Starting phenix.real_space_refine on Tue Sep 24 05:34:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/09_2024/8xb8_38214.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/09_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_38214/09_2024/8xb8_38214.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/09_2024/8xb8_38214.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/09_2024/8xb8_38214.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xb8_38214/09_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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 50400 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "D" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "E" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "H" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "I" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "J" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "K" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "L" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "M" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "N" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "O" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "P" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Q" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "R" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "S" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "T" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "U" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "V" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "W" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "X" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Y" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Z" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "a" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "b" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "c" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "d" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "e" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "f" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "g" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "h" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "i" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "j" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "k" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "l" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "m" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "n" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "o" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "p" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "q" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "r" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "s" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "t" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "u" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "v" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "w" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "x" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "y" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "z" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "0" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "1" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "2" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "3" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "4" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "5" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "6" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "7" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 840 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Time building chain proxies: 20.55, per 1000 atoms: 0.41 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: 8.81 Conformation dependent library (CDL) restraints added in 4.4 seconds 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11640 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 60 sheets defined 53.1% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 1 through 36 Processing helix chain 'A' and resid 68 through 84 Processing helix chain 'B' and resid 2 through 36 Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 68 through 84 Processing helix chain 'C' and resid 2 through 36 Processing helix chain 'C' and resid 68 through 84 Processing helix chain 'D' and resid 2 through 36 Processing helix chain 'D' and resid 68 through 84 Processing helix chain 'E' and resid 2 through 36 Processing helix chain 'E' and resid 68 through 84 Processing helix chain 'F' and resid 2 through 37 Processing helix chain 'F' and resid 68 through 84 Processing helix chain 'G' and resid 2 through 36 Processing helix chain 'G' and resid 64 through 67 Processing helix chain 'G' and resid 68 through 84 Processing helix chain 'H' and resid 2 through 36 Processing helix chain 'H' and resid 68 through 84 Processing helix chain 'I' and resid 2 through 36 Processing helix chain 'I' and resid 68 through 84 Processing helix chain 'J' and resid 2 through 36 Processing helix chain 'J' and resid 68 through 84 Processing helix chain 'K' and resid 2 through 37 Processing helix chain 'K' and resid 68 through 84 Processing helix chain 'L' and resid 2 through 36 Processing helix chain 'L' and resid 64 through 67 Processing helix chain 'L' and resid 68 through 84 Processing helix chain 'M' and resid 2 through 36 Processing helix chain 'M' and resid 68 through 84 Processing