Starting phenix.real_space_refine on Tue Jan 14 19:11:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xb8_38214/01_2025/8xb8_38214.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xb8_38214/01_2025/8xb8_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/cci-nas-00/data/ceres_data/8xb8_38214/01_2025/8xb8_38214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xb8_38214/01_2025/8xb8_38214.map" model { file = "/net/cci-nas-00/data/ceres_data/8xb8_38214/01_2025/8xb8_38214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xb8_38214/01_2025/8xb8_38214.cif" } 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. Time to flip 2 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 20.28, per 1000 atoms: 0.40 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.23 Conformation dependent library (CDL) restraints added in 4.4 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: 4.25 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: 15.66 Time building geometry restraints manager: 10.88 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: 0.00 - 1.68: 68704 1.68 - 3.35: 868 3.35 - 5.03: 122 5.03 - 6.70: 24 6.70 - 8.38: 2 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 3.040 nonbonded pdb=" O LEU F 79 " pdb=" OG SER F 83 " model vdw 2.258 3.040 nonbonded pdb=" O LEU K 79 " pdb=" OG SER K 83 " model vdw 2.260 3.040 nonbonded pdb=" O LEU A 79 " pdb=" OG SER A 83 " model vdw 2.278 3.040 nonbonded pdb=" O HIS a 62 " pdb=" NE2 HIS a 66 " model vdw 2.281 3.120 ... (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 Time spend for trying shortcut: 0.01 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.470 Check model and map are aligned: 0.290 Set scattering table: 0.340 Process input model: 79.800 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.510 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:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.270 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 17 poor density : 656 time to evaluate : 4.220 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: 0.5520 time to fit residues: 583.2192 Evaluate side-chains 665 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 652 time to evaluate : 4.244 ------------------------------------------------------------------------------- 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: 2.9990 chunk 409 optimal weight: 0.0000 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 423 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 257 optimal weight: 0.0570 chunk 315 optimal weight: 1.9990 chunk 490 optimal weight: 3.9990 overall best weight: 1.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.167469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146674 restraints weight = 56896.013| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.89 r_work: 0.3514 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.0513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 51720 Z= 0.233 Angle : 0.496 7.388 69720 Z= 0.276 Chirality : 0.045 0.317 7500 Planarity : 0.003 0.028 8820 Dihedral : 4.551 41.095 6321 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.99 % Allowed : 17.24 % Favored : 79.77 % 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: 1.44 (0.10), residues: 5820 helix: 2.23 (0.08), residues: 3060 sheet: -0.27 (0.11), residues: 1440 loop : -0.54 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 24 HIS 0.003 0.001 HIS W 62 PHE 0.013 0.001 PHE V 96 TYR 0.007 0.001 TYR I 44 ARG 0.005 0.001 ARG T 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 849 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 682 time to evaluate : 4.196 Fit side-chains REVERT: A 67 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: F 58 THR cc_start: 0.8484 (m) cc_final: 0.8280 (p) REVERT: F 67 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: K 58 THR cc_start: 0.8510 (m) cc_final: 0.8287 (p) REVERT: K 67 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: L 9 ASP cc_start: 0.7828 (t0) cc_final: 0.7321 (t0) REVERT: S 9 ASP cc_start: 0.7992 (t0) cc_final: 0.7634 (t0) REVERT: W 90 LYS cc_start: 0.7969 (ptpt) cc_final: 0.7755 (ptpt) REVERT: f 36 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7060 (mt-10) REVERT: j 67 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: s 1 MET cc_start: 0.7282 (tpt) cc_final: 0.7081 (tpt) REVERT: s 9 ASP cc_start: 0.7927 (t0) cc_final: 0.7626 (t0) REVERT: s 36 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: z 36 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: 7 36 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6950 (mp0) outliers start: 167 outliers final: 116 residues processed: 725 average time/residue: 0.5476 time to fit residues: 632.0832 Evaluate side-chains 797 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 673 time to evaluate : 4.800 ------------------------------------------------------------------------------- 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 E residue 50 THR 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 H residue 88 VAL 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 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 O residue 50 THR 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 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 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 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 88 VAL Chi-restraints excluded: chain g residue 50 THR 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 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 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 36 