Starting phenix.real_space_refine on Mon Mar 25 18:06:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/03_2024/8xb8_38214.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/03_2024/8xb8_38214.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/8xb8_38214/03_2024/8xb8_38214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/03_2024/8xb8_38214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/03_2024/8xb8_38214.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/03_2024/8xb8_38214.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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 300 5.16 5 C 32700 2.51 5 N 8400 2.21 5 O 9000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "o TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50400 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "D" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "E" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "H" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "I" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "J" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "K" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "L" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "M" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "N" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "O" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "P" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Q" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "R" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "S" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "T" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "U" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "V" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "W" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "X" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Y" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Z" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "a" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "b" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "c" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "d" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "e" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "f" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "g" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "h" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "i" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "j" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "k" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "l" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "m" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "n" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "o" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "p" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "q" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "r" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "s" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "t" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "u" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "v" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "w" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "x" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "y" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "z" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "0" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "1" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "2" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "3" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "4" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "5" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "6" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "7" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Time building chain proxies: 23.91, per 1000 atoms: 0.47 Number of scatterers: 50400 At special positions: 0 Unit cell: (204.88, 204.88, 205.92, 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 300 16.00 O 9000 8.00 N 8400 7.00 C 32700 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: 18.74 Conformation dependent library (CDL) restraints added in 8.5 seconds 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11640 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 60 sheets defined 53.1% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.84 Creating SS restraints... Processing helix chain 'A' and resid 1 through 36 Processing helix chain 'A' and resid 68 through 84 Processing helix chain 'B' and resid 2 through 36 Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 68 through 84 Processing helix chain 'C' and resid 2 through 36 Processing helix chain 'C' and resid 68 through 84 Processing helix chain 'D' and resid 2 through 36 Processing helix chain 'D' and resid 68 through 84 Processing helix chain 'E' and resid 2 through 36 Processing helix chain 'E' and resid 68 through 84 Processing helix chain 'F' and resid 2 through 37 Processing helix chain 'F' and resid 68 through 84 Processing helix chain 'G' and resid 2 through 36 Processing helix chain 'G' and resid 64 through 67 Processing helix chain 'G' and resid 68 through 84 Processing helix chain 'H' and resid 2 through 36 Processing helix chain 'H' and resid 68 through 84 Processing helix chain 'I' and resid 2 through 36 Processing helix chain 'I' and resid 68 through 84 Processing helix chain 'J' and resid 2 through 36 Processing helix chain 'J' and resid 68 through 84 Processing helix chain 'K' and resid 2 through 37 Processing helix chain 'K' and resid 68 through 84 Processing helix chain 'L' and resid 2 through 36 Processing helix chain 'L' and resid 64 through 67 Processing helix chain 'L' and resid 68 through 84 Processing helix chain 'M' and resid 2 through 36 Processing helix chain 'M' and resid 68 through 84 Processing helix chain 'N' and resid 2 through 36 Processing helix chain 'N' and resid 68 through 84 Processing helix chain 'O' and resid 2 through 37 Processing helix chain 'O' and resid 68 through 84 Processing helix chain 'P' and resid 2 through 37 Processing helix chain 'P' and resid 64 through 67 Processing helix chain 'P' and resid 68 through 84 Processing helix chain 'Q' and resid 2 through 36 Processing helix chain 'Q' and resid 68 through 84 Processing helix chain 'R' and resid 2 through 36 Processing helix chain 'R' and resid 68 through 84 Processing helix chain 'S' and resid 2 through 36 Processing helix chain 'S' and resid 68 through 84 Processing helix chain 'T' and resid 2 through 36 Processing helix chain 'T' and resid 68 through 84 Processing helix chain 'U' and resid 2 through 37 Processing helix chain 'U' and resid 68 through 84 Processing helix chain 'V' and resid 2 through 36 Processing helix chain 'V' and resid 68 through 84 Processing helix chain 'W' and resid 2 through 36 Processing helix chain 'W' and resid 68 through 84 Processing helix chain 'X' and resid 2 through 36 Processing