helix chain 'N' and resid 2 through 36 Processing helix chain 'N' and resid 68 through 84 Processing helix chain 'O' and resid 2 through 37 Processing helix chain 'O' and resid 68 through 84 Processing helix chain 'P' and resid 2 through 37 Processing helix chain 'P' and resid 64 through 67 Processing helix chain 'P' and resid 68 through 84 Processing helix chain 'Q' and resid 2 through 36 Processing helix chain 'Q' and resid 68 through 84 Processing helix chain 'R' and resid 2 through 36 Processing helix chain 'R' and resid 68 through 84 Processing helix chain 'S' and resid 2 through 36 Processing helix chain 'S' and resid 68 through 84 Processing helix chain 'T' and resid 2 through 36 Processing helix chain 'T' and resid 68 through 84 Processing helix chain 'U' and resid 2 through 37 Processing helix chain 'U' and resid 68 through 84 Processing helix chain 'V' and resid 2 through 36 Processing helix chain 'V' and resid 68 through 84 Processing helix chain 'W' and resid 2 through 36 Processing helix chain 'W' and resid 68 through 84 Processing helix chain 'X' and resid 2 through 36 Processing helix chain 'X' and resid 68 through 84 Processing helix chain 'Y' and resid 2 through 36 Processing helix chain 'Y' and resid 68 through 84 Processing helix chain 'Z' and resid 2 through 36 Processing helix chain 'Z' and resid 68 through 84 Processing helix chain 'a' and resid 2 through 36 Processing helix chain 'a' and resid 68 through 84 Processing helix chain 'b' and resid 2 through 36 Processing helix chain 'b' and resid 68 through 84 Processing helix chain 'c' and resid 2 through 36 Processing helix chain 'c' and resid 68 through 84 Processing helix chain 'd' and resid 2 through 37 Processing helix chain 'd' and resid 68 through 84 Processing helix chain 'e' and resid 2 through 37 Processing helix chain 'e' and resid 68 through 84 Processing helix chain 'f' and resid 2 through 36 Processing helix chain 'f' and resid 68 through 84 Processing helix chain 'g' and resid 2 through 36 Processing helix chain 'g' and resid 68 through 84 Processing helix chain 'h' and resid 2 through 36 Processing helix chain 'h' and resid 68 through 84 Processing helix chain 'i' and resid 2 through 37 Processing helix chain 'i' and resid 68 through 84 Processing helix chain 'j' and resid 2 through 37 Processing helix chain 'j' and resid 68 through 84 Processing helix chain 'k' and resid 2 through 36 Processing helix chain 'k' and resid 64 through 67 Processing helix chain 'k' and resid 68 through 84 Processing helix chain 'l' and resid 2 through 36 Processing helix chain 'l' and resid 68 through 84 Processing helix chain 'm' and resid 2 through 36 Processing helix chain 'm' and resid 68 through 84 Processing helix chain 'n' and resid 2 through 36 Processing helix chain 'n' and resid 68 through 84 Processing helix chain 'o' and resid 2 through 37 Processing helix chain 'o' and resid 68 through 84 Processing helix chain 'p' and resid 2 through 36 Processing helix chain 'p' and resid 68 through 84 Processing helix chain 'q' and resid 2 through 36 Processing helix chain 'q' and resid 68 through 84 Processing helix chain 'r' and resid 2 through 36 Processing helix chain 'r' and resid 68 through 84 Processing helix chain 's' and resid 2 through 37 Processing helix chain 's' and resid 68 through 84 Processing helix chain 't' and resid 2 through 37 Processing helix chain 't' and resid 68 through 84 Processing helix chain 'u' and resid 2 through 36 Processing helix chain 'u' and resid 68 through 84 Processing helix chain 'v' and resid 2 through 36 Processing helix chain 'v' and resid 68 through 84 Processing helix chain 'w' and resid 2 through 36 Processing helix chain 'w' and resid 68 through 84 Processing helix chain 'x' and resid 2 through 37 Processing helix chain 'x' and resid 68 through 84 Processing helix chain 'y' and resid 2 through 37 Processing helix chain 'y' and resid 68 through 84 Processing helix chain 'z' and resid 2 through 36 Processing helix chain 'z' and resid 68 through 84 Processing helix chain '0' and resid 2 through 36 Processing helix chain '0' and resid 68 through 84 Processing helix chain '1' and resid 2 through 36 Processing helix chain '1' and resid 68 through 84 Processing helix chain '2' and resid 2 through 37 Processing helix chain '2' and resid 68 through 84 Processing helix chain '3' and resid 2 through 37 Processing helix chain '3' and resid 68 through 84 Processing helix chain '4' and resid 2 through 36 Processing helix chain '4' and resid 68 through 84 Processing helix chain '5' and resid 2 through 36 Processing helix chain '5' and resid 68 through 84 Processing helix chain '6' and resid 2 through 36 Processing helix chain '6' and resid 68 through 84 Processing helix chain '7' and resid 2 through 36 Processing helix chain '7' and resid 68 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 47 Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 47 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 47 Processing sheet with id=AA4, first strand: chain 'D' and resid 42 through 47 Processing sheet with id=AA5, first strand: chain 'E' and resid 42 through 47 Processing sheet with id=AA6, first strand: chain 'F' and resid 42 through 47 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 47 Processing sheet with id=AA8, first strand: chain 'H' and resid 42 through 47 Processing sheet with id=AA9, first strand: chain 'I' and resid 42 through 47 Processing sheet with id=AB1, first strand: chain 'J' and resid 42 through 47 Processing sheet with id=AB2, first