 0.8957 (t80) cc_final: 0.8713 (t80) REVERT: e 13 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8435 (mm-40) REVERT: e 34 ASN cc_start: 0.8685 (t0) cc_final: 0.8363 (t0) outliers start: 176 outliers final: 149 residues processed: 1675 average time/residue: 0.3864 time to fit residues: 968.6726 Evaluate side-chains 1763 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1603 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain O residue 15 MET Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 36 GLU Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain S residue 8 SER Chi-restraints excluded: chain S residue 15 MET Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 60 LYS Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain W residue 2 ASN Chi-restraints excluded: chain W residue 32 VAL Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 71 LYS Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 26 ASP Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain c residue 13 GLN Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 15 MET Chi-restraints excluded: chain d residue 18 THR Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain d residue 55 ILE Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 74 LYS Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 43 CYS Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 257 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 250 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 249 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 77 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN E 82 GLN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN H 82 GLN I 67 ASN I 77 ASN J 67 ASN K 34 ASN L 67 ASN L 82 GLN M 31 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN O 67 ASN Q 67 ASN S 39 ASN ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 ASN ** W 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 82 GLN X 67 ASN Y 67 ASN Z 2 ASN a 2 ASN b 22 GLN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 67 ASN b 82 GLN d 39 ASN d 67 ASN ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 82 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23095 Z= 0.227 Angle : 0.653 8.265 31000 Z= 0.359 Chirality : 0.043 0.222 3472 Planarity : 0.004 0.046 3937 Dihedral : 4.111 25.629 2914 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.75 % Allowed : 29.97 % Favored : 64.28 % 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: 0.73 (0.16), residues: 2728 helix: 0.87 (0.10), residues: 2480 sheet: None (None), residues: 0 loop : -2.81 (0.24), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP V 30 HIS 0.003 0.001 HIS U 56 PHE 0.023 0.001 PHE C 3 TYR 0.015 0.002 TYR D 78 ARG 0.010 0.001 ARG d 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1818 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1670 time to evaluate : 2.824 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: A 17 MET cc_start: 0.8429 (tpp) cc_final: 0.8158 (tpt) REVERT: A 34 ASN cc_start: 0.8180 (t0) cc_final: 0.7191 (t0) REVERT: A 37 GLU cc_start: 0.8807 (mp0) cc_final: 0.8308 (mp0) REVERT: A 60 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8433 (mtpt) REVERT: B 2 ASN cc_start: 0.8402 (m-40) cc_final: 0.8183 (m-40) REVERT: B 34 ASN cc_start: 0.8469 (p0) cc_final: 0.8189 (p0) REVERT: B 45 LYS cc_start: 0.8361 (tttt) cc_final: 0.8054 (tttt) REVERT: B 60 LYS cc_start: 0.8432 (mttt) cc_final: 0.8208 (mttp) REVERT: C 1 MET cc_start: 0.6350 (tpt) cc_final: 0.5688 (tpt) REVERT: C 42 CYS cc_start: 0.7887 (m) cc_final: 0.7659 (t) REVERT: C 