Starting phenix.real_space_refine on Mon Nov 18 18:21:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/11_2024/8xb8_38214.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/11_2024/8xb8_38214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/11_2024/8xb8_38214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/11_2024/8xb8_38214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/11_2024/8xb8_38214.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/11_2024/8xb8_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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 25.37, per 1000 atoms: 0.50 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: 10.96 Conformation dependent library (CDL) restraints added in 5.9 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: 5.32 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: 22.09 Time building geometry restraints manager: 12.88 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: 0.00 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: 3.850 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: 1.900 Check model and map are aligned: 0.370 Set scattering table: 0.450 Process input model: 100.610 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.610 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.250 ------------------------------------------------------------------------------- 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 : 5.390 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: 0.6716 time to fit residues: 709.9422 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 : 5.672 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 5.175 Fit side-chains REVERT: A 67 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: F 67 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: K 67 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: L 9 ASP cc_start: 0.7544 (t0) cc_final: 0.7093 (t0) REVERT: S 9 ASP cc_start: 0.7737 (t0) cc_final: 0.7351 (t0) REVERT: b 28 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8055 (mtpp) REVERT: f 36 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6754 (mt-10) REVERT: j 67 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: s 1 MET cc_start: 0.7224 (tpt) cc_final: 0.7018 (tpt) REVERT: s 9 ASP cc_start: 0.7648 (t0) cc_final: 0.7371 (t0) REVERT: s 36 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: z 36 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6762 (mt-10) REVERT: 7 36 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6772 (mp0) outliers start: 167 outliers final: 116 residues processed: 725 average time/residue: 0.6783 time to fit residues: 782.8455 Evaluate side-chains 798 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 673 time to evaluate : 5.326 ------------------------------------------------------------------------------- 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 28 LYS Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 53 MET Chi-restraints excluded: chain f residue 4 VAL Chi-restraints excluded: chain f residue 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 272 optimal weight: 2.9990 chunk 152 optimal weight: 0.2980 chunk 408 optimal weight: 0.1980 chunk 333 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 491 optimal weight: 0.7980 chunk 530 optimal weight: 2.9990 chunk 437 optimal weight: 0.0170 chunk 487 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 394 optimal weight: 0.9990 overall best weight: 0.4620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 51720 Z= 0.163 Angle : 0.457 7.414 69720 Z= 0.252 Chirality : 0.043 0.349 7500 Planarity : 0.003 0.031 8820 Dihedral : 4.274 26.003 6303 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.17 % Allowed : 18.06 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.10), residues: 5820 helix: 2.46 (0.08), residues: 3060 sheet: -0.13 (0.11), residues: 1440 loop : -0.57 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 24 HIS 0.004 0.001 HIS y 62 PHE 0.011 0.001 PHE V 96 TYR 0.009 0.000 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 891 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 714 time to evaluate : 5.631 Fit side-chains REVERT: A 67 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: F 67 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: K 67 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: L 9 ASP cc_start: 0.7459 (t0) cc_final: 0.7057 (t0) REVERT: V 36 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6459 (mt-10) REVERT: W 1 MET cc_start: 0.7046 (tmm) cc_final: 0.6531 (tpt) REVERT: Z 9 ASP cc_start: 0.7560 (t0) cc_final: 0.7285 (t0) REVERT: b 28 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7998 (mtpp) REVERT: p 36 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6432 (mt-10) REVERT: q 1 MET cc_start: 0.7043 (tmm) cc_final: 0.6549 (tpt) REVERT: s 36 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: t 9 ASP cc_start: 0.7540 (t0) cc_final: 0.7262 (t0) REVERT: v 28 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8059 (mtpp) REVERT: w 36 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6292 (mt-10) REVERT: 4 36 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6445 (mt-10) REVERT: 5 1 MET cc_start: 0.7012 (tmm) cc_final: 0.6540 (tpt) REVERT: 7 1 MET cc_start: 