strand: chain 'K' and resid 42 through 47 Processing sheet with id=AB3, first strand: chain 'L' and resid 42 through 47 Processing sheet with id=AB4, first strand: chain 'M' and resid 42 through 47 Processing sheet with id=AB5, first strand: chain 'N' and resid 42 through 47 Processing sheet with id=AB6, first strand: chain 'O' and resid 42 through 47 Processing sheet with id=AB7, first strand: chain 'P' and resid 42 through 47 Processing sheet with id=AB8, first strand: chain 'Q' and resid 42 through 47 Processing sheet with id=AB9, first strand: chain 'R' and resid 42 through 47 Processing sheet with id=AC1, first strand: chain 'S' and resid 42 through 47 Processing sheet with id=AC2, first strand: chain 'T' and resid 42 through 47 Processing sheet with id=AC3, first strand: chain 'U' and resid 42 through 47 Processing sheet with id=AC4, first strand: chain 'V' and resid 42 through 47 Processing sheet with id=AC5, first strand: chain 'W' and resid 42 through 47 Processing sheet with id=AC6, first strand: chain 'X' and resid 42 through 47 Processing sheet with id=AC7, first strand: chain 'Y' and resid 42 through 47 Processing sheet with id=AC8, first strand: chain 'Z' and resid 42 through 47 Processing sheet with id=AC9, first strand: chain 'a' and resid 42 through 47 Processing sheet with id=AD1, first strand: chain 'b' and resid 42 through 47 Processing sheet with id=AD2, first strand: chain 'c' and resid 42 through 47 Processing sheet with id=AD3, first strand: chain 'd' and resid 42 through 47 Processing sheet with id=AD4, first strand: chain 'e' and resid 42 through 47 Processing sheet with id=AD5, first strand: chain 'f' and resid 42 through 47 Processing sheet with id=AD6, first strand: chain 'g' and resid 42 through 47 Processing sheet with id=AD7, first strand: chain 'h' and resid 42 through 47 Processing sheet with id=AD8, first strand: chain 'i' and resid 42 through 47 Processing sheet with id=AD9, first strand: chain 'j' and resid 42 through 47 Processing sheet with id=AE1, first strand: chain 'k' and resid 42 through 47 Processing sheet with id=AE2, first strand: chain 'l' and resid 42 through 47 Processing sheet with id=AE3, first strand: chain 'm' and resid 42 through 47 Processing sheet with id=AE4, first strand: chain 'n' and resid 42 through 47 Processing sheet with id=AE5, first strand: chain 'o' and resid 42 through 47 Processing sheet with id=AE6, first strand: chain 'p' and resid 42 through 47 Processing sheet with id=AE7, first strand: chain 'q' and resid 42 through 47 Processing sheet with id=AE8, first strand: chain 'r' and resid 42 through 47 Processing sheet with id=AE9, first strand: chain 's' and resid 42 through 47 Processing sheet with id=AF1, first strand: chain 't' and resid 42 through 47 Processing sheet with id=AF2, first strand: chain 'u' and resid 42 through 47 Processing sheet with id=AF3, first strand: chain 'v' and resid 42 through 47 Processing sheet with id=AF4, first strand: chain 'w' and resid 42 through 47 Processing sheet with id=AF5, first strand: chain 'x' and resid 42 through 47 Processing sheet with id=AF6, first strand: chain 'y' and resid 42 through 47 Processing sheet with id=AF7, first strand: chain 'z' and resid 42 through 47 Processing sheet with id=AF8, first strand: chain '0' and resid 42 through 47 Processing sheet with id=AF9, first strand: chain '1' and resid 42 through 47 Processing sheet with id=AG1, first strand: chain '2' and resid 42 through 47 Processing sheet with id=AG2, first strand: chain '3' and resid 42 through 47 Processing sheet with id=AG3, first strand: chain '4' and resid 42 through 47 Processing sheet with id=AG4, first strand: chain '5' and resid 42 through 47 Processing sheet with id=AG5, first strand: chain '6' and resid 42 through 47 Processing sheet with id=AG6, first strand: chain '7' and resid 42 through 47 3622 hydrogen bonds defined for protein. 10311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.46 Time building geometry restraints manager: 10.58 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: 1.820 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: 0.040 Extract box with map and model: 1.420 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 86.770 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.820 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: 0.030 Load rotamer database and sin/cos tables:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 51720 Z= 0.199 Angle : 0.500 8.380 69720 Z= 0.275 Chirality : 0.045 0.445 7500 Planarity : 0.003 0.039 8820 Dihedral : 16.094 74.505 19380 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.30 % Allowed : 18.48 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.10), residues: 5820 helix: 2.25 (0.08), residues: 3060 sheet: -0.21 (0.11), residues: 1440 loop : -0.60 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 24 HIS 0.005 0.001 HIS y 62 PHE 0.014 0.001 PHE 4 96 TYR 0.011 0.001 TYR P 44 ARG 0.009 0.000 ARG 6 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 656 time to evaluate : 4.261 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: 0.5518 time to fit residues: 583.3536 Evaluate side-chains 665 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 652 time to evaluate : 4.283 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 167 poor density : 682 time to evaluate : 4.263 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: 0.5558 time to fit residues: 641.2420 Evaluate side-chains 798 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 673 time to evaluate : 4.271 ------------------------------------------------------------------------------- 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: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 51720 Z= 0.164 Angle : 0.457 7.430 69720 Z= 0.252 Chirality : 0.043 0.351 7500 Planarity : 0.003 0.031 8820 Dihedral : 4.274 25.996 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 : 3.14 % Allowed : 18.10 % 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 0.003 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 l 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 890 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 715 time to evaluate : 4.335 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: 0.7468 (mt-10) REVERT: K 67 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: L 9 ASP cc_start: 0.7484 (t0) cc_final: 0.7042 (t0) REVERT: V 36 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6453 (mt-10) REVERT: W 1 MET cc_start: 0.7045 (tmm) cc_final: 0.6531 (tpt) REVERT: Z 9 ASP cc_start: 0.7560 (t0) cc_final: 0.7288 (t0) REVERT: b 28 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7999 (mtpp) REVERT: p 36 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6429 (mt-10) REVERT: q 1 MET cc_start: 0.7043 (tmm) cc_final: 0.6552 (tpt) REVERT: s 36 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: t 9 ASP cc_start: 0.7540 (t0) cc_final: 0.7263 (t0) REVERT: v 28 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.8059 (mtpp) REVERT: w 36 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6291 (mt-10) REVERT: 4 36 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6450 (mt-10) REVERT: 5 1 MET cc_start: 0.7012 (tmm) cc_final: 0.6541 (tpt) REVERT: 7 1 MET cc_start: 0.7321 (tpt) cc_final: 0.7091 (tpt) REVERT: 7 36 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6688 (mp0) outliers start: 175 outliers final: 82 residues processed: 782 average time/residue: 0.5542 time to fit residues: 694.7521 Evaluate side-chains 764 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 671 time to evaluate : 4.338 ------------------------------------------------------------------------------- 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 53 MET Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 28 LYS Chi-restraints excluded: chain R residue 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 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: 1.9990 chunk 254 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 329 optimal weight: 5.9990 chunk 493 optimal weight: 0.9980 chunk 521 optimal weight: 0.9990 chunk 257 optimal weight: 3.9990 chunk 467 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 51720 Z= 0.285 Angle : 0.518 6.303 69720 Z= 0.286 Chirality : 0.047 0.375 7500 Planarity : 0.003 0.025 8820 Dihedral : 4.434 28.147 6303 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.15 % Allowed : 18.87 % Favored : 77.97 % 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: 1.36 (0.10), residues: 5820 helix: 2.16 (0.08), residues: 3060 sheet: -0.27 (0.11), residues: 1440 loop : -0.62 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP l 24 HIS 0.004 0.001 HIS W 62 PHE 0.018 0.002 PHE d 96 TYR 0.009 0.001 TYR P 44 ARG 0.005 0.001 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 890 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 714 time to evaluate : 5.564 Fit side-chains REVERT: A 67 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: B 9 ASP cc_start: 0.7692 (t0) cc_final: 0.7222 (t0) REVERT: C 9 ASP cc_start: 0.8020 (t0) cc_final: 0.7796 (t0) REVERT: F 67 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: H 9 ASP cc_start: 0.8042 (t0) cc_final: 0.7806 (t0) REVERT: K 9 ASP cc_start: 0.7584 (t0) cc_final: 0.7335 (t0) REVERT: K 67 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: L 9 ASP cc_start: 0.7586 (t0) cc_final: 0.7133 (t0) REVERT: R 9 ASP cc_start: 0.7924 (t0) cc_final: 0.7685 (t0) REVERT: S 13 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6958 (mtpp) REVERT: X 12 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7257 (tp30) REVERT: Z 1 MET cc_start: 0.7332 (tpt) cc_final: 0.6990 (tpt) REVERT: Z 9 ASP cc_start: 0.7717 (t0) cc_final: 0.7445 (t0) REVERT: b 28 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8043 (mtpp) REVERT: c 12 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: c 36 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6256 (mt-10) REVERT: g 9 ASP cc_start: 0.7735 (t0) cc_final: 0.7514 (t0) REVERT: h 36 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6088 (mp0) REVERT: l 9 ASP cc_start: 0.8027 (t0) cc_final: 0.7814 (t0) REVERT: r 12 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7139 (tp30) REVERT: s 9 ASP cc_start: 0.7718 (t0) cc_final: 0.7361 (t0) REVERT: s 36 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: t 1 MET cc_start: 0.7313 (tpt) cc_final: 0.6979 (tpt) REVERT: t 9 ASP cc_start: 0.7693 (t0) cc_final: 0.7411 (t0) REVERT: v 28 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8068 (mtpp) REVERT: w 36 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6268 (mt-10) REVERT: z 36 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6773 (mt-10) REVERT: 0 9 ASP cc_start: 0.7732 (t0) cc_final: 0.7498 (t0) REVERT: 1 36 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: 6 12 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7262 (tp30) REVERT: 7 9 ASP cc_start: 0.7716 (t0) cc_final: 0.7369 (t0) REVERT: 7 36 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6769 (mp0) outliers start: 176 outliers final: 134 residues processed: 