47 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7136 (tt0) REVERT: C 56 HIS cc_start: 0.7852 (m-70) cc_final: 0.7594 (m-70) REVERT: C 60 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8140 (mttt) REVERT: C 71 LYS cc_start: 0.9351 (ttmm) cc_final: 0.9139 (ptmt) REVERT: C 82 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8130 (mm-40) REVERT: D 13 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8589 (mm-40) REVERT: D 35 ARG cc_start: 0.7950 (tpp80) cc_final: 0.7680 (tpp-160) REVERT: D 39 ASN cc_start: 0.8335 (m110) cc_final: 0.7915 (m110) REVERT: D 74 LYS cc_start: 0.8998 (tttt) cc_final: 0.8642 (ttpp) REVERT: D 78 TYR cc_start: 0.8595 (t80) cc_final: 0.7879 (t80) REVERT: D 82 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8220 (mp10) REVERT: E 9 ARG cc_start: 0.8608 (mtp-110) cc_final: 0.8260 (mtp-110) REVERT: E 35 ARG cc_start: 0.7569 (tpp80) cc_final: 0.7223 (tpp80) REVERT: E 39 ASN cc_start: 0.8314 (m110) cc_final: 0.7475 (m110) REVERT: E 57 MET cc_start: 0.8291 (mtm) cc_final: 0.7900 (mtp) REVERT: E 60 LYS cc_start: 0.8562 (mtmt) cc_final: 0.8272 (mtpp) REVERT: E 78 TYR cc_start: 0.8734 (t80) cc_final: 0.8415 (t80) REVERT: F 34 ASN cc_start: 0.8127 (t0) cc_final: 0.7028 (t0) REVERT: G 37 GLU cc_start: 0.8596 (pm20) cc_final: 0.8385 (pm20) REVERT: H 35 ARG cc_start: 0.7908 (ttm170) cc_final: 0.7553 (tpp80) REVERT: H 36 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: H 44 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8087 (mm-30) REVERT: H 67 ASN cc_start: 0.8703 (m-40) cc_final: 0.8384 (m-40) REVERT: H 82 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8318 (mp10) REVERT: I 66 CYS cc_start: 0.8439 (t) cc_final: 0.8072 (m) REVERT: J 9 ARG cc_start: 0.8266 (mtp-110) cc_final: 0.8001 (mtp-110) REVERT: J 39 ASN cc_start: 0.8515 (m-40) cc_final: 0.8049 (m-40) REVERT: J 82 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8497 (mm-40) REVERT: J 87 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7585 (mm-40) REVERT: K 17 MET cc_start: 0.8242 (tpp) cc_final: 0.7854 (tpt) REVERT: K 21 LYS cc_start: 0.8963 (mttt) cc_final: 0.8695 (mttp) REVERT: K 25 ASP cc_start: 0.8206 (m-30) cc_final: 0.7744 (m-30) REVERT: K 60 LYS cc_start: 0.8568 (mtmt) cc_final: 0.8329 (mtpp) REVERT: K 83 ASP cc_start: 0.8687 (t70) cc_final: 0.8103 (t0) REVERT: L 36 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: L 66 CYS cc_start: 0.8258 (m) cc_final: 0.7925 (m) REVERT: L 74 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8690 (ttpp) REVERT: M 58 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8771 (tp) REVERT: M 71 LYS cc_start: 0.9282 (ptmt) cc_final: 0.9056 (ptmt) REVERT: O 1 MET cc_start: 0.6339 (tpp) cc_final: 0.5890 (tpt) REVERT: O 9 ARG cc_start: 0.8581 (mtp-110) cc_final: 0.8357 (mtp-110) REVERT: O 35 ARG cc_start: 0.7595 (tpp80) cc_final: 0.6814 (tpp80) REVERT: O 39 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.7779 (m110) REVERT: O 44 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7944 (mm-30) REVERT: O 52 ARG cc_start: 0.7522 (mtm-85) cc_final: 0.7234 (mtt-85) REVERT: O 60 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8037 (mtpt) REVERT: P 60 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8615 (mtpt) REVERT: P 71 LYS cc_start: 0.9479 (ttmt) cc_final: 0.9267 (tttt) REVERT: Q 5 LYS cc_start: 0.8787 (tptm) cc_final: 0.8585 (tptm) REVERT: Q 66 CYS cc_start: 0.8416 (m) cc_final: 0.7844 (m) REVERT: Q 71 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8996 (ttpt) REVERT: R 35 ARG cc_start: 0.7948 (ttp-110) cc_final: 0.7706 (tpp80) REVERT: R 44 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7630 (mm-30) REVERT: R 60 LYS cc_start: 0.8937 (mtmt) cc_final: 0.8621 (mttt) REVERT: R 74 LYS cc_start: 0.9064 (ttmm) cc_final: 0.8722 (ttpp) REVERT: S 9 ARG cc_start: 0.8479 (mtp-110) cc_final: 0.8271 (mtp-110) REVERT: S 66 CYS cc_start: 0.8663 (m) cc_final: 0.8274 (m) REVERT: T 1 MET cc_start: 0.6806 (tpp) cc_final: 0.6380 (tpt) REVERT: T 39 ASN cc_start: 0.8136 (m110) cc_final: 0.7790 (t0) REVERT: T 52 ARG cc_start: 0.7686 (mtt-85) cc_final: 0.7385 (mtt-85) REVERT: U 35 ARG cc_start: 0.7605 (ttm110) cc_final: 0.7249 (ttm110) REVERT: U 39 ASN cc_start: 0.8337 (m110) cc_final: 0.7669 (m-40) REVERT: U 49 ASP cc_start: 0.8213 (m-30) cc_final: 0.7878 (m-30) REVERT: U 74 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8724 (ptmm) REVERT: V 39 ASN cc_start: 0.8122 (m-40) cc_final: 0.7671 (t0) REVERT: V 56 HIS cc_start: 0.7846 (m-70) cc_final: 0.7455 (m-70) REVERT: V 66 CYS cc_start: 0.8428 (m) cc_final: 0.8060 (m) REVERT: V 82 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8447 (mm110) REVERT: V 87 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7957 (mp10) REVERT: W 47 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: W 60 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8296 (mtmm) REVERT: W 66 CYS cc_start: 0.7977 (t) cc_final: 0.7408 (m) REVERT: X 7 ASN cc_start: 0.8974 (m-40) cc_final: 0.8498 (m110) REVERT: X 14 ARG cc_start: 0.7693 (mtt180) cc_final: 0.6177 (tpt170) REVERT: X 21 LYS cc_start: 0.9127 (mttp) cc_final: 0.8478 (mttp) REVERT: X 22 GLN cc_start: 0.8602 (mt0) cc_final: 0.8270 (mt0) REVERT: X 25 ASP cc_start: 0.8091 (m-30) cc_final: 0.7514 (m-30) REVERT: X 66 CYS cc_start: 0.8689 (m) cc_final: 0.8007 (m) REVERT: X 78 TYR cc_start: 0.8932 (t80) cc_final: 0.8517 (t80) REVERT: Y 3 PHE cc_start: 0.9044 (t80) cc_final: 0.8741 (t80) REVERT: Y 7 ASN cc_start: 0.8646 (m-40) cc_final: 0.7934 (m110) REVERT: Y 8 SER cc_start: 0.8688 (m) cc_final: 0.8400 (m) REVERT: Y 42 CYS cc_start: 0.7833 (m) cc_final: 0.7370 (t) REVERT: Y 60 LYS cc_start: 0.9041 (mtmt) cc_final: 0.7972 (tmtt) REVERT: Y 82 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8122 (mp10) REVERT: Z 36 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: Z 74 LYS cc_start: 0.9102 (ttpt) cc_final: 0.8819 (ttpp) REVERT: Z 82 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8292 (mp10) REVERT: a 5 LYS cc_start: 0.8819 (tttm) cc_final: 0.8540 (tptt) REVERT: a 9 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7464 (mmt-90) REVERT: a 39 ASN cc_start: 0.8660 (m-40) cc_final: 0.8381 (m-40) REVERT: a 60 LYS cc_start: 0.8999 (mtmt) cc_final: 0.7525 (tptm) REVERT: b 1 MET cc_start: 0.6052 (tpt) cc_final: 0.5828 (tpt) REVERT: b 20 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8998 (mp) REVERT: b 26 ASP cc_start: 0.8166 (t70) cc_final: 0.7703 (t0) REVERT: b 39 ASN cc_start: 0.8189 (m110) cc_final: 0.7539 (m110) REVERT: b 71 LYS cc_start: 0.9415 (ptmt) cc_final: 0.9169 (ptmt) REVERT: b 74 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8805 (ptmm) REVERT: b 78 TYR cc_start: 0.9002 (t80) cc_final: 0.8694 (t80) REVERT: c 9 ARG cc_start: 0.4656 (mmt-90) cc_final: 0.4152 (mtt-85) REVERT: c 20 ILE cc_start: 0.9287 (mp) cc_final: 0.9000 (mp) REVERT: c 39 ASN cc_start: 0.8740 (m-40) cc_final: 0.7849 (m110) REVERT: c 58 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9109 (tp) REVERT: c 87 GLN cc_start: 0.7143 (mp10) cc_final: 0.6692 (mp10) REVERT: d 9 ARG cc_start: 0.8560 (mtp-110) cc_final: 0.8357 (mtp-110) REVERT: d 13 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8704 (mm110) REVERT: d 15 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7345 (ttm) REVERT: d 26 ASP cc_start: 0.8670 (t70) cc_final: 0.8149 (t0) REVERT: d 39 ASN cc_start: 0.8692 (m-40) cc_final: 0.8364 (m110) REVERT: d 60 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8050 (mtpt) REVERT: d 74 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8751 (ttpp) REVERT: d 78 TYR cc_start: 0.8813 (t80) cc_final: 0.8528 (t80) REVERT: e 12 ILE cc_start: 0.9069 (mt) cc_final: 0.8842 (mm) REVERT: e 13 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8406 (mm-40) REVERT: e 26 ASP cc_start: 0.8615 (t0) cc_final: 0.8271 (t0) REVERT: e 34 ASN cc_start: 0.8668 (t0) cc_final: 0.8387 (t0) REVERT: e 71 LYS cc_start: 0.9319 (ptmt) cc_final: 0.9082 (ptmt) REVERT: e 74 LYS cc_start: 0.9064 (tttt) cc_final: 0.8752 (ttpp) REVERT: e 78 TYR cc_start: 0.8771 (t80) cc_final: 0.8283 (t80) REVERT: e 82 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8314 (mm110) outliers start: 148 outliers final: 113 residues processed: 1699 average time/residue: 0.3757 time to fit residues: 951.1772 Evaluate side-chains 1745 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1618 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 89 LEU Chi-restraints excluded: chain O residue 39 ASN Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 36 GLU Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain S residue 15 MET Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain T residue 70 LEU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain W residue 2 ASN Chi-restraints excluded: chain W residue 32 VAL Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 71 LYS Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 26 ASP Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 64 GLU Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 15 MET Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 74 LYS Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain e residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 264 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 184 optimal weight: 0.0030 chunk 277 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 overall best weight: 2.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN G 67 ASN I 67 ASN I 77 ASN I 82 GLN J 2 ASN J 22 GLN J 67 ASN ** K 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN L 67 ASN M 31 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 ASN O 67 ASN P 82 GLN Q 2 ASN Q 67 ASN ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN U 67 ASN ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 2 ASN ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 ASN ** W 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN X 67 ASN Y 67 ASN Z 2 ASN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 67 ASN b 82 GLN d 67 ASN ** e 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.6345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 23095 Z= 0.252 Angle : 0.676 7.734 31000 Z= 0.371 Chirality : 0.044 0.226 3472 Planarity : 0.004 0.045 3937 Dihedral : 4.166 24.410 2914 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.01 % Allowed : 30.98 % Favored : 64.01 % 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: 0.52 (0.16), residues: 2728 helix: 0.69 (0.10), residues: 2511 sheet: None (None), residues: 0 loop : -2.87 (0.26), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V 30 HIS 0.004 0.001 HIS U 56 PHE 0.028 0.001 PHE D 3 TYR 0.023 0.002 TYR a 78 ARG 0.012 0.001 ARG Y 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1765 