helix chain 'X' and resid 68 through 84 Processing helix chain 'Y' and resid 2 through 36 Processing helix chain 'Y' and resid 68 through 84 Processing helix chain 'Z' and resid 2 through 36 Processing helix chain 'Z' and resid 68 through 84 Processing helix chain 'a' and resid 2 through 36 Processing helix chain 'a' and resid 68 through 84 Processing helix chain 'b' and resid 2 through 36 Processing helix chain 'b' and resid 68 through 84 Processing helix chain 'c' and resid 2 through 36 Processing helix chain 'c' and resid 68 through 84 Processing helix chain 'd' and resid 2 through 37 Processing helix chain 'd' and resid 68 through 84 Processing helix chain 'e' and resid 2 through 37 Processing helix chain 'e' and resid 68 through 84 Processing helix chain 'f' and resid 2 through 36 Processing helix chain 'f' and resid 68 through 84 Processing helix chain 'g' and resid 2 through 36 Processing helix chain 'g' and resid 68 through 84 Processing helix chain 'h' and resid 2 through 36 Processing helix chain 'h' and resid 68 through 84 Processing helix chain 'i' and resid 2 through 37 Processing helix chain 'i' and resid 68 through 84 Processing helix chain 'j' and resid 2 through 37 Processing helix chain 'j' and resid 68 through 84 Processing helix chain 'k' and resid 2 through 36 Processing helix chain 'k' and resid 64 through 67 Processing helix chain 'k' and resid 68 through 84 Processing helix chain 'l' and resid 2 through 36 Processing helix chain 'l' and resid 68 through 84 Processing helix chain 'm' and resid 2 through 36 Processing helix chain 'm' and resid 68 through 84 Processing helix chain 'n' and resid 2 through 36 Processing helix chain 'n' and resid 68 through 84 Processing helix chain 'o' and resid 2 through 37 Processing helix chain 'o' and resid 68 through 84 Processing helix chain 'p' and resid 2 through 36 Processing helix chain 'p' and resid 68 through 84 Processing helix chain 'q' and resid 2 through 36 Processing helix chain 'q' and resid 68 through 84 Processing helix chain 'r' and resid 2 through 36 Processing helix chain 'r' and resid 68 through 84 Processing helix chain 's' and resid 2 through 37 Processing helix chain 's' and resid 68 through 84 Processing helix chain 't' and resid 2 through 37 Processing helix chain 't' and resid 68 through 84 Processing helix chain 'u' and resid 2 through 36 Processing helix chain 'u' and resid 68 through 84 Processing helix chain 'v' and resid 2 through 36 Processing helix chain 'v' and resid 68 through 84 Processing helix chain 'w' and resid 2 through 36 Processing helix chain 'w' and resid 68 through 84 Processing helix chain 'x' and resid 2 through 37 Processing helix chain 'x' and resid 68 through 84 Processing helix chain 'y' and resid 2 through 37 Processing helix chain 'y' and resid 68 through 84 Processing helix chain 'z' and resid 2 through 36 Processing helix chain 'z' and resid 68 through 84 Processing helix chain '0' and resid 2 through 36 Processing helix chain '0' and resid 68 through 84 Processing helix chain '1' and resid 2 through 36 Processing helix chain '1' and resid 68 through 84 Processing helix chain '2' and resid 2 through 37 Processing helix chain '2' and resid 68 through 84 Processing helix chain '3' and resid 2 through 37 Processing helix chain '3' and resid 68 through 84 Processing helix chain '4' and resid 2 through 36 Processing helix chain '4' and resid 68 through 84 Processing helix chain '5' and resid 2 through 36 Processing helix chain '5' and resid 68 through 84 Processing helix chain '6' and resid 2 through 36 Processing helix chain '6' and resid 68 through 84 Processing helix chain '7' and resid 2 through 36 Processing helix chain '7' and resid 68 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 47 Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 47 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 47 Processing sheet with id=AA4, first strand: chain 'D' and resid 42 through 47 Processing sheet with id=AA5, first strand: chain 'E' and resid 42 through 47 Processing sheet with id=AA6, first strand: chain 'F' and resid 42 through 47 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 47 Processing sheet with id=AA8, first strand: chain 'H' and resid 42 through 47 Processing sheet with id=AA9, first strand: chain 'I' and resid 42 through 47 Processing sheet with id=AB1, first strand: chain 'J' and resid 42 through 47 Processing sheet with id=AB2, first strand: chain 'K' and resid 42 through 47 Processing sheet with id=AB3, first strand: chain 'L' and resid 42 through 47 Processing sheet with id=AB4, first strand: chain 'M' and resid 42 through 47 Processing sheet with id=AB5, first strand: chain 'N' and resid 42 through 47 Processing sheet with id=AB6, first strand: chain 'O' and resid 42 through 47 Processing sheet with id=AB7, first strand: chain 'P' and resid 42 through 47 Processing sheet with id=AB8, first strand: chain 'Q' and resid 42 through 47 Processing sheet with id=AB9, first strand: chain 'R' and resid 42 through 47 Processing sheet with id=AC1, first strand: chain 'S' and resid 42 through 47 Processing sheet with id=AC2, first strand: chain 'T' and resid 42 through 47 Processing sheet with id=AC3, first strand: chain 'U' and resid 42 through 47 Processing sheet with id=AC4, first strand: chain 'V' and resid 42 through 47 Processing sheet with id=AC5, first strand: chain 'W' and resid 42 through 47 Processing sheet with id=AC6, first strand: chain 'X' and resid 42 through 47 Processing sheet with id=AC7, first strand: chain 'Y' and resid 42 through 47 Processing sheet with id=AC8, first strand: chain 'Z' and resid 42 through 47 Processing sheet with id=AC9, first strand: chain 'a' and resid 42 through 47 Processing sheet with id=AD1, first strand: chain 'b' and resid 42 through 47 Processing sheet with id=AD2, first strand: chain 'c' and resid 42 through 47 Processing sheet with id=AD3, first strand: chain 'd' and resid 42 through 47 Processing sheet with id=AD4, first strand: chain 'e' and resid 42 through 47 Processing sheet with id=AD5, first strand: chain 'f' and resid 42 through 47 Processing sheet with id=AD6, first strand: chain 'g' and resid 42 through 47 Processing sheet with id=AD7, first strand: chain 'h' and resid 42 through 47 Processing sheet with id=AD8, first strand: chain 'i' and resid 42 through 47 Processing sheet with id=AD9, first strand: chain 'j' and resid 42 through 47 Processing sheet with id=AE1, first strand: chain 'k' and resid 42 through 47 Processing sheet with id=AE2, first strand: chain 'l' and resid 42 through 47 Processing sheet with id=AE3, first strand: chain 'm' and resid 42 through 47 Processing sheet with id=AE4, first strand: chain 'n' and resid 42 through 47 Processing sheet with id=AE5, first strand: chain 'o' and resid 42 through 47 Processing sheet with id=AE6, first strand: chain 'p' and resid 42 through 47 Processing sheet with id=AE7, first strand: chain 'q' and resid 42 through 47 Processing sheet with id=AE8, first strand: chain 'r' and