0.7341 (tpt) cc_final: 0.7130 (tpt) REVERT: 7 36 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6683 (mp0) outliers start: 177 outliers final: 82 residues processed: 782 average time/residue: 0.6810 time to fit residues: 856.5009 Evaluate side-chains 761 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 668 time to evaluate : 5.454 ------------------------------------------------------------------------------- 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 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 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 50 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 28 LYS Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 53 MET Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain f residue 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 88 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 50 THR Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 88 VAL Chi-restraints excluded: chain 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 r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain v residue 28 LYS Chi-restraints excluded: chain v residue 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 88 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 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 88 VAL Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 36 GLU Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 1.9990 chunk 369 optimal weight: 0.8980 chunk 254 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 chunk 329 optimal weight: 5.9990 chunk 493 optimal weight: 0.7980 chunk 521 optimal weight: 0.7980 chunk 257 optimal weight: 2.9990 chunk 467 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 51720 Z= 0.206 Angle : 0.481 6.629 69720 Z= 0.265 Chirality : 0.045 0.365 7500 Planarity : 0.003 0.026 8820 Dihedral : 4.311 27.947 6303 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.05 % Allowed : 18.85 % Favored : 78.10 % 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: 1.64 (0.10), residues: 5820 helix: 2.41 (0.08), residues: 3060 sheet: -0.16 (0.11), residues: 1440 loop : -0.58 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 24 HIS 0.004 0.001 HIS W 62 PHE 0.016 0.001 PHE r 96 TYR 0.009 0.001 TYR P 44 ARG 0.005 0.000 ARG R 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 850 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 680 time to evaluate : 5.613 Fit side-chains REVERT: B 9 ASP cc_start: 0.7705 (t0) cc_final: 0.7240 (t0) REVERT: G 9 ASP cc_start: 0.7625 (t0) cc_final: 0.7165 (t0) REVERT: H 9 ASP cc_start: 0.8003 (t0) cc_final: 0.7766 (t0) REVERT: L 9 ASP cc_start: 0.7529 (t0) cc_final: 0.7076 (t0) REVERT: R 9 ASP cc_start: 0.7921 (t0) cc_final: 0.7699 (t0) REVERT: S 9 ASP cc_start: 0.7687 (t0) cc_final: 0.7251 (t0) REVERT: S 13 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6965 (mtpp) REVERT: W 1 MET cc_start: 0.7224 (tmm) cc_final: 0.6515 (tpt) REVERT: Z 1 MET cc_start: 0.7323 (tpt) cc_final: 0.7055 (tpt) REVERT: b 28 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.8007 (mtpp) REVERT: c 12 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: c 36 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6294 (mt-10) REVERT: f 36 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6725 (mt-10) REVERT: h 36 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6166 (mp0) REVERT: l 9 ASP cc_start: 0.7993 (t0) cc_final: 0.7761 (t0) REVERT: q 1 MET cc_start: 0.7117 (tmm) cc_final: 0.6571 (tpt) REVERT: s 9 ASP cc_start: 0.7624 (t0) cc_final: 0.7270 (t0) REVERT: s 36 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: t 1 MET cc_start: 0.7303 (tpt) cc_final: 0.7034 (tpt) REVERT: v 28 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8050 (mtpp) REVERT: w 36 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6298 (mt-10) REVERT: z 36 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6726 (mt-10) REVERT: 1 36 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6159 (mp0) REVERT: 5 1 MET cc_start: 0.7093 (tmm) cc_final: 0.6562 (tpt) REVERT: 7 9 ASP cc_start: 0.7654 (t0) cc_final: 0.7333 (t0) REVERT: 7 36 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6753 (mp0) outliers start: 170 outliers final: 123 residues processed: 730 average time/residue: 0.6681 time to fit residues: 781.3117 Evaluate side-chains 808 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 673 time to evaluate : 5.615 ------------------------------------------------------------------------------- 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 28 LYS 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 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 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 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 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 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 28 LYS 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 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 50 THR Chi-restraints excluded: chain l residue 28 LYS Chi-restraints excluded: chain l residue 50 THR Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 88 VAL Chi-restraints excluded: chain 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 28 