GLU Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR 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 88 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 284 optimal weight: 5.9990 chunk 453 optimal weight: 0.8980 chunk 272 optimal weight: 2.9990 chunk 385 optimal weight: 0.8980 chunk 462 optimal weight: 1.9990 chunk 474 optimal weight: 2.9990 chunk 334 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 242 optimal weight: 0.5980 chunk 440 optimal weight: 1.9990 chunk 359 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.168848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148159 restraints weight = 57040.263| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.89 r_work: 0.3529 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 51720 Z= 0.206 Angle : 0.477 7.022 69720 Z= 0.264 Chirality : 0.044 0.341 7500 Planarity : 0.003 0.029 8820 Dihedral : 4.368 25.913 6303 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.51 % Allowed : 17.85 % Favored : 78.64 % 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: 2.28 (0.08), residues: 3060 sheet: -0.26 (0.11), residues: 1440 loop : -0.62 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 24 HIS 0.004 0.001 HIS w 62 PHE 0.012 0.001 PHE V 96 TYR 0.009 0.001 TYR P 44 ARG 0.005 0.000 ARG M 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 884 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 688 time to evaluate : 4.315 Fit side-chains REVERT: A 67 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: F 67 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: K 67 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: L 9 ASP cc_start: 0.7830 (t0) cc_final: 0.7325 (t0) REVERT: V 36 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6679 (mt-10) REVERT: W 1 MET cc_start: 0.7169 (tmm) cc_final: 0.6509 (tpt) REVERT: W 90 LYS cc_start: 0.7973 (ptpt) cc_final: 0.7764 (ptpt) REVERT: Z 9 ASP cc_start: 0.7870 (t0) cc_final: 0.7565 (t0) REVERT: c 36 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6530 (mt-10) REVERT: j 1 MET cc_start: 0.7006 (tmm) cc_final: 0.6533 (tmm) REVERT: j 67 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: p 36 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6740 (mt-10) REVERT: q 1 MET cc_start: 0.7196 (tmm) cc_final: 0.6597 (tpt) REVERT: s 9 ASP cc_start: 0.7901 (t0) cc_final: 0.7574 (t0) REVERT: s 36 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: t 9 ASP cc_start: 0.7851 (t0) cc_final: 0.7535 (t0) REVERT: w 36 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6495 (mt-10) REVERT: 4 36 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: 5 1 MET cc_start: 0.7174 (tmm) cc_final: 0.6590 (tpt) REVERT: 7 1 MET cc_start: 0.7503 (tpt) cc_final: 0.7262 (tpt) REVERT: 7 36 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6910 (mp0) outliers start: 196 outliers final: 111 residues processed: 755 average time/residue: 0.5397 time to fit residues: 652.0520 Evaluate side-chains 793 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 671 time to evaluate : 4.209 ------------------------------------------------------------------------------- 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 88 VAL Chi-restraints excluded: chain E residue 50 THR 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 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 1 MET 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 50 THR 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 50 THR Chi-restraints excluded: chain T residue 88 VAL 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 88 VAL Chi-restraints excluded: chain W residue 4 VAL 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 88 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 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 1 MET Chi-restraints excluded: chain g residue 50 THR 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 67 GLU Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 1 MET 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 n 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 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 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 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 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 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 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 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 145 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 492 optimal weight: 2.9990 chunk 533 optimal weight: 3.9990 chunk 307 optimal weight: 0.6980 chunk 184 optimal weight: 0.7980 chunk 487 optimal weight: 0.9980 chunk 409 optimal weight: 5.9990 chunk 376 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 531 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.168196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.147458 restraints weight = 57086.121| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.90 r_work: 0.3521 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 51720 Z= 0.216 Angle : 0.482 6.632 69720 Z= 0.267 Chirality : 0.045 0.360 7500 Planarity : 0.003 0.028 8820 Dihedral : 4.374 28.374 6303 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.33 % Allowed : 18.66 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.10), residues: 5820 helix: 2.26 (0.08), residues: 3060 sheet: -0.28 (0.11), residues: 1440 loop : -0.66 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP u 24 HIS 0.004 0.001 HIS 5 62 PHE 0.016 0.001 PHE r 96 TYR 0.009 0.001 TYR P 44 ARG 0.005 0.000 ARG T 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 875 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 