766 average time/residue: 0.5768 time to fit residues: 709.9399 Evaluate side-chains 851 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 700 time to evaluate : 4.378 ------------------------------------------------------------------------------- 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 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 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 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 53 MET Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 28 LYS Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 82 ILE Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 82 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 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 12 GLU Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain Z residue 88 VAL Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain b residue 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 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 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 12 GLU Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain t residue 88 VAL Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain v residue 28 LYS Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 36 GLU Chi-restraints excluded: chain w residue 50 THR Chi-restraints excluded: chain w residue 53 MET Chi-restraints excluded: chain x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 53 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 82 ILE Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 50 THR Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 50 THR Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 12 GLU Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 36 GLU Chi-restraints excluded: chain 7 residue 50 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 0.5980 chunk 296 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 445 optimal weight: 0.0570 chunk 360 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 468 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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** ** 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: 0.7382 moved from start: 0.0828 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= 0.180 Angle : 0.473 6.773 69720 Z= 0.260 Chirality : 0.045 0.375 7500 Planarity : 0.003 0.027 8820 Dihedral : 4.308 29.594 6303 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.32 % Allowed : 18.75 % Favored : 77.94 % 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: 1.53 (0.10), residues: 5820 helix: 2.35 (0.08), residues: 3060 sheet: -0.23 (0.11), residues: 1440 loop : -0.65 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 24 HIS 0.004 0.001 HIS W 62 PHE 0.013 0.001 PHE K 96 TYR 0.009 0.001 TYR P 44 ARG 0.006 0.000 ARG r 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11640 Ramachandran restraints generated. 5820 Oldfield, 0 Emsley, 5820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 689 time to evaluate : 4.367 Fit side-chains REVERT: B 9 ASP cc_start: 0.7522 (t0) cc_final: 0.7037 (t0) REVERT: H 9 ASP cc_start: 0.8012 (t0) cc_final: 0.7756 (t0) REVERT: L 9 ASP cc_start: 0.7504 (t0) cc_final: 0.7030 (t0) REVERT: R 9 ASP cc_start: 0.7942 (t0) cc_final: 0.7694 (t0) REVERT: V 36 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6460 (mt-10) REVERT: W 1 MET cc_start: 0.7235 (tmm) cc_final: 0.6539 (tpt) REVERT: Z 9 ASP cc_start: 0.7692 (t0) cc_final: 0.7443 (t0) REVERT: b 28 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7991 (mtpp) REVERT: c 36 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6286 (mt-10) REVERT: f 36 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: h 36 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6079 (mp0) REVERT: p 36 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6437 (mt-10) REVERT: q 1 MET cc_start: 0.7111 (tmm) cc_final: 0.6555 (tpt) REVERT: s 9 ASP cc_start: 0.7625 (t0) cc_final: 0.7285 (t0) REVERT: s 36 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: t 9 ASP cc_start: 0.7663 (t0) cc_final: 0.7407 (t0) REVERT: v 28 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.8034 (mtpp) REVERT: w 36 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6293 (mt-10) REVERT: z 36 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6776 (mt-10) REVERT: 1 36 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6118 (mp0) REVERT: 4 36 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6460 (mt-10) REVERT: 5 1 MET cc_start: 0.7094 (tmm) cc_final: 0.6546 (tpt) REVERT: 7 36 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6771 (mp0) outliers start: 185 outliers final: 119 residues processed: 751 average time/residue: 0.5822 time to fit residues: 700.9361 Evaluate side-chains 798 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 666 time to evaluate : 4.