LYS Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 28 LYS Chi-restraints excluded: chain w residue 36 GLU Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 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 434 optimal weight: 0.8980 chunk 296 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 0.1980 chunk 445 optimal weight: 0.0270 chunk 360 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 266 optimal weight: 5.9990 chunk 468 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 51720 Z= 0.205 Angle : 0.479 6.567 69720 Z= 0.264 Chirality : 0.045 0.398 7500 Planarity : 0.003 0.026 8820 Dihedral : 4.296 29.418 6303 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.46 % Allowed : 18.42 % Favored : 78.12 % 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: 1.60 (0.10), residues: 5820 helix: 2.39 (0.08), residues: 3060 sheet: -0.18 (0.11), residues: 1440 loop : -0.61 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP l 24 HIS 0.004 0.001 HIS q 62 PHE 0.013 0.001 PHE K 96 TYR 0.009 0.001 TYR P 44 ARG 0.006 0.000 ARG T 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 874 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 681 time to evaluate : 5.700 Fit side-chains REVERT: B 9 ASP cc_start: 0.7610 (t0) cc_final: 0.7117 (t0) REVERT: C 9 ASP cc_start: 0.8000 (t0) cc_final: 0.7749 (t0) REVERT: G 9 ASP cc_start: 0.7526 (t0) cc_final: 0.7037 (t0) REVERT: H 9 ASP cc_start: 0.8024 (t0) cc_final: 0.7798 (t0) REVERT: K 9 ASP cc_start: 0.7509 (t0) cc_final: 0.7286 (t0) REVERT: L 9 ASP cc_start: 0.7506 (t0) cc_final: 0.7095 (t0) REVERT: R 9 ASP cc_start: 0.7954 (t0) cc_final: 0.7692 (t0) REVERT: S 9 ASP cc_start: 0.7554 (t0) cc_final: 0.7080 (t0) REVERT: V 36 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6479 (mt-10) REVERT: W 1 MET cc_start: 0.7185 (tmm) cc_final: 0.6562 (tpt) REVERT: X 12 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7122 (tp30) REVERT: b 28 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7990 (mtpp) REVERT: c 12 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: c 36 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6296 (mt-10) REVERT: f 36 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6768 (mt-10) REVERT: g 9 ASP cc_start: 0.7747 (t0) cc_final: 0.7460 (t0) REVERT: h 36 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6106 (mp0) REVERT: l 9 ASP cc_start: 0.8013 (t0) cc_final: 0.7780 (t0) REVERT: p 36 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6468 (mt-10) REVERT: q 1 MET cc_start: 0.7241 (tmm) cc_final: 0.6552 (tpt) REVERT: r 12 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7111 (tp30) REVERT: s 9 ASP cc_start: 0.7644 (t0) cc_final: 0.7306 (t0) REVERT: s 36 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: u 9 ASP cc_start: 0.7943 (t0) cc_final: 0.7724 (t0) REVERT: v 28 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8052 (mtpp) REVERT: w 36 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6302 (mt-10) REVERT: z 36 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6789 (mt-10) REVERT: 0 9 ASP cc_start: 0.7754 (t0) cc_final: 0.7472 (t0) REVERT: 1 36 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6108 (mp0) REVERT: 4 36 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6486 (mt-10) REVERT: 5 1 MET cc_start: 0.7216 (tmm) cc_final: 0.6544 (tpt) REVERT: 6 12 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7141 (tp30) REVERT: 6 36 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6741 (mt-10) REVERT: 7 9 ASP cc_start: 0.7674 (t0) cc_final: 0.7338 (t0) REVERT: 7 36 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6739 (mp0) outliers start: 193 outliers final: 135 residues processed: 742 average time/residue: 0.6909 time to fit residues: 823.1645 Evaluate side-chains 826 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 673 time to evaluate : 5.499 ------------------------------------------------------------------------------- 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 28 LYS 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 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 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 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 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 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 a residue 50 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 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 36 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 28 LYS Chi-restraints excluded: chain l residue 50 THR Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 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 u residue 50 THR Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain v residue 28 LYS Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 28 LYS Chi-restraints excluded: chain w residue 36 GLU Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 53 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 82 ILE Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 12 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 0.0970 chunk 470 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 522 optimal weight: 0.9990 chunk 433 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 274 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 