689 time to evaluate : 4.217 Fit side-chains REVERT: B 9 ASP cc_start: 0.7908 (t0) cc_final: 0.7415 (t0) REVERT: G 9 ASP cc_start: 0.7960 (t0) cc_final: 0.7490 (t0) REVERT: H 9 ASP cc_start: 0.8239 (t0) cc_final: 0.8013 (t0) REVERT: K 9 ASP cc_start: 0.7801 (t0) cc_final: 0.7575 (t0) REVERT: L 9 ASP cc_start: 0.7843 (t0) cc_final: 0.7334 (t0) REVERT: R 9 ASP cc_start: 0.8153 (t0) cc_final: 0.7923 (t0) REVERT: S 9 ASP cc_start: 0.8024 (t0) cc_final: 0.7621 (t0) REVERT: W 90 LYS cc_start: 0.8024 (ptpt) cc_final: 0.7819 (ptpt) REVERT: Z 1 MET cc_start: 0.7287 (tpt) cc_final: 0.7041 (tpt) REVERT: Z 9 ASP cc_start: 0.7939 (t0) cc_final: 0.7614 (t0) REVERT: c 12 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: c 36 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6533 (mt-10) REVERT: f 36 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7045 (mt-10) REVERT: h 36 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6306 (mp0) REVERT: s 9 ASP cc_start: 0.7925 (t0) cc_final: 0.7562 (t0) REVERT: s 36 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: t 1 MET cc_start: 0.7327 (tpt) cc_final: 0.7119 (tpt) REVERT: t 9 ASP cc_start: 0.7920 (t0) cc_final: 0.7591 (t0) REVERT: u 9 ASP cc_start: 0.8198 (t0) cc_final: 0.7953 (t0) REVERT: w 12 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: w 36 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6495 (mt-10) REVERT: z 36 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7067 (mt-10) REVERT: 1 36 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: 5 1 MET cc_start: 0.7225 (tmm) cc_final: 0.6507 (tpt) REVERT: 5 90 LYS cc_start: 0.7915 (ptpt) cc_final: 0.7637 (ptpt) REVERT: 7 9 ASP cc_start: 0.7921 (t0) cc_final: 0.7595 (t0) REVERT: 7 36 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6918 (mp0) outliers start: 186 outliers final: 130 residues processed: 743 average time/residue: 0.5403 time to fit residues: 640.8664 Evaluate side-chains 814 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 674 time to evaluate : 4.201 ------------------------------------------------------------------------------- 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 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 1 MET 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 1 MET 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 50 THR 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 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 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 50 THR Chi-restraints excluded: chain b residue 53 MET Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 12 GLU 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 1 MET 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 1 MET 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 n residue 50 THR 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 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 50 THR 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 12 GLU 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 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 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 327 optimal weight: 0.0060 chunk 14 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 340 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 443 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.164213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143213 restraints weight = 57608.399| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.92 r_work: 0.3482 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 51720 Z= 0.286 Angle : 0.517 6.187 69720 Z= 0.286 Chirality : 0.047 0.415 7500 Planarity : 0.003 0.031 8820 Dihedral : 4.480 29.473 6303 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.48 % Allowed : 19.21 % Favored : 77.31 % 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: 1.22 (0.10), residues: 5820 helix: 2.07 (0.09), residues: 3060 sheet: -0.37 (0.11), residues: 1440 loop : -0.70 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP l 24 HIS 0.005 0.001 HIS W 62 PHE 0.017 0.002 PHE K 96 TYR 0.010 0.001 TYR P 44 ARG 0.006 0.001 ARG R 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 913 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 719 time to evaluate : 4.265 Fit side-chains REVERT: C 9 ASP cc_start: 0.8274 (t0) cc_final: 0.8035 (t0) REVERT: H 9 ASP cc_start: 0.8283 (t0) cc_final: 0.8065 (t0) REVERT: R 9 ASP cc_start: 0.8209 (t0) cc_final: 0.7930 (t0) REVERT: V 36 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: X 12 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: Z 9 ASP cc_start: 0.7987 (t0) cc_final: 0.7743 (t0) REVERT: c 12 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: c 36 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6550 (mt-10) REVERT: f 36 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: g 9 ASP cc_start: 0.8070 (t0) cc_final: 0.7753 (t0) REVERT: h 36 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: l 9 ASP cc_start: 0.8261 (t0) cc_final: 0.8038 (t0) REVERT: p 36 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6741 (mt-10) REVERT: q 90 LYS cc_start: 0.8016 (ptpt) cc_final: 0.7783 (ptpt) REVERT: r 12 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7333 (tp30) REVERT: s 36 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: t 9 ASP cc_start: 0.7987 (t0) cc_final: 0.7700 (t0) REVERT: w 12 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: w 36 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6518 (mt-10) REVERT: z 9 ASP cc_start: 0.8085 (t0) cc_final: 0.7820 (t0) REVERT: z 36 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7056 (mt-10) REVERT: 0 9 ASP cc_start: 0.8089 (t0) cc_final: 0.7758 (t0) REVERT: 1 36 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6307 (mp0) REVERT: 4 36 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6689 (mt-10) REVERT: 5 90 LYS cc_start: 0.7994 (ptpt) cc_final: 0.7746 (ptpt) REVERT: 6 12 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7355 (tp30) REVERT: 7 36 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6350 (mp0) outliers start: 194 outliers final: 144 residues processed: 777 average time/residue: 0.5418 time to fit residues: 669.0104 Evaluate side-chains 870 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 710 time to evaluate : 5.634 ------------------------------------------------------------------------------- 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 53 MET 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 1 MET 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 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 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 50 THR 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 O residue 50 THR 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 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 12 GLU 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 12 GLU 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 1 MET 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 50 THR 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 n residue 50 THR 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 12 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 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 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 12 GLU 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 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 1 MET 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 52 LYS 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 12 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 94 optimal weight: 0.0670 chunk 498 optimal weight: 0.9990 chunk 322 optimal weight: 0.8980 chunk 339 optimal weight: 4.9990 chunk 243 optimal weight: 0.9980 chunk 495 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 420 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 490 optimal weight: 4.9990 chunk 430 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.168752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.148133 restraints weight = 57013.107| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.90 r_work: 0.3531 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.0884 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= 0.191 Angle : 0.479 6.690 69720 Z= 0.264 Chirality : 0.045 0.386 7500 Planarity : 0.003 0.029 8820 Dihedral : 4.360 30.160 6303 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.23 % Allowed : 19.66 % Favored : 77.11 % 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: 1.41 (0.10), residues: 5820 helix: 2.28 (0.08), residues: 3060 sheet: -0.30 (0.11), residues: 1440 loop : -0.74 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 24 HIS 0.004 0.001 HIS y 62 PHE 0.014 0.001 PHE K 96 TYR 0.010 0.001 TYR P 44 ARG 0.007 0.000 ARG F 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 883 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 703 time to evaluate : 4.354 Fit side-chains REVERT: D 36 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6627 (mt-10) REVERT: D 53 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6865 (ptm) REVERT: H 9 ASP cc_start: 0.8248 (t0) cc_final: 0.8024 (t0) REVERT: I 53 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6897 (ptm) REVERT: N 53 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6940 (ptm) REVERT: R 9 ASP cc_start: 0.8189 (t0) cc_final: 0.7933 (t0) REVERT: S 13 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.6917 (mtpp) REVERT: V 36 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6694 (mt-10) REVERT: W 1 MET cc_start: 0.7105 (tmm) cc_final: 0.6587 (tpt) REVERT: X 12 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7376 (tp30) REVERT: Z 9 ASP cc_start: 0.7953 (t0) cc_final: 0.7656 (t0) REVERT: c 12 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: f 36 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7035 (mt-10) REVERT: g 9 ASP cc_start: 0.8056 (t0) cc_final: 0.7703 (t0) REVERT: h 36 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6383 (mp0) REVERT: j 1 MET cc_start: 0.6884 (tmm) cc_final: 0.6508 (tmm) REVERT: l 9 ASP cc_start: 0.8231 (t0) cc_final: 0.8000 (t0) REVERT: m 36 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6649 (mt-10) REVERT: m 53 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6890 (ptm) REVERT: p 36 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6768 (mt-10) REVERT: q 1 MET cc_start: 0.7157 (tmm) cc_final: 0.6592 (tpt) REVERT: r 12 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: s 36 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: t 9 ASP cc_start: 0.7937 (t0) cc_final: 0.7632 (t0) REVERT: w 12 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: w 36 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6490 (mt-10) REVERT: z 36 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: 0 9 ASP cc_start: 0.8089 (t0) cc_final: 0.7769 (t0) REVERT: 1 36 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: 4 36 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6713 (mt-10) REVERT: 5 1 MET cc_start: 0.7129 (tmm) cc_final: 0.6560 (tpt) REVERT: 6 12 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7402 (tp30) REVERT: 7 36 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6945 (mp0) outliers