resid 42 through 47 Processing sheet with id=AE9, first strand: chain 's' and resid 42 through 47 Processing sheet with id=AF1, first strand: chain 't' and resid 42 through 47 Processing sheet with id=AF2, first strand: chain 'u' and resid 42 through 47 Processing sheet with id=AF3, first strand: chain 'v' and resid 42 through 47 Processing sheet with id=AF4, first strand: chain 'w' and resid 42 through 47 Processing sheet with id=AF5, first strand: chain 'x' and resid 42 through 47 Processing sheet with id=AF6, first strand: chain 'y' and resid 42 through 47 Processing sheet with id=AF7, first strand: chain 'z' and resid 42 through 47 Processing sheet with id=AF8, first strand: chain '0' and resid 42 through 47 Processing sheet with id=AF9, first strand: chain '1' and resid 42 through 47 Processing sheet with id=AG1, first strand: chain '2' and resid 42 through 47 Processing sheet with id=AG2, first strand: chain '3' and resid 42 through 47 Processing sheet with id=AG3, first strand: chain '4' and resid 42 through 47 Processing sheet with id=AG4, first strand: chain '5' and resid 42 through 47 Processing sheet with id=AG5, first strand: chain '6' and resid 42 through 47 Processing sheet with id=AG6, first strand: chain '7' and resid 42 through 47 3622 hydrogen bonds defined for protein. 10311 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: 19.60 Time building geometry restraints manager: 20.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 15960 1.34 - 1.46: 11504 1.46 - 1.58: 23836 1.58 - 1.69: 0 1.69 - 1.81: 420 Bond restraints: 51720 Sorted by residual: bond pdb=" N ASP k 9 " pdb=" CA ASP k 9 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.85e+00 bond pdb=" CB ASP g 9 " pdb=" CG ASP g 9 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.12e+00 bond pdb=" CB ASP 0 9 " pdb=" CG ASP 0 9 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 bond pdb=" CB ILE X 37 " pdb=" CG2 ILE X 37 " ideal model delta sigma weight residual 1.521 1.554 -0.033 3.30e-02 9.18e+02 9.86e-01 bond pdb=" CB ILE g 37 " pdb=" CG2 ILE g 37 " ideal model delta sigma weight residual 1.521 1.553 -0.032 3.30e-02 9.18e+02 9.29e-01 ... (remaining 51715 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.63: 1260 106.63 - 113.48: 28010 113.48 - 120.33: 20062 120.33 - 127.18: 19728 127.18 - 134.03: 660 Bond angle restraints: 69720 Sorted by residual: angle pdb=" CA ASP k 9 " pdb=" C ASP k 9 " pdb=" O ASP k 9 " ideal model delta sigma weight residual 120.82 118.06 2.76 1.05e+00 9.07e-01 6.90e+00 angle pdb=" C LYS 6 52 " pdb=" N MET 6 53 " pdb=" CA MET 6 53 " ideal model delta sigma weight residual 122.87 118.71 4.16 1.61e+00 3.86e-01 6.68e+00 angle pdb=" C THR Q 50 " pdb=" N LYS Q 51 " pdb=" CA LYS Q 51 " ideal model delta sigma weight residual 122.46 125.90 -3.44 1.41e+00 5.03e-01 5.96e+00 angle pdb=" CA LEU y 8 " pdb=" CB LEU y 8 " pdb=" CG LEU y 8 " ideal model delta sigma weight residual 116.30 124.68 -8.38 3.50e+00 8.16e-02 5.73e+00 angle pdb=" CA LEU e 8 " pdb=" CB LEU e 8 " pdb=" CG LEU e 8 " ideal model delta sigma weight residual 116.30 124.68 -8.38 3.50e+00 8.16e-02 5.73e+00 ... (remaining 69715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 25702 14.90 - 29.80: 3892 29.80 - 44.70: 1007 44.70 - 59.60: 331 59.60 - 74.50: 88 Dihedral angle restraints: 31020 sinusoidal: 13380 harmonic: 17640 Sorted by residual: dihedral pdb=" N LYS e 28 " pdb=" CA LYS e 28 " pdb=" CB LYS e 28 " pdb=" CG LYS e 28 " ideal model delta sinusoidal sigma weight residual -60.00 -119.99 59.99 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LYS W 28 " pdb=" CA LYS W 28 " pdb=" CB LYS W 28 " pdb=" CG LYS W 28 " ideal model delta sinusoidal sigma weight residual -180.00 -120.01 -59.99 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LYS b 28 " pdb=" CA LYS b 28 " pdb=" CB LYS b 28 " pdb=" CG LYS b 28 " ideal model delta sinusoidal sigma weight residual -60.00 -119.98 59.98 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 31017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 7196 0.089 - 0.178: 263 0.178 - 0.267: 24 0.267 - 0.356: 3 0.356 - 0.445: 14 Chirality restraints: 7500 Sorted by residual: chirality pdb=" CB ILE X 37 " pdb=" CA ILE X 37 " pdb=" CG1 ILE X 37 " pdb=" CG2 ILE X 37 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" CB ILE g 37 " pdb=" CA ILE g 37 " pdb=" CG1 ILE g 37 " pdb=" CG2 ILE g 37 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CB ILE 0 37 " pdb=" CA ILE 0 37 " pdb=" CG1 ILE 0 37 " pdb=" CG2 ILE 0 37 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.60e+00 ... (remaining 7497 not shown) Planarity restraints: 8820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP v 9 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" CG ASP v 9 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP v 9 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP v 9 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 9 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.25e+00 pdb=" CG ASP H 9 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP H 9 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP H 9 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP l 9 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.25e+00 pdb=" CG ASP l 9 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASP l 9 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP l 9 " 0.009 2.00e-02 2.50e+03 ... (remaining 8817 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 8961 2.77 - 3.30: 47569 3.30 - 3.84: 88231 3.84 - 4.37: 96857 4.37 - 4.90: 179252 Nonbonded interactions: 420870 Sorted by model distance: nonbonded pdb=" O LEU j 79 " pdb=" OG SER j 83 " model vdw 2.241 2.440 nonbonded pdb=" O LEU F 79 " pdb=" OG SER F 83 " model vdw 2.258 2.440 nonbonded pdb=" O LEU K 79 " pdb=" OG SER K 83 " model vdw 2.260 2.440 nonbonded pdb=" O LEU A 79 " pdb=" OG SER A 83 " model vdw 2.278 2.440 nonbonded pdb=" O HIS a 62 " pdb=" NE2 HIS a 66 " model vdw 2.281 2.520 ... (remaining 420865 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = 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' 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' } 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 12.600 Check model and map are aligned: 0.790 Set scattering table: 0.500 Process input model: 124.010 Find NCS groups from input model: 3.560 Set up NCS constraints: 0.870 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.003 0.033 51720 Z= 0.199 Angle : 0.500 8.380 69720 Z= 0.275 Chirality : 0.045 0.445 7500 Planarity : 0.003 0.039 8820 Dihedral : 16.094 74.505 19380 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.30 % Allowed : 18.48 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.10), residues: 5820 helix: 2.25 (0.08), residues: 3060 sheet: -0.21 (0.11), residues: 1440 loop : -0.60 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 24 HIS 0.005 0.001 HIS y 62 PHE 0.014 0.001 PHE 4 96 TYR 0.011 0.001 TYR P 44 ARG 0.009 0.000 ARG 6 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 656 time to evaluate : 6.026 Fit side-chains REVERT: u 36 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6384 (mt-10) REVERT: 3 67 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6895 (mt-10) outliers start: 17 outliers final: 11 residues processed: 662 average time/residue: 0.6904 time to fit residues: 731.3598 Evaluate side-chains 665 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 652 time to evaluate : 5.