51720 Z= 0.194 Angle : 0.474 6.477 69720 Z= 0.262 Chirality : 0.045 0.381 7500 Planarity : 0.003 0.030 8820 Dihedral : 4.283 29.378 6303 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.51 % Allowed : 18.66 % Favored : 77.83 % 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: 1.63 (0.10), residues: 5820 helix: 2.43 (0.08), residues: 3060 sheet: -0.18 (0.11), residues: 1440 loop : -0.62 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP u 24 HIS 0.004 0.001 HIS w 62 PHE 0.012 0.001 PHE K 96 TYR 0.010 0.001 TYR P 44 ARG 0.007 0.000 ARG R 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 889 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 693 time to evaluate : 5.661 Fit side-chains REVERT: B 9 ASP cc_start: 0.7610 (t0) cc_final: 0.7111 (t0) REVERT: C 9 ASP cc_start: 0.8004 (t0) cc_final: 0.7751 (t0) REVERT: G 9 ASP cc_start: 0.7530 (t0) cc_final: 0.7036 (t0) REVERT: H 9 ASP cc_start: 0.8036 (t0) cc_final: 0.7806 (t0) REVERT: K 9 ASP cc_start: 0.7526 (t0) cc_final: 0.7318 (t0) REVERT: L 9 ASP cc_start: 0.7503 (t0) cc_final: 0.7092 (t0) REVERT: R 9 ASP cc_start: 0.7965 (t0) cc_final: 0.7696 (t0) REVERT: S 9 ASP cc_start: 0.7538 (t0) cc_final: 0.7037 (t0) REVERT: V 36 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6503 (mt-10) REVERT: X 12 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7258 (tp30) REVERT: Z 9 ASP cc_start: 0.7548 (t0) cc_final: 0.7331 (t0) REVERT: b 28 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7988 (mtpp) REVERT: c 12 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: c 36 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6297 (mt-10) REVERT: f 36 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6777 (mt-10) REVERT: g 9 ASP cc_start: 0.7748 (t0) cc_final: 0.7482 (t0) REVERT: h 36 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6101 (mp0) REVERT: l 9 ASP cc_start: 0.8022 (t0) cc_final: 0.7803 (t0) REVERT: p 36 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6469 (mt-10) REVERT: r 12 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7231 (tp30) REVERT: s 1 MET cc_start: 0.7264 (tpt) cc_final: 0.7024 (tpt) REVERT: s 9 ASP cc_start: 0.7634 (t0) cc_final: 0.7301 (t0) REVERT: s 36 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: t 9 ASP cc_start: 0.7533 (t0) cc_final: 0.7310 (t0) REVERT: v 28 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.8033 (mtpp) REVERT: w 36 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6299 (mt-10) REVERT: z 36 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: 0 9 ASP cc_start: 0.7759 (t0) cc_final: 0.7489 (t0) REVERT: 1 36 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6115 (mp0) REVERT: 4 36 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6481 (mt-10) REVERT: 6 12 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: 6 36 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6758 (mt-10) REVERT: 7 9 ASP cc_start: 0.7675 (t0) cc_final: 0.7315 (t0) REVERT: 7 36 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6765 (mp0) outliers start: 196 outliers final: 134 residues processed: 759 average time/residue: 0.6610 time to fit residues: 805.4006 Evaluate side-chains 828 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 676 time to evaluate : 5.425 ------------------------------------------------------------------------------- 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 28 LYS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 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 28 LYS 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 28 LYS Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain 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 a residue 50 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 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 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 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 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 u residue 50 THR Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain v residue 4 VAL Chi-restraints excluded: chain v residue 28 LYS Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 28 LYS Chi-restraints excluded: chain w residue 36 GLU Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 12 GLU Chi-restraints excluded: chain 6 residue 36 GLU Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 36 GLU Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 297 optimal weight: 4.9990 chunk 381 optimal weight: 0.5980 chunk 295 optimal weight: 1.9990 chunk 439 optimal weight: 0.9980 chunk 291 optimal weight: 0.0370 chunk 520 optimal weight: 0.9980 chunk 325 optimal weight: 2.9990 chunk 317 optimal weight: 0.7980 chunk 240 optimal weight: 0.0370 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 51720 Z= 0.166 Angle : 0.470 7.219 69720 Z= 0.257 Chirality : 0.044 0.426 7500 Planarity : 0.003 0.031 8820 Dihedral : 4.235 29.733 6303 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.80 % Allowed : 19.55 % Favored : 77.65 % 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: 1.77 (0.10), residues: 5820 helix: 2.55 (0.08), residues: 3060 sheet: -0.12 (0.11), residues: 1440 loop : -0.59 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 24 HIS 0.004 0.001 HIS y 62 PHE 0.015 0.001 PHE z 96 TYR 0.011 0.001 