start: 180 outliers final: 115 residues processed: 758 average time/residue: 0.5392 time to fit residues: 651.9209 Evaluate side-chains 801 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 664 time to evaluate : 4.195 ------------------------------------------------------------------------------- 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 4 VAL 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 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 88 VAL 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 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 53 MET 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 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 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 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 50 THR Chi-restraints excluded: chain X residue 12 GLU 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 53 MET Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 12 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 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 1 MET 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 1 MET 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 n residue 50 THR 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 r residue 1 MET Chi-restraints excluded: chain r residue 12 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 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 12 GLU 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 88 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 53 MET 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 88 VAL Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 12 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 414 optimal weight: 0.6980 chunk 334 optimal weight: 0.7980 chunk 537 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 384 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 411 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.168602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147922 restraints weight = 57097.606| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.89 r_work: 0.3529 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.0920 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= 0.203 Angle : 0.486 6.397 69720 Z= 0.269 Chirality : 0.046 0.400 7500 Planarity : 0.003 0.032 8820 Dihedral : 4.362 29.673 6303 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.39 % Allowed : 19.96 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.10), residues: 5820 helix: 2.31 (0.08), residues: 3060 sheet: -0.33 (0.11), residues: 1440 loop : -0.74 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 24 HIS 0.004 0.001 HIS O 62 PHE 0.015 0.001 PHE f 96 TYR 0.010 0.001 TYR P 44 ARG 0.007 0.000 ARG T 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 873 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 684 time to evaluate : 4.264 Fit side-chains REVERT: C 9 ASP cc_start: 0.8247 (t0) cc_final: 0.8026 (t0) REVERT: H 9 ASP cc_start: 0.8273 (t0) cc_final: 0.8067 (t0) REVERT: I 36 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6614 (mt-10) REVERT: R 9 ASP cc_start: 0.8192 (t0) cc_final: 0.7936 (t0) REVERT: V 36 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6679 (mt-10) REVERT: W 1 MET cc_start: 0.7132 (tmm) cc_final: 0.6642 (tpt) REVERT: Y 36 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: Z 9 ASP cc_start: 0.7992 (t0) cc_final: 0.7723 (t0) REVERT: c 12 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: c 36 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6528 (mt-10) REVERT: g 9 ASP cc_start: 0.8033 (t0) cc_final: 0.7671 (t0) REVERT: h 36 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6311 (mp0) REVERT: j 1 MET cc_start: 0.6934 (tmm) cc_final: 0.6510 (tmm) REVERT: l 9 ASP cc_start: 0.8248 (t0) cc_final: 0.8036 (t0) REVERT: p 36 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: q 1 MET cc_start: 0.7124 (tmm) cc_final: 0.6661 (tpt) REVERT: s 36 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: w 12 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: w 36 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6491 (mt-10) REVERT: z 36 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7083 (mt-10) REVERT: 0 9 ASP cc_start: 0.8076 (t0) cc_final: 0.7693 (t0) REVERT: 1 36 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: 1 61 PHE cc_start: 0.8271 (m-80) cc_final: 0.8057 (m-80) REVERT: 4 36 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6687 (mt-10) REVERT: 5 1 MET cc_start: 0.7088 (tmm) cc_final: 0.6633 (tpt) REVERT: 7 1 MET cc_start: 0.7289 (tpt) cc_final: 0.6951 (tpt) REVERT: 7 36 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6971 (mp0) outliers start: 189 outliers final: 138 residues processed: 752 average time/residue: 0.5755 time to fit residues: 697.3556 Evaluate side-chains 822 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 670 time to evaluate : 4.229 ------------------------------------------------------------------------------- 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 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 1 MET Chi-restraints excluded: chain H residue 28 LYS 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 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 O residue 50 THR 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 50 THR Chi-restraints excluded: chain Q residue 71 CYS Chi-restraints excluded: chain R residue 1 MET 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 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 W residue 71 CYS 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 