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1636 time to evaluate : 3.315 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: A 17 MET cc_start: 0.8425 (tpp) cc_final: 0.8037 (tpt) REVERT: A 34 ASN cc_start: 0.8076 (t0) cc_final: 0.7080 (t0) REVERT: A 37 GLU cc_start: 0.8802 (mp0) cc_final: 0.8263 (mp0) REVERT: A 60 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8513 (mtpt) REVERT: B 2 ASN cc_start: 0.8414 (m-40) cc_final: 0.8205 (m-40) REVERT: B 34 ASN cc_start: 0.8375 (p0) cc_final: 0.7898 (p0) REVERT: B 60 LYS cc_start: 0.8409 (mttt) cc_final: 0.8197 (mttp) REVERT: B 81 PHE cc_start: 0.9213 (t80) cc_final: 0.8586 (t80) REVERT: C 1 MET cc_start: 0.6601 (tpt) cc_final: 0.6104 (tpt) REVERT: C 47 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: C 56 HIS cc_start: 0.7729 (m-70) cc_final: 0.7497 (m-70) REVERT: C 60 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8145 (mttt) REVERT: C 71 LYS cc_start: 0.9349 (ttmm) cc_final: 0.9145 (ptmt) REVERT: D 13 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8586 (mm-40) REVERT: D 35 ARG cc_start: 0.7934 (tpp80) cc_final: 0.7658 (tpp-160) REVERT: D 39 ASN cc_start: 0.8230 (m110) cc_final: 0.7859 (m110) REVERT: D 74 LYS cc_start: 0.8987 (tttt) cc_final: 0.8648 (ttpp) REVERT: D 78 TYR cc_start: 0.8632 (t80) cc_final: 0.8371 (t80) REVERT: E 35 ARG cc_start: 0.7572 (tpp80) cc_final: 0.7231 (tpp80) REVERT: E 39 ASN cc_start: 0.8333 (m110) cc_final: 0.7424 (m110) REVERT: E 57 MET cc_start: 0.8300 (mtm) cc_final: 0.7987 (mtp) REVERT: E 60 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8261 (mtpp) REVERT: H 14 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7249 (mtp180) REVERT: H 35 ARG cc_start: 0.8037 (ttm170) cc_final: 0.7403 (tpp80) REVERT: H 36 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: H 44 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8084 (mm-30) REVERT: H 78 TYR cc_start: 0.8881 (t80) cc_final: 0.8532 (t80) REVERT: H 82 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8234 (mp10) REVERT: I 66 CYS cc_start: 0.8342 (t) cc_final: 0.8025 (m) REVERT: J 39 ASN cc_start: 0.8482 (m-40) cc_final: 0.8003 (m-40) REVERT: J 82 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8494 (mm-40) REVERT: J 87 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7678 (mm-40) REVERT: K 17 MET cc_start: 0.8274 (tpp) cc_final: 0.7907 (tpt) REVERT: K 21 LYS cc_start: 0.8901 (mttt) cc_final: 0.8644 (mttp) REVERT: K 25 ASP cc_start: 0.8212 (m-30) cc_final: 0.7735 (m-30) REVERT: K 60 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8317 (mtpp) REVERT: K 83 ASP cc_start: 0.8585 (t70) cc_final: 0.7986 (t0) REVERT: L 36 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: L 66 CYS cc_start: 0.8240 (m) cc_final: 0.7895 (m) REVERT: L 74 LYS cc_start: 0.8981 (ttmm) cc_final: 0.8750 (ttpp) REVERT: M 35 ARG cc_start: 0.7981 (tpp-160) cc_final: 0.7643 (tpp-160) REVERT: M 39 ASN cc_start: 0.8301 (m110) cc_final: 0.7021 (m110) REVERT: M 44 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7549 (mm-30) REVERT: M 58 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8861 (tp) REVERT: M 71 LYS cc_start: 0.9294 (ptmt) cc_final: 0.9055 (ptmt) REVERT: N 37 GLU cc_start: 0.8739 (pm20) cc_final: 0.8479 (pm20) REVERT: N 44 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7534 (mm-30) REVERT: O 9 ARG cc_start: 0.8607 (mtp-110) cc_final: 0.8196 (mtp-110) REVERT: O 35 ARG cc_start: 0.7705 (tpp80) cc_final: 0.7252 (tpp80) REVERT: O 39 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.7972 (m110) REVERT: O 44 