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain l residue 50 THR Chi-restraints excluded: chain u residue 4 VAL Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain 3 residue 67 GLU Chi-restraints excluded: chain 6 residue 88 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 455 optimal weight: 3.9990 chunk 409 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 276 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 423 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 chunk 315 optimal weight: 1.9990 chunk 490 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.0542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 51720 Z= 0.284 Angle : 0.504 6.956 69720 Z= 0.279 Chirality : 0.046 0.324 7500 Planarity : 0.003 0.028 8820 Dihedral : 4.571 40.791 6321 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.85 % Allowed : 17.58 % Favored : 79.57 % 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: 1.35 (0.10), residues: 5820 helix: 2.12 (0.09), residues: 3060 sheet: -0.30 (0.11), residues: 1440 loop : -0.51 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 24 HIS 0.005 0.001 HIS W 62 PHE 0.013 0.002 PHE V 96 TYR 0.008 0.001 TYR 2 44 ARG 0.005 0.000 ARG 6 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 691 time to evaluate : 5.570 Fit side-chains REVERT: A 67 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7432 (mt-10) REVERT: F 67 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: K 67 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: L 9 ASP cc_start: 0.7588 (t0) cc_final: 0.7143 (t0) REVERT: M 9 ASP cc_start: 0.8008 (t0) cc_final: 0.7795 (t0) REVERT: S 9 ASP cc_start: 0.7708 (t0) cc_final: 0.7288 (t0) REVERT: b 28 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8093 (mtpp) REVERT: j 67 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: s 9 ASP cc_start: 0.7655 (t0) cc_final: 0.7389 (t0) REVERT: s 36 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: 7 9 ASP cc_start: 0.7696 (t0) cc_final: 0.7400 (t0) REVERT: 7 36 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6770 (mp0) outliers start: 159 outliers final: 118 residues processed: 725 average time/residue: 0.6584 time to fit residues: 763.2644 Evaluate side-chains 801 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 676 time to evaluate : 5.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 53 MET Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 53 MET Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 28 LYS Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain Z residue 88 VAL Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 53 MET Chi-restraints excluded: chain f residue 4 VAL Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain g residue 88 VAL Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 52 LYS Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 67 GLU Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 53 MET Chi-restraints excluded: chain m residue 88 VAL Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 88 VAL Chi-restraints excluded: chain p residue 4 VAL Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain t residue 88 VAL Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 53 MET Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 36 GLU Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 408 optimal weight: 0.0970 chunk 333 optimal weight: 0.0020 chunk 135 optimal weight: 5.9990 chunk 491 optimal weight: 3.9990 chunk 530 optimal weight: 0.4980 chunk 437 optimal weight: 0.8980 chunk 487 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 394 optimal weight: 1.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.0484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 51720 Z= 0.159 Angle : 0.442 7.507 69720 Z= 0.244 Chirality : 0.042 0.335 7500 Planarity : 0.003 0.031 8820 Dihedral : 4.238 24.884 6302 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.92 % Allowed : 18.21 % Favored : 78.87 % 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: 1.69 (0.10), residues: 5820 helix: 2.44 (0.08), residues: 3060 sheet: -0.14 (0.11), residues: 1440 loop : -0.49 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 24 HIS 0.003 0.001 HIS W 62 PHE 0.011 0.001 PHE V 96 TYR 0.008 0.000 TYR P 44 ARG 0.005 0.000 ARG R 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 698 time to evaluate : 5.452 Fit side-chains REVERT: C 41 ARG cc_start: 0.8761 (ttm110) cc_final: 0.8540 (ttm110) REVERT: K 67 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: V 36 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6510 (mt-10) REVERT: W 1 MET cc_start: 0.6859 (tmm) cc_final: 0.6291 (tpt) REVERT: b 28 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.8014 (mtpp) REVERT: f 36 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6741 (mt-10) REVERT: h 36 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6174 (mp0) REVERT: k 1 MET cc_start: 0.7182 (tpt) cc_final: 0.6879 (tpt) REVERT: p 36 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6499 (mt-10) REVERT: q 1 MET cc_start: 0.6950 (tmm) cc_final: 0.6492 (tpt) REVERT: s 36 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6743 (mp0) REVERT: v 28 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.8032 (mtpp) REVERT: w 28 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7854 (mtpt) REVERT: z 36 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6748 (mt-10) REVERT: 1 36 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6187 (mp0) REVERT: 4 36 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6513 (mt-10) REVERT: 5 1 MET cc_start: 0.6929 (tmm) cc_final: 0.6474 (tpt) REVERT: 7 36 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6679 (mp0) outliers start: 163 outliers final: 79 residues processed: 760 average time/residue: 0.6786 time to fit residues: 830.3465 Evaluate side-chains 755 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 663 time to evaluate : 5.