36 GLU 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 53 MET Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 12 GLU 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 50 THR Chi-restraints excluded: chain f residue 71 CYS Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain g residue 1 MET 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 1 MET 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 n residue 50 THR 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 q residue 71 CYS 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 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 12 GLU 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 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 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 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 5 residue 71 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 257 optimal weight: 0.7980 chunk 221 optimal weight: 0.8980 chunk 307 optimal weight: 2.9990 chunk 366 optimal weight: 0.7980 chunk 219 optimal weight: 0.4980 chunk 186 optimal weight: 1.9990 chunk 349 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 492 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.169005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148251 restraints weight = 57257.196| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.90 r_work: 0.3531 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.0983 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= 0.200 Angle : 0.492 6.462 69720 Z= 0.270 Chirality : 0.046 0.419 7500 Planarity : 0.003 0.034 8820 Dihedral : 4.354 29.415 6303 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.17 % Allowed : 20.54 % 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: 1.47 (0.10), residues: 5820 helix: 2.35 (0.08), residues: 3060 sheet: -0.33 (0.11), residues: 1440 loop : -0.72 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP u 24 HIS 0.004 0.001 HIS y 62 PHE 0.016 0.001 PHE f 96 TYR 0.011 0.001 TYR P 44 ARG 0.009 0.000 ARG z 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 863 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 686 time to evaluate : 4.299 Fit side-chains REVERT: C 9 ASP cc_start: 0.8249 (t0) cc_final: 0.8018 (t0) REVERT: H 9 ASP cc_start: 0.8272 (t0) cc_final: 0.8065 (t0) REVERT: R 9 ASP cc_start: 0.8195 (t0) cc_final: 0.7928 (t0) REVERT: V 36 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6709 (mt-10) REVERT: W 1 MET cc_start: 0.7138 (tmm) cc_final: 0.6633 (tpt) REVERT: Y 42 CYS cc_start: 0.7935 (p) cc_final: 0.7682 (p) REVERT: Z 1 MET cc_start: 0.7369 (tpt) cc_final: 0.6986 (tpt) REVERT: Z 9 ASP cc_start: 0.7995 (t0) cc_final: 0.7712 (t0) REVERT: c 12 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: c 36 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6495 (mt-10) REVERT: g 9 ASP cc_start: 0.8040 (t0) cc_final: 0.7629 (t0) REVERT: h 36 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6407 (mp0) REVERT: j 1 MET cc_start: 0.6949 (tmm) cc_final: 0.6486 (tmm) REVERT: k 1 MET cc_start: 0.7361 (tpt) cc_final: 0.7102 (tpt) REVERT: l 9 ASP cc_start: 0.8245 (t0) cc_final: 0.8029 (t0) REVERT: p 36 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6778 (mt-10) REVERT: q 1 MET cc_start: 0.7130 (tmm) cc_final: 0.6645 (tpt) REVERT: s 36 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: s 42 CYS cc_start: 0.7970 (p) cc_final: 0.7715 (p) REVERT: t 1 MET cc_start: 0.7328 (tpt) cc_final: 0.6931 (tpt) REVERT: t 98 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8432 (mttt) REVERT: w 12 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: w 36 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6438 (mt-10) REVERT: z 36 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7072 (mt-10) REVERT: 0 9 ASP cc_start: 0.8063 (t0) cc_final: 0.7671 (t0) REVERT: 1 36 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: 1 61 PHE cc_start: 0.8267 (m-80) cc_final: 0.8053 (m-80) REVERT: 4 36 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6700 (mt-10) REVERT: 5 1 MET cc_start: 0.7089 (tmm) cc_final: 0.6613 (tpt) REVERT: 7 1 MET cc_start: 0.7255 (tpt) cc_final: 0.6979 (tpt) REVERT: 7 36 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6999 (mp0) outliers start: 177 outliers final: 139 residues processed: 746 average time/residue: 0.5486 time to fit residues: 649.7681 Evaluate side-chains 827 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 676 time to evaluate : 4.294 ------------------------------------------------------------------------------- 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 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 28 LYS 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 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 O residue 50 THR 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 Q residue 71 CYS Chi-restraints excluded: chain R residue 1 MET 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 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 W residue 71 CYS 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 53 MET Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 12 GLU 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 50 THR Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain g residue 1 MET 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 1 MET 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 n residue 50 THR 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 71 CYS 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 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 12 GLU 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 