TYR P 44 ARG 0.008 0.000 ARG o 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 828 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 672 time to evaluate : 5.366 Fit side-chains REVERT: C 9 ASP cc_start: 0.7991 (t0) cc_final: 0.7728 (t0) REVERT: H 9 ASP cc_start: 0.8031 (t0) cc_final: 0.7790 (t0) REVERT: L 9 ASP cc_start: 0.7479 (t0) cc_final: 0.7071 (t0) REVERT: R 9 ASP cc_start: 0.7974 (t0) cc_final: 0.7699 (t0) REVERT: S 9 ASP cc_start: 0.7508 (t0) cc_final: 0.7004 (t0) REVERT: V 36 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6490 (mt-10) REVERT: X 12 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7147 (tp30) REVERT: g 9 ASP cc_start: 0.7720 (t0) cc_final: 0.7371 (t0) REVERT: h 36 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6245 (mp0) REVERT: j 9 ASP cc_start: 0.7495 (t0) cc_final: 0.7289 (t0) REVERT: l 9 ASP cc_start: 0.8004 (t0) cc_final: 0.7791 (t0) REVERT: p 36 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6461 (mt-10) REVERT: r 12 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7127 (tp30) REVERT: s 36 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: v 28 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7939 (mtpp) REVERT: 0 9 ASP cc_start: 0.7721 (t0) cc_final: 0.7388 (t0) REVERT: 1 36 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6262 (mp0) REVERT: 4 36 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6467 (mt-10) REVERT: 6 36 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6759 (mt-10) REVERT: 7 1 MET cc_start: 0.7136 (tpt) cc_final: 0.6819 (tpt) REVERT: 7 9 ASP cc_start: 0.7641 (t0) cc_final: 0.7324 (t0) REVERT: 7 36 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6770 (mp0) outliers start: 156 outliers final: 111 residues processed: 730 average time/residue: 0.6816 time to fit residues: 797.5115 Evaluate side-chains 781 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 659 time to evaluate : 5.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 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 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 28 LYS Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 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 W residue 28 LYS 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 b residue 4 VAL Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 28 LYS 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 50 THR Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 50 THR Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 88 VAL Chi-restraints excluded: chain 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 4 VAL 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 v residue 4 VAL Chi-restraints excluded: chain v residue 28 LYS Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 28 LYS Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain y residue 28 LYS Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 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 6 residue 1 MET Chi-restraints excluded: chain 6 residue 36 GLU Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 36 GLU Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 0.0010 chunk 207 optimal weight: 4.9990 chunk 310 optimal weight: 0.0270 chunk 156 optimal weight: 0.0040 chunk 102 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 330 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 409 optimal weight: 4.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 51720 Z= 0.152 Angle : 0.468 6.678 69720 Z= 0.255 Chirality : 0.044 0.426 7500 Planarity : 0.003 0.037 8820 Dihedral : 4.191 29.711 6303 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.56 % Allowed : 19.71 % Favored : 77.72 % 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: 1.95 (0.10), residues: 5820 helix: 2.70 (0.08), residues: 3060 sheet: -0.02 (0.11), residues: 1440 loop : -0.54 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP u 24 HIS 0.004 0.001 HIS E 62 PHE 0.015 0.001 PHE f 96 TYR 0.010 0.001 TYR P 44 ARG 0.008 0.001 ARG d 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 813 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 670 time to evaluate : 5.542 Fit side-chains REVERT: C 9 ASP cc_start: 0.7983 (t0) cc_final: 0.7762 (t0) REVERT: L 9 ASP cc_start: 0.7458 (t0) cc_final: 0.7043 (t0) REVERT: R 9 ASP cc_start: 0.7969 (t0) cc_final: 0.7677 (t0) REVERT: S 9 ASP cc_start: 0.7460 (t0) cc_final: 0.7006 (t0) REVERT: V 36 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6470 (mt-10) REVERT: g 9 ASP cc_start: 0.7663 (t0) cc_final: 0.7269 (t0) REVERT: h 36 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6361 (mp0) REVERT: p 36 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6456 (mt-10) REVERT: s 36 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: v 28 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7942 (mtpp) REVERT: w 28 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7901 (mtpt) REVERT: y 28 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7728 (mtpt) REVERT: 0 9 ASP cc_start: 0.7668 (t0) cc_final: 0.7267 (t0) REVERT: 0 86 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7333 (ttt-90) REVERT: 1 36 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6395 (mp0) REVERT: 4 36 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6465 (mt-10) REVERT: 6 36 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6751 (mt-10) REVERT: 7 1 MET cc_start: 0.7104 (tpt) cc_final: 0.6871 (tpt) outliers start: 143 outliers final: 115 residues processed: 715 average time/residue: 0.6743 time to fit residues: 772.7127 Evaluate side-chains 777 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 652 time to evaluate : 5.579 ------------------------------------------------------------------------------- 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 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 67 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain 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 28 LYS Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 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 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 50 THR Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 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 4 VAL Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain v residue 28 LYS Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 28 LYS Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain 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 50 THR Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 36 GLU Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 2.9990 chunk 498 optimal weight: 0.0970 chunk 454 optimal weight: 0.0770 chunk 485 optimal weight: 0.6980 chunk 291 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 380 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 438 optimal weight: 2.9990 chunk 458 optimal weight: 0.7980 chunk 483 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1146 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= 0.169 Angle : 0.476 6.410 69720 Z= 0.259 Chirality : 0.045 0.424 7500 Planarity : 0.003 0.036 8820 Dihedral : 4.191 29.040 6303 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.76 % Allowed : 19.57 % Favored : 77.67 % 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: 2.00 (0.10), residues: 5820 helix: 2.74 (0.08), residues: 3060 sheet: 0.00 (0.11), residues: 1440 loop : -0.51 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 24 HIS 0.005 0.001 HIS E 62 PHE 0.014 0.001 PHE f 96 TYR 0.009 0.001 TYR b 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 814 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 660 time to evaluate : 5.523 Fit side-chains REVERT: B 9 ASP cc_start: 0.7581 (t0) cc_final: 0.7106 (t0) REVERT: C 9 ASP cc_start: 0.8000 (t0) cc_final: 0.7780 (t0) REVERT: G 9 ASP cc_start: 0.7507 (t0) cc_final: 0.7036 (t0) REVERT: L 9 ASP cc_start: 0.7477 (t0) cc_final: 0.7068 (t0) REVERT: M 9 ASP cc_start: 0.7954 (t0) cc_final: 0.7720 (t0) REVERT: R 9 ASP cc_start: 0.7856 (t0) cc_final: 0.7541 (t0) REVERT: S 9 ASP cc_start: 0.7564 (t0) cc_final: 0.7017 (t0) REVERT: S 86 ARG cc_start: 0.7731 (ttt-90) cc_final: 0.7278 (ttt-90) REVERT: V 36 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6527 (mt-10) REVERT: c 36 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6376 (mt-10) REVERT: g 9 ASP cc_start: 0.7687 (t0) cc_final: 0.7280 (t0) REVERT: h 36 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6276 (mp0) REVERT: k 1 MET cc_start: 0.7139 (tpt) cc_final: 0.6771 (tpt) REVERT: p 36 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6472 (mt-10) REVERT: s 9 ASP cc_start: 0.7479 (t0) cc_final: 0.7091 (t0) REVERT: s 36 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: v 28 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7943 (mtpp) REVERT: w 28 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7905 (mtpt) REVERT: y 28 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7724 (mtpt) REVERT: 0 9 ASP cc_start: 0.7690 (t0) cc_final: 0.7282 (t0) REVERT: 0 86 ARG cc_start: 0.7579 (ttp80) cc_final: 0.7266 (ttt-90) REVERT: 1 36 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6332 (mp0) REVERT: 4 36 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6488 (mt-10) REVERT: 6 12 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7112 (tp30) REVERT: 6 36 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6759 (mt-10) REVERT: 7 9 ASP cc_start: 0.7664 (t0) cc_final: 0.7303 (t0) outliers start: 154 outliers final: 126 residues processed: 706 average time/residue: 0.6601 time to fit residues: 746.1032 Evaluate side-chains 794 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 656 time to evaluate : 5.330 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 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 28 LYS Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain 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 Z residue 50 THR Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 28 LYS Chi-restraints excluded: chain e residue 50 THR 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 50 THR Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 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 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 v residue 4 VAL Chi-restraints excluded: chain v residue 28 LYS Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 28 LYS Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain 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 50 THR Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 