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain P residue 53 MET Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 28 LYS Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 50 THR Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 88 VAL Chi-restraints excluded: chain o residue 88 VAL Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain v residue 28 LYS Chi-restraints excluded: chain v residue 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 28 LYS Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 36 GLU Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 0.8980 chunk 369 optimal weight: 0.6980 chunk 254 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 329 optimal weight: 0.9990 chunk 493 optimal weight: 0.9980 chunk 521 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 467 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.0549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 51720 Z= 0.201 Angle : 0.467 6.672 69720 Z= 0.257 Chirality : 0.044 0.369 7500 Planarity : 0.003 0.028 8820 Dihedral : 4.262 26.560 6302 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.94 % Allowed : 18.78 % Favored : 78.28 % 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: 1.68 (0.10), residues: 5820 helix: 2.42 (0.08), residues: 3060 sheet: -0.15 (0.11), residues: 1440 loop : -0.46 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP l 24 HIS 0.004 0.001 HIS W 62 PHE 0.016 0.001 PHE d 96 TYR 0.009 0.001 TYR P 44 ARG 0.005 0.000 ARG K 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 672 time to evaluate : 6.689 Fit side-chains REVERT: K 67 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: L 9 ASP cc_start: 0.7515 (t0) cc_final: 0.7111 (t0) REVERT: M 9 ASP cc_start: 0.7874 (t0) cc_final: 0.7602 (t0) REVERT: S 13 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6920 (mtpp) REVERT: V 36 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6439 (mt-10) REVERT: W 1 MET cc_start: 0.6916 (tmm) cc_final: 0.6387 (tpt) REVERT: Z 9 ASP cc_start: 0.7622 (t0) cc_final: 0.7339 (t0) REVERT: b 28 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.8032 (mtpp) REVERT: c 36 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6294 (mt-10) REVERT: f 36 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6778 (mt-10) REVERT: h 36 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6140 (mp0) REVERT: p 36 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6437 (mt-10) REVERT: s 9 ASP cc_start: 0.7627 (t0) cc_final: 0.7307 (t0) REVERT: s 36 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: t 9 ASP cc_start: 0.7605 (t0) cc_final: 0.7325 (t0) REVERT: u 41 ARG cc_start: 0.8711 (ttm110) cc_final: 0.8487 (ttm110) REVERT: v 28 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8061 (mtpp) REVERT: w 36 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6282 (mt-10) REVERT: z 36 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6747 (mt-10) REVERT: 1 36 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6145 (mp0) REVERT: 4 36 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6452 (mt-10) REVERT: 7 1 MET cc_start: 0.7247 (tpt) cc_final: 0.7028 (tpt) REVERT: 7 36 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6683 (mp0) outliers start: 164 outliers final: 124 residues processed: 721 average time/residue: 0.6600 time to fit residues: 759.5110 Evaluate side-chains 808 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 669 time to evaluate : 5.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 53 MET Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 28 LYS Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 53 MET Chi-restraints excluded: chain f residue 4 VAL Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 28 LYS Chi-restraints excluded: chain l residue 50 THR Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 88 VAL Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 88 VAL Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain v residue 4 VAL Chi-restraints excluded: chain v residue 28 LYS Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 36 GLU Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 36 GLU Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 0.6980 chunk 296 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 445 optimal weight: 0.9990 chunk 360 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 266 optimal weight: 5.9990 chunk 468 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 51720 Z= 0.298 Angle : 0.518 6.080 69720 Z= 0.286 Chirality : 0.046 0.373 7500 Planarity : 0.003 0.029 8820 Dihedral : 4.434 28.264 6302 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.41 % Allowed : 19.07 % Favored : 77.53 % 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: 1.31 (0.10), residues: 5820 helix: 2.10 (0.08), residues: 3060 sheet: -0.34 (0.11), residues: 1440 loop : -0.53 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP u 24 HIS 0.005 0.001 HIS e 85 PHE 0.014 0.002 PHE 6 96 TYR 0.010 0.001 TYR P 44 ARG 0.005 0.000 ARG a 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 750 time to evaluate : 5.968 Fit side-chains REVERT: C 41 ARG cc_start: 0.8779 (ttm110) cc_final: 0.8559 (ttm110) REVERT: D 36 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6458 (mt-10) REVERT: I 36 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6451 (mt-10) REVERT: K 67 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: N 36 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6422 (mt-10) REVERT: R 9 ASP cc_start: 0.7971 (t0) cc_final: 0.7717 (t0) REVERT: V 36 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6448 (mt-10) REVERT: c 36 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6268 (mt-10) REVERT: f 36 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: h 36 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.5983 (mp0) REVERT: m 36 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6410 (mt-10) REVERT: p 36 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6437 (mt-10) REVERT: s 1 MET cc_start: 0.7464 (tpt) cc_final: 0.7210 (tpt) REVERT: s 36 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: v 28 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8111 (mtpp) REVERT: w 36 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6277 (mt-10) REVERT: z 36 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6769 (mt-10) REVERT: 1 36 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6048 (mp0) REVERT: 4 36 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6453 (mt-10) REVERT: 6 36 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6776 (mt-10) REVERT: 6 67 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: 7 36 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6172 (mp0) outliers start: 190 outliers final: 141 residues processed: 810 average time/residue: 0.7268 time to fit residues: 939.7626 Evaluate side-chains 895 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 735 time to evaluate : 5.