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 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 71 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 288 optimal weight: 1.9990 chunk 371 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 500 optimal weight: 4.9990 chunk 346 optimal weight: 3.9990 chunk 465 optimal weight: 0.9980 chunk 468 optimal weight: 2.9990 chunk 509 optimal weight: 4.9990 chunk 521 optimal weight: 1.9990 chunk 339 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.164833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.143782 restraints weight = 57588.034| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.92 r_work: 0.3486 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 51720 Z= 0.277 Angle : 0.529 6.325 69720 Z= 0.290 Chirality : 0.048 0.435 7500 Planarity : 0.003 0.039 8820 Dihedral : 4.479 29.294 6303 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.21 % Allowed : 20.59 % Favored : 76.20 % 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: 1.19 (0.10), residues: 5820 helix: 2.12 (0.08), residues: 3060 sheet: -0.49 (0.11), residues: 1440 loop : -0.77 (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 q 62 PHE 0.016 0.002 PHE f 96 TYR 0.011 0.001 TYR P 44 ARG 0.008 0.001 ARG r 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 896 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 717 time to evaluate : 5.339 Fit side-chains REVERT: I 36 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6565 (mt-10) REVERT: N 36 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6622 (mt-10) REVERT: V 36 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6679 (mt-10) REVERT: Y 36 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: Y 42 CYS cc_start: 0.7937 (p) cc_final: 0.7694 (p) REVERT: Z 1 MET cc_start: 0.7392 (tpt) cc_final: 0.7043 (tpt) REVERT: c 12 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: c 36 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6532 (mt-10) REVERT: h 36 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6254 (mp0) REVERT: k 1 MET cc_start: 0.7433 (tpt) cc_final: 0.7207 (tpt) REVERT: p 36 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6748 (mt-10) REVERT: r 12 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7270 (tp30) REVERT: s 36 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: s 42 CYS cc_start: 0.7991 (p) cc_final: 0.7790 (p) REVERT: t 1 MET cc_start: 0.7339 (tpt) cc_final: 0.7000 (tpt) REVERT: t 98 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8459 (mttt) REVERT: w 12 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: w 36 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6502 (mt-10) REVERT: z 36 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7067 (mt-10) REVERT: 1 36 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: 4 36 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6634 (mt-10) REVERT: 6 36 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: 7 1 MET cc_start: 0.7316 (tpt) cc_final: 0.7100 (tpt) REVERT: 7 36 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7056 (mp0) outliers start: 179 outliers final: 144 residues processed: 775 average time/residue: 0.5528 time to fit residues: 677.1897 Evaluate side-chains 862 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 701 time to evaluate : 4.274 ------------------------------------------------------------------------------- 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 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 1 MET 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 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 O residue 50 THR 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 Q residue 71 CYS Chi-restraints excluded: chain R residue 1 MET 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 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 W residue 53 MET Chi-restraints excluded: chain W residue 71 CYS 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 36 GLU 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 53 MET Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 12 GLU 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 50 THR Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain g residue 1 MET 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 1 MET 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 n residue 50 THR 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 q residue 71 CYS Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 12 GLU Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 28 LYS 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 12 GLU 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 71 CYS Chi-restraints excluded: chain z residue 82 ILE 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 5 residue 71 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 128 optimal weight: 0.6980 chunk 283 optimal weight: 1.9990 chunk 524 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 516 optimal weight: 0.0000 chunk 65 optimal weight: 0.7980 chunk 533 optimal weight: 1.