12 GLU 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 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 3.9990 chunk 512 optimal weight: 0.7980 chunk 313 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 356 optimal weight: 0.7980 chunk 537 optimal weight: 2.9990 chunk 495 optimal weight: 0.8980 chunk 428 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 330 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 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 : 0.003 0.035 51720 Z= 0.212 Angle : 0.498 6.336 69720 Z= 0.273 Chirality : 0.046 0.424 7500 Planarity : 0.003 0.040 8820 Dihedral : 4.270 28.215 6303 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.63 % Allowed : 19.93 % Favored : 77.44 % 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: 1.81 (0.10), residues: 5820 helix: 2.58 (0.08), residues: 3060 sheet: -0.13 (0.11), residues: 1440 loop : -0.54 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP u 24 HIS 0.005 0.001 HIS J 62 PHE 0.015 0.002 PHE f 96 TYR 0.011 0.001 TYR P 44 ARG 0.010 0.001 ARG d 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 841 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 694 time to evaluate : 5.681 Fit side-chains REVERT: A 2 GLU cc_start: 0.7475 (tp30) cc_final: 0.7212 (mm-30) REVERT: R 9 ASP cc_start: 0.8007 (t0) cc_final: 0.7667 (t0) REVERT: S 86 ARG cc_start: 0.7749 (ttt-90) cc_final: 0.7306 (ttt-90) REVERT: V 36 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6462 (mt-10) REVERT: Y 9 ASP cc_start: 0.7718 (t0) cc_final: 0.7353 (t0) REVERT: c 36 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6371 (mt-10) REVERT: f 9 ASP cc_start: 0.7909 (t0) cc_final: 0.7655 (t0) REVERT: g 9 ASP cc_start: 0.7569 (t0) cc_final: 0.7143 (t0) REVERT: h 12 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7256 (tm-30) REVERT: h 36 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6148 (mp0) REVERT: k 9 ASP cc_start: 0.7633 (t0) cc_final: 0.7204 (t0) REVERT: p 36 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6456 (mt-10) REVERT: s 9 ASP cc_start: 0.7632 (t0) cc_final: 0.7213 (t0) REVERT: s 36 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: v 28 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7966 (mtpp) REVERT: z 9 ASP cc_start: 0.7839 (t0) cc_final: 0.7582 (t0) REVERT: 0 9 ASP cc_start: 0.7576 (t0) cc_final: 0.7147 (t0) REVERT: 0 86 ARG cc_start: 0.7577 (ttp80) cc_final: 0.7249 (ttt-90) REVERT: 1 12 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7443 (tm-30) REVERT: 1 36 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6276 (mp0) REVERT: 4 36 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6466 (mt-10) REVERT: 6 36 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: 7 9 ASP cc_start: 0.7635 (t0) cc_final: 0.7256 (t0) outliers start: 147 outliers final: 125 residues processed: 735 average time/residue: 0.6677 time to fit residues: 782.8974 Evaluate side-chains 826 residues out of total 5580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 692 time to evaluate : 5.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain 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 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 R residue 1 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 28 LYS Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain 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 50 THR Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 50 THR Chi-restraints excluded: chain l residue 88 VAL Chi-restraints excluded: chain m residue 50 THR Chi-restraints excluded: chain m residue 88 VAL Chi-restraints excluded: chain 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 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain v residue 4 VAL Chi-restraints excluded: chain v residue 28 LYS Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 28 LYS Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain y residue 50 THR 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 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 36 GLU Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 2.9990 chunk 456 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 395 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 429 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 440 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.169361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148694 restraints weight = 56902.105| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 1.88 r_work: 0.3562 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 51720 Z= 0.192 Angle : 0.493 6.576 69720 Z= 0.268 Chirality : 0.046 0.449 7500 Planarity : 0.003 0.039 8820 Dihedral : 4.250 28.457 6303 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.63 % Allowed : 20.38 % Favored : 76.99 % 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: 1.82 (0.10), residues: 5820 helix: 2.61 (0.08), residues: 3060 sheet: -0.12 (0.11), residues: 1440 loop : -0.56 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP u 24 HIS 0.005 0.001 HIS J 62 PHE 0.014 0.001 PHE f 96 TYR 0.009 0.001 TYR b 44 ARG 0.009 0.001 ARG d 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13154.52 seconds wall clock time: 234 minutes 22.77 seconds (14062.77 seconds total)