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 53 MET Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 53 MET Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 53 MET Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 28 LYS Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 82 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 82 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain Z residue 88 VAL Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 53 MET Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 53 MET Chi-restraints excluded: chain f residue 4 VAL Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 28 LYS Chi-restraints excluded: chain l residue 50 THR Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain m residue 36 GLU Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 53 MET Chi-restraints excluded: chain m residue 88 VAL Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 88 VAL Chi-restraints excluded: chain p residue 4 VAL Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 28 LYS Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain t residue 88 VAL Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain v residue 4 VAL Chi-restraints excluded: chain v residue 28 LYS Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 36 GLU Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 53 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 82 ILE Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 36 GLU Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 67 GLU Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 36 GLU Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 0.1980 chunk 470 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 522 optimal weight: 0.9980 chunk 433 optimal weight: 4.9990 chunk 241 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 chunk 274 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 51720 Z= 0.166 Angle : 0.466 6.918 69720 Z= 0.254 Chirality : 0.044 0.407 7500 Planarity : 0.003 0.029 8820 Dihedral : 4.261 29.677 6302 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.33 % Allowed : 19.52 % Favored : 77.15 % 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: 1.66 (0.10), residues: 5820 helix: 2.43 (0.08), residues: 3060 sheet: -0.18 (0.11), residues: 1440 loop : -0.54 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP f 24 HIS 0.004 0.001 HIS q 62 PHE 0.011 0.001 PHE K 96 TYR 0.010 0.001 TYR P 44 ARG 0.007 0.000 ARG u 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 700 time to evaluate : 6.272 Fit side-chains REVERT: D 36 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6487 (mt-10) REVERT: I 36 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6467 (mt-10) REVERT: K 67 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: N 36 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6463 (mt-10) REVERT: V 36 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6497 (mt-10) REVERT: W 1 MET cc_start: 0.6918 (tmm) cc_final: 0.6383 (tpt) REVERT: f 36 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6730 (mt-10) REVERT: h 36 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6219 (mp0) REVERT: j 1 MET cc_start: 0.6618 (tmm) cc_final: 0.6357 (tmm) REVERT: m 36 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6469 (mt-10) REVERT: p 36 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6461 (mt-10) REVERT: s 1 MET cc_start: 0.7193 (tpt) cc_final: 0.6992 (tpt) REVERT: s 36 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: w 36 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6265 (mt-10) REVERT: z 36 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6754 (mt-10) REVERT: 1 36 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6265 (mp0) REVERT: 4 36 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6473 (mt-10) REVERT: 6 36 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6756 (mt-10) REVERT: 7 36 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6715 (mp0) outliers start: 186 outliers final: 119 residues processed: 765 average time/residue: 0.6665 time to fit residues: 808.5731 Evaluate side-chains 803 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 668 time to evaluate : 5.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 28 LYS Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 53 MET Chi-restraints excluded: chain f residue 4 VAL Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain m residue 36 GLU Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 88 VAL Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 88 VAL Chi-restraints excluded: chain p residue 4 VAL Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain v residue 4 VAL Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 36 GLU Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 4 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 36 GLU Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 36 GLU Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 297 optimal weight: 3.9990 chunk 381 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 439 optimal weight: 1.9990 chunk 291 optimal weight: 0.9980 chunk 520 optimal weight: 0.7980 chunk 325 optimal weight: 1.9990 chunk 317 optimal weight: 3.9990 chunk 240 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 51720 Z= 0.236 Angle : 0.497 6.157 69720 Z= 0.274 Chirality : 0.046 0.421 7500 Planarity : 0.003 0.032 8820 Dihedral : 4.348 28.698 6302 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.01 % Allowed : 20.59 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.10), residues: 5820 helix: 2.33 (0.08), residues: 3060 sheet: -0.24 (0.11), residues: 1440 loop : -0.52 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP o 24 HIS 0.003 0.001 HIS q 62 PHE 0.016 0.002 PHE f 96 TYR 0.011 0.001 TYR P 44 ARG 0.008 0.001 ARG j 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 699 time to evaluate : 5.667 Fit side-chains REVERT: I 36 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6458 (mt-10) REVERT: K 67 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: N 36 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6484 (mt-10) REVERT: R 9 ASP cc_start: 0.7982 (t0) cc_final: 0.7724 (t0) REVERT: V 36 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6464 (mt-10) REVERT: W 1 MET cc_start: 0.6884 (tmm) cc_final: 0.6393 (tpt) REVERT: Z 1 MET cc_start: 0.7193 (tpt) cc_final: 0.6934 (tpt) REVERT: c 36 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6247 (mt-10) REVERT: f 36 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6746 (mt-10) REVERT: h 36 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6097 (mp0) REVERT: j 1 MET cc_start: 0.6759 (tmm) cc_final: 0.6376 (tmm) REVERT: k 1 MET cc_start: 0.7346 (tpt) cc_final: 0.7034 (tpt) REVERT: m 36 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6469 (mt-10) REVERT: p 36 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6431 (mt-10) REVERT: q 1 MET cc_start: 0.7369 (tpt) cc_final: 0.7160 (tpt) REVERT: r 36 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6737 (mt-10) REVERT: s 36 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6784 (mp0) REVERT: w 36 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6243 (mt-10) REVERT: z 36 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: 1 36 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6110 (mp0) REVERT: 4 36 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6422 (mt-10) REVERT: 5 1 MET cc_start: 0.7347 (tpt) cc_final: 0.7147 (tpt) REVERT: 6 36 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6737 (mt-10) REVERT: 7 36 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6759 (mp0) outliers start: 168 outliers final: 131 residues processed: 758 average time/residue: 0.6890 time to fit residues: 822.5610 Evaluate side-chains 827 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 679 time to evaluate : 5.