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.170646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149839 restraints weight = 57447.549| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.91 r_work: 0.3551 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1132 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= 0.179 Angle : 0.490 6.668 69720 Z= 0.268 Chirality : 0.045 0.436 7500 Planarity : 0.003 0.037 8820 Dihedral : 4.367 30.205 6303 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.94 % Allowed : 20.93 % Favored : 76.13 % 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: 1.49 (0.10), residues: 5820 helix: 2.40 (0.08), residues: 3060 sheet: -0.36 (0.11), residues: 1440 loop : -0.76 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 24 HIS 0.004 0.001 HIS W 62 PHE 0.013 0.001 PHE f 96 TYR 0.011 0.001 TYR P 44 ARG 0.009 0.000 ARG 6 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 871 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 707 time to evaluate : 4.255 Fit side-chains REVERT: I 36 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6631 (mt-10) REVERT: N 36 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6658 (mt-10) REVERT: R 41 ARG cc_start: 0.8727 (ttm110) cc_final: 0.8514 (ttm110) REVERT: V 36 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6778 (mt-10) REVERT: W 1 MET cc_start: 0.7122 (tmm) cc_final: 0.6620 (tpt) REVERT: X 86 ARG cc_start: 0.8231 (ttt-90) cc_final: 0.7995 (ttt-90) REVERT: Y 36 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: Y 42 CYS cc_start: 0.7783 (p) cc_final: 0.7559 (p) REVERT: Z 1 MET cc_start: 0.7271 (tpt) cc_final: 0.6978 (tpt) REVERT: c 12 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: c 36 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6511 (mt-10) REVERT: h 36 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6391 (mp0) REVERT: j 1 MET cc_start: 0.6772 (tmm) cc_final: 0.6448 (tmm) REVERT: k 1 MET cc_start: 0.7329 (tpt) cc_final: 0.7125 (tpt) REVERT: p 36 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6872 (mt-10) REVERT: q 1 MET cc_start: 0.7168 (tmm) cc_final: 0.6597 (tpt) REVERT: r 86 ARG cc_start: 0.8268 (ttt-90) cc_final: 0.8020 (ttt-90) REVERT: s 36 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: s 42 CYS cc_start: 0.7981 (p) cc_final: 0.7767 (p) REVERT: t 1 MET cc_start: 0.7240 (tpt) cc_final: 0.6921 (tpt) REVERT: u 61 PHE cc_start: 0.8286 (m-80) cc_final: 0.8060 (m-80) REVERT: w 12 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: w 28 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8236 (mtpt) REVERT: w 36 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6459 (mt-10) REVERT: z 36 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7063 (mt-10) REVERT: 1 36 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6419 (mp0) REVERT: 4 36 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6790 (mt-10) REVERT: 5 1 MET cc_start: 0.7071 (tmm) cc_final: 0.6675 (tpt) REVERT: 6 36 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7029 (mt-10) REVERT: 7 1 MET cc_start: 0.7235 (tpt) cc_final: 0.7014 (tpt) REVERT: 7 36 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7088 (mp0) outliers start: 164 outliers final: 140 residues processed: 762 average time/residue: 0.5899 time to fit residues: 711.6948 Evaluate side-chains 847 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 690 time to evaluate : 4.221 ------------------------------------------------------------------------------- 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 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 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 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 O residue 50 THR Chi-restraints excluded: chain O residue 71 CYS 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 Q residue 71 CYS Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 82 ILE 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 W residue 53 MET 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 36 GLU 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 12 GLU 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 c residue 71 CYS 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 50 THR Chi-restraints excluded: chain f residue 71 CYS Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain g residue 1 MET 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 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 n residue 50 THR Chi-restraints excluded: chain n residue 71 CYS 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 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 12 GLU 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 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 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 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 5 residue 71 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 347 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 238 optimal weight: 0.9990 chunk 284 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 489 optimal weight: 0.6980 chunk 138 optimal weight: 0.4980 chunk 244 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 517 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.169339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.148356 restraints weight = 56919.630| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.90 r_work: 0.3545 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1188 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= 0.193 Angle : 0.498 6.363 69720 Z= 0.272 Chirality : 0.046 0.435 7500 Planarity : 0.003 0.039 8820 Dihedral : 4.374 29.693 6303 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.99 % Allowed : 21.16 % Favored : 75.84 % 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: 1.51 (0.10), residues: 5820 helix: 2.45 (0.08), residues: 3060 sheet: -0.41 (0.11), residues: 1440 loop : -0.75 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 24 HIS 0.005 0.001 HIS 5 62 PHE 0.017 0.001 PHE d 96 TYR 0.009 0.001 TYR b 44 ARG 0.009 0.001 ARG X 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18439.91 seconds wall clock time: 319 minutes 13.22 seconds (19153.22 seconds total)