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8066 (mm-30) REVERT: O 60 LYS cc_start: 0.8543 (mtpt) cc_final: 0.8021 (mtpt) REVERT: P 60 LYS cc_start: 0.8893 (mtmt) cc_final: 0.8300 (mtpt) REVERT: Q 5 LYS cc_start: 0.8831 (tptm) cc_final: 0.8618 (tptm) REVERT: Q 14 ARG cc_start: 0.8248 (mtp180) cc_final: 0.7898 (mtp180) REVERT: Q 71 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8915 (ttpp) REVERT: R 35 ARG cc_start: 0.7989 (ttp-110) cc_final: 0.7592 (tpp80) REVERT: R 44 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7641 (mm-30) REVERT: R 60 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8546 (mttt) REVERT: R 74 LYS cc_start: 0.9093 (ttmm) cc_final: 0.8881 (ttpp) REVERT: S 9 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.7813 (ttm110) REVERT: S 66 CYS cc_start: 0.8643 (m) cc_final: 0.8088 (m) REVERT: T 1 MET cc_start: 0.6928 (tpp) cc_final: 0.6492 (tpt) REVERT: T 39 ASN cc_start: 0.8098 (m110) cc_final: 0.7752 (t0) REVERT: T 52 ARG cc_start: 0.7632 (mtt-85) cc_final: 0.7267 (mtt-85) REVERT: U 35 ARG cc_start: 0.7701 (ttm110) cc_final: 0.7274 (ttm110) REVERT: U 39 ASN cc_start: 0.8306 (m110) cc_final: 0.7650 (m-40) REVERT: U 49 ASP cc_start: 0.8265 (m-30) cc_final: 0.7935 (m-30) REVERT: V 35 ARG cc_start: 0.7920 (tpp80) cc_final: 0.7161 (tpp80) REVERT: V 39 ASN cc_start: 0.8137 (m-40) cc_final: 0.7747 (m110) REVERT: V 56 HIS cc_start: 0.7628 (m-70) cc_final: 0.7291 (m-70) REVERT: V 66 CYS cc_start: 0.8444 (m) cc_final: 0.8084 (m) REVERT: V 87 GLN cc_start: 0.8194 (mm-40) cc_final: 0.7969 (mp10) REVERT: W 36 GLU cc_start: 0.8619 (tp30) cc_final: 0.7659 (tp30) REVERT: W 47 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: W 66 CYS cc_start: 0.8134 (t) cc_final: 0.7403 (m) REVERT: W 82 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8665 (mm-40) REVERT: X 7 ASN cc_start: 0.8984 (m-40) cc_final: 0.8570 (m110) REVERT: X 14 ARG cc_start: 0.7708 (mtt180) cc_final: 0.6222 (tpt170) REVERT: X 21 LYS cc_start: 0.9127 (mttp) cc_final: 0.8485 (mttp) REVERT: X 22 GLN cc_start: 0.8612 (mt0) cc_final: 0.8292 (mt0) REVERT: X 25 ASP cc_start: 0.8093 (m-30) cc_final: 0.7501 (m-30) REVERT: X 66 CYS cc_start: 0.8647 (m) cc_final: 0.7950 (m) REVERT: X 78 TYR cc_start: 0.8934 (t80) cc_final: 0.8538 (t80) REVERT: Y 8 SER cc_start: 0.8696 (m) cc_final: 0.8413 (m) REVERT: Y 14 ARG cc_start: 0.7668 (mtp180) cc_final: 0.7461 (mtp-110) REVERT: Y 42 CYS cc_start: 0.7828 (m) cc_final: 0.7381 (t) REVERT: Y 60 LYS cc_start: 0.9039 (mtmt) cc_final: 0.7963 (tmtt) REVERT: Y 82 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8210 (mp10) REVERT: Z 36 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: Z 74 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8752 (ttpp) REVERT: Z 82 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8306 (mp10) REVERT: a 5 LYS cc_start: 0.8808 (tttm) cc_final: 0.8541 (tptt) REVERT: a 9 ARG cc_start: 0.7985 (mtp180) cc_final: 0.7483 (mmt-90) REVERT: a 39 ASN cc_start: 0.8508 (m-40) cc_final: 0.8250 (m-40) REVERT: a 60 LYS cc_start: 0.8994 (mtmt) cc_final: 0.7509 (tptm) REVERT: b 20 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8978 (mp) REVERT: b 26 ASP cc_start: 0.8176 (t70) cc_final: 0.7841 (t0) REVERT: b 39 ASN cc_start: 0.8050 (m110) cc_final: 0.7400 (m110) REVERT: b 71 LYS cc_start: 0.9411 (ptmt) cc_final: 0.9207 (ptmt) REVERT: b 74 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8821 (ptmm) REVERT: c 9 ARG cc_start: 0.4665 (mmt-90) cc_final: 0.4171 (mtt-85) REVERT: c 20 ILE cc_start: 0.9238 (mp) cc_final: 0.8988 (mp) REVERT: c 36 GLU cc_start: 0.7374 (tt0) cc_final: 0.7155 (pt0) REVERT: c 39 ASN cc_start: 0.8667 (m-40) cc_final: 0.7346 (m110) REVERT: c 58 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9087 (tp) REVERT: d 5 LYS cc_start: 0.8865 (tttm) cc_final: 0.8630 (tttm) REVERT: d 9 ARG cc_start: 0.8570 (mtp-110) cc_final: 0.8283 (mtp-110) REVERT: d 13 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8660 (mm110) REVERT: d 26 ASP cc_start: 0.8671 (t70) cc_final: 0.8186 (t0) REVERT: d 37 GLU cc_start: 0.8686 (mp0) cc_final: 0.8220 (mp0) REVERT: d 39 ASN cc_start: 0.8828 (m-40) cc_final: 0.8591 (m110) REVERT: d 60 LYS cc_start: 0.8506 (mtmt) cc_final: 0.7998 (mtpt) REVERT: d 74 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8771 (ttpp) REVERT: d 78 TYR cc_start: 0.8729 (t80) cc_final: 0.8437 (t80) REVERT: e 12 ILE cc_start: 0.9072 (mt) cc_final: 0.8834 (mm) REVERT: e 13 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8380 (mm-40) REVERT: e 34 ASN cc_start: 0.8699 (t0) cc_final: 0.8388 (t0) REVERT: e 74 LYS cc_start: 0.9069 (tttt) cc_final: 0.8735 (ttpp) REVERT: e 78 TYR cc_start: 0.8724 (t80) cc_final: 0.8252 (t80) outliers start: 129 outliers final: 104 residues processed: 1666 average time/residue: 0.3667 time to fit residues: 913.0514 Evaluate side-chains 1717 residues out of total 2573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1601 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain L residue 2 ASN Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 39 ASN Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 36 GLU Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain S residue 15 MET Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain W residue 2 ASN Chi-restraints excluded: chain W residue 32 VAL Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 71 LYS Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 64 GLU Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 15 MET Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 74 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 227 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN I 67 ASN I 82 GLN J 2 ASN ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN L 67 ASN L 82 GLN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 ASN O 13 GLN O 67 ASN P 67 ASN ** P 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN V 2 ASN ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 ASN ** W 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 67 ASN Y 67 ASN Z 2 ASN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 67 ASN b 82 GLN d 67 ASN e 82 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.094348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.082106 restraints weight = 38495.702| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.33 r_work: 0.2854 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 23095 Z= 0.264 Angle : 0.698 7.598 31000 Z= 0.383 Chirality : 0.045 0.229 3472 Planarity : 0.004 0.044 3937 Dihedral : 4.249 21.425 2914 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.94 % Allowed : 31.17 % Favored : 63.89 % 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: 0.42 (0.16), residues: 2728 helix: 0.63 (0.10), residues: 2511 sheet: None (None), residues: 0 loop : -2.87 (0.26), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 30 HIS 0.004 0.001 HIS Z 56 PHE 0.028 0.001 PHE D 3 TYR 0.017 0.002 TYR D 78 ARG 0.012 0.001 ARG Y 9 =============================================================================== Job complete usr+sys time: 11786.87 seconds wall clock time: 208 minutes 46.65 seconds (12526.65 seconds total)