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 36 GLU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 36 GLU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 28 LYS Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 53 MET Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 53 MET Chi-restraints excluded: chain f residue 4 VAL Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 50 THR Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain m residue 36 GLU Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 88 VAL Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 88 VAL Chi-restraints excluded: chain p residue 4 VAL Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 36 GLU Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 28 LYS Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain v residue 4 VAL Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 28 LYS Chi-restraints excluded: chain w residue 36 GLU Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 36 GLU Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 36 GLU Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 310 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 330 optimal weight: 0.0970 chunk 354 optimal weight: 0.7980 chunk 257 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 409 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 51720 Z= 0.188 Angle : 0.479 6.440 69720 Z= 0.262 Chirality : 0.046 0.421 7500 Planarity : 0.003 0.033 8820 Dihedral : 4.295 29.138 6302 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.89 % Allowed : 21.09 % Favored : 76.02 % 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: 1.66 (0.10), residues: 5820 helix: 2.45 (0.08), residues: 3060 sheet: -0.21 (0.11), residues: 1440 loop : -0.55 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP u 24 HIS 0.003 0.001 HIS q 62 PHE 0.014 0.001 PHE f 96 TYR 0.011 0.001 TYR P 44 ARG 0.008 0.000 ARG X 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 687 time to evaluate : 5.805 Fit side-chains REVERT: R 9 ASP cc_start: 0.7982 (t0) cc_final: 0.7747 (t0) REVERT: V 36 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6572 (mt-10) REVERT: W 1 MET cc_start: 0.6987 (tmm) cc_final: 0.6317 (tpt) REVERT: c 36 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6245 (mt-10) REVERT: f 36 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6730 (mt-10) REVERT: h 36 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6213 (mp0) REVERT: j 1 MET cc_start: 0.6791 (tmm) cc_final: 0.6470 (tmm) REVERT: k 1 MET cc_start: 0.7275 (tpt) cc_final: 0.7035 (tpt) REVERT: p 36 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6504 (mt-10) REVERT: q 28 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7828 (mtpt) REVERT: r 36 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6719 (mt-10) REVERT: s 36 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: w 36 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6252 (mt-10) REVERT: z 36 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6748 (mt-10) REVERT: 1 36 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: 4 36 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6461 (mt-10) REVERT: 6 36 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6728 (mt-10) REVERT: 7 36 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6758 (mp0) outliers start: 161 outliers final: 130 residues processed: 737 average time/residue: 0.6835 time to fit residues: 796.0044 Evaluate side-chains 816 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 672 time to evaluate : 5.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 28 LYS Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 28 LYS Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 53 MET Chi-restraints excluded: chain f residue 4 VAL Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 50 THR Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 88 VAL Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 88 VAL Chi-restraints excluded: chain p residue 4 VAL Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 28 LYS Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 36 GLU Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain v residue 4 VAL Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 28 LYS Chi-restraints excluded: chain w residue 36 GLU Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 4 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 36 GLU Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 36 GLU Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 2.9990 chunk 498 optimal weight: 2.9990 chunk 454 optimal weight: 0.0970 chunk 485 optimal weight: 0.7980 chunk 291 optimal weight: 0.7980 chunk 211 optimal weight: 0.0060 chunk 380 optimal weight: 0.6980 chunk 148 optimal weight: 0.0570 chunk 438 optimal weight: 0.9990 chunk 458 optimal weight: 2.9990 chunk 483 optimal weight: 1.9990 overall best weight: 0.3312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 51720 Z= 0.152 Angle : 0.466 6.810 69720 Z= 0.253 Chirality : 0.045 0.421 7500 Planarity : 0.003 0.033 8820 Dihedral : 4.207 30.022 6302 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.60 % Allowed : 21.11 % Favored : 76.29 % 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: 1.94 (0.10), residues: 5820 helix: 2.69 (0.08), residues: 3060 sheet: -0.09 (0.11), residues: 1440 loop : -0.47 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP f 24 HIS 0.003 0.001 HIS 2 62 PHE 0.013 0.001 PHE f 96 TYR 0.011 0.001 TYR P 44 ARG 0.007 0.000 ARG T 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 705 time to evaluate : 5.634 Fit side-chains REVERT: G 86 ARG cc_start: 0.7688 (ttt-90) cc_final: 0.7482 (ttt-90) REVERT: R 9 ASP cc_start: 0.7844 (t0) cc_final: 0.7491 (t0) REVERT: V 36 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6568 (mt-10) REVERT: X 86 ARG cc_start: 0.7850 (ttt-90) cc_final: 0.7614 (ttt-90) REVERT: c 36 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6322 (mt-10) REVERT: e 28 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7844 (mtpt) REVERT: f 36 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6758 (mt-10) REVERT: h 36 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6213 (mp0) REVERT: j 1 MET cc_start: 0.6597 (tmm) cc_final: 0.6332 (tmm) REVERT: p 36 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6509 (mt-10) REVERT: r 36 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6701 (mt-10) REVERT: s 36 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: u 36 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6392 (mt-10) REVERT: w 28 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7806 (mtpt) REVERT: w 36 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6342 (mt-10) REVERT: x 86 ARG cc_start: 0.7793 (ttt-90) cc_final: 0.7585 (ttt-90) REVERT: y 28 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7821 (mtpt) REVERT: z 36 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6781 (mt-10) REVERT: 1 36 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6268 (mp0) REVERT: 4 36 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6521 (mt-10) REVERT: 5 28 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7993 (mtpt) REVERT: 6 36 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6749 (mt-10) REVERT: 7 36 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6786 (mp0) outliers start: 145 outliers final: 106 residues processed: 759 average time/residue: 0.6924 time to fit residues: 827.0781 Evaluate side-chains 814 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 690 time to evaluate : 5.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 28 LYS Chi-restraints excluded: chain e residue 53 MET Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain g residue 4 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 50 THR Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 88 VAL Chi-restraints excluded: chain o residue 88 VAL Chi-restraints excluded: chain p residue 4 VAL Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain r residue 36 GLU Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 4 VAL Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain v residue 4 VAL Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 28 LYS Chi-restraints excluded: chain w residue 36 GLU Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain y residue 28 LYS Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 71 CYS Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 4 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 28 LYS Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 36 GLU Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 36 GLU Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 2.9990 chunk 512 optimal weight: 3.9990 chunk 313 optimal weight: 0.3980 chunk 243 optimal weight: 0.8980 chunk 356 optimal weight: 0.4980 chunk 537 optimal weight: 0.5980 chunk 495 optimal weight: 3.9990 chunk 428 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 330 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 85 HIS ** y 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 51720 Z= 0.211 Angle : 0.495 6.233 69720 Z= 0.270 Chirality : 0.047 0.433 7500 Planarity : 0.003 0.039 8820 Dihedral : 4.259 31.669 6301 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.47 % Allowed : 21.51 % Favored : 76.02 % 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: 1.84 (0.10), residues: 5820 helix: 2.60 (0.08), residues: 3060 sheet: -0.16 (0.11), residues: 1440 loop : -0.43 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP l 24 HIS 0.003 0.001 HIS q 62 PHE 0.020 0.001 PHE x 96 TYR 0.010 0.001 TYR b 44 ARG 0.008 0.001 ARG X 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 688 time to evaluate : 5.782 Fit side-chains REVERT: D 36 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6466 (mt-10) REVERT: O 28 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7892 (mtpt) REVERT: R 9 ASP cc_start: 0.7871 (t0) cc_final: 0.7555 (t0) REVERT: V 36 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6558 (mt-10) REVERT: c 36 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6333 (mt-10) REVERT: f 36 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6793 (mt-10) REVERT: h 36 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6155 (mp0) REVERT: h 86 ARG cc_start: 0.7899 (ttt-90) cc_final: 0.7650 (ttt-90) REVERT: j 1 MET cc_start: 0.6761 (tmm) cc_final: 0.6445 (tmm) REVERT: p 36 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6541 (mt-10) REVERT: r 36 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6709 (mt-10) REVERT: s 36 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: u 36 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6430 (mt-10) REVERT: w 36 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6352 (mt-10) REVERT: y 28 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7824 (mtpt) REVERT: z 36 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: 1 36 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6320 (mp0) REVERT: 1 86 ARG cc_start: 0.7899 (ttt-90) cc_final: 0.7633 (ttt-90) REVERT: 4 36 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6559 (mt-10) REVERT: 5 28 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7971 (mtpt) REVERT: 6 36 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6769 (mt-10) REVERT: 7 36 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6831 (mp0) outliers start: 138 outliers final: 114 residues processed: 737 average time/residue: 0.7074 time to fit residues: 823.9286 Evaluate side-chains 817 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 685 time to evaluate : 5.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 28 LYS Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain O residue 28 LYS Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain W residue 71 CYS Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 28 LYS Chi-restraints excluded: chain e residue 53 MET Chi-restraints excluded: chain f residue 4 VAL Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 50 THR Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 88 VAL Chi-restraints excluded: chain o residue 88 VAL Chi-restraints excluded: chain p residue 4 VAL Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 36 GLU Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain u residue 36 GLU Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 28 LYS Chi-restraints excluded: chain w residue 36 GLU Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain y residue 28 LYS Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 71 CYS Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 4 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 28 LYS Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 5 residue 71 CYS Chi-restraints excluded: chain 6 residue 36 GLU Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 36 GLU Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 0.5980 chunk 456 optimal weight: 0.0980 chunk 131 optimal weight: 3.9990 chunk 395 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 429 optimal weight: 0.9980 chunk 179 optimal weight: 0.0170 chunk 440 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.171891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.151120 restraints weight = 56528.338| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.88 r_work: 0.3581 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 51720 Z= 0.165 Angle : 0.476 6.948 69720 Z= 0.258 Chirality : 0.046 0.452 7500 Planarity : 0.003 0.037 8820 Dihedral : 4.192 31.650 6301 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.46 % Allowed : 21.38 % Favored : 76.16 % 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: 1.99 (0.10), residues: 5820 helix: 2.72 (0.08), residues: 3060 sheet: -0.08 (0.11), residues: 1440 loop : -0.38 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 24 HIS 0.003 0.001 HIS 5 62 PHE 0.017 0.001 PHE x 96 TYR 0.010 0.000 TYR P 44 ARG 0.008 0.000 ARG X 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13390.87 seconds wall clock time: 240 minutes 35.72 seconds (14435.72 seconds total)