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 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 4 VAL Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 53 MET Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 28 LYS Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 82 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 53 MET Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 53 MET Chi-restraints excluded: chain f residue 4 VAL Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 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 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 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 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 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 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: 4.9990 chunk 470 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 306 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 522 optimal weight: 0.6980 chunk 433 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 274 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.7421 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 51720 Z= 0.235 Angle : 0.496 6.287 69720 Z= 0.274 Chirality : 0.046 0.381 7500 Planarity : 0.003 0.030 8820 Dihedral : 4.367 29.460 6303 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.12 % Allowed : 19.53 % Favored : 77.35 % 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: 1.42 (0.10), residues: 5820 helix: 2.25 (0.08), residues: 3060 sheet: -0.30 (0.11), residues: 1440 loop : -0.66 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP l 24 HIS 0.004 0.001 HIS W 62 PHE 0.016 0.002 PHE z 96 TYR 0.010 0.001 TYR P 44 ARG 0.007 0.001 ARG T 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 861 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 687 time to evaluate : 4.345 Fit side-chains REVERT: B 9 ASP cc_start: 0.7569 (t0) cc_final: 0.7068 (t0) REVERT: C 9 ASP cc_start: 0.8031 (t0) cc_final: 0.7787 (t0) REVERT: H 9 ASP cc_start: 0.8052 (t0) cc_final: 0.7838 (t0) REVERT: K 9 ASP cc_start: 0.7589 (t0) cc_final: 0.7337 (t0) REVERT: L 9 ASP cc_start: 0.7555 (t0) cc_final: 0.7094 (t0) REVERT: R 9 ASP cc_start: 0.7983 (t0) cc_final: 0.7721 (t0) REVERT: V 36 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6456 (mt-10) REVERT: W 1 MET cc_start: 0.7203 (tmm) cc_final: 0.6592 (tpt) REVERT: Z 9 ASP cc_start: 0.7738 (t0) cc_final: 0.7485 (t0) REVERT: b 28 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.8009 (mtpp) REVERT: c 12 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: c 36 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6287 (mt-10) REVERT: f 36 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6812 (mt-10) REVERT: g 9 ASP cc_start: 0.7794 (t0) cc_final: 0.7462 (t0) REVERT: h 36 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6084 (mp0) REVERT: j 9 ASP cc_start: 0.7572 (t0) cc_final: 0.7336 (t0) REVERT: l 9 ASP cc_start: 0.8038 (t0) cc_final: 0.7808 (t0) REVERT: p 36 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6430 (mt-10) REVERT: q 1 MET cc_start: 0.7116 (tmm) cc_final: 0.6542 (tpt) REVERT: s 1 MET cc_start: 0.7217 (tpt) cc_final: 0.6975 (tpt) REVERT: s 9 ASP cc_start: 0.7673 (t0) cc_final: 0.7341 (t0) REVERT: s 36 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: t 9 ASP cc_start: 0.7709 (t0) cc_final: 0.7458 (t0) REVERT: w 36 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6291 (mt-10) REVERT: 0 9 ASP cc_start: 0.7797 (t0) cc_final: 0.7471 (t0) REVERT: 1 36 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6121 (mp0) REVERT: 4 36 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6455 (mt-10) REVERT: 5 1 MET cc_start: 0.7096 (tmm) cc_final: 0.6530 (tpt) REVERT: 7 9 ASP cc_start: 0.7717 (t0) cc_final: 0.7366 (t0) REVERT: 7 36 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6795 (mp0) outliers start: 174 outliers final: 135 residues processed: 741 average time/residue: 0.5480 time to fit residues: 645.9700 Evaluate side-chains 824 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 677 time to evaluate : 4.313 ------------------------------------------------------------------------------- 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 88 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 88 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 53 MET Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 28 LYS Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 82 ILE Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 53 MET Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 12 GLU Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 53 MET Chi-restraints excluded: chain f residue 4 VAL Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 50 THR Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 50 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 36 GLU Chi-restraints excluded: chain h residue 50 THR Chi-restraints excluded: chain h residue 88 VAL Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k residue 4 VAL Chi-restraints excluded: chain k residue 50 THR Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 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 36 GLU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain u residue 88 VAL Chi-restraints excluded: chain v residue 4 VAL Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 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 50 THR Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 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 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: 0.7980 chunk 58 optimal weight: 5.9990 chunk 297 optimal weight: 0.0870 chunk 381 optimal weight: 0.8980 chunk 295 optimal weight: 1.9990 chunk 439 optimal weight: 0.6980 chunk 291 optimal weight: 0.8980 chunk 520 optimal weight: 1.9990 chunk 325 optimal weight: 2.9990 chunk 317 optimal weight: 0.9980 chunk 240 optimal weight: 0.0670 overall best weight: 0.5096 ------------------------------------------------------------------------------- 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: 0.7361 moved from start: 0.0976 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= 0.169 Angle : 0.467 6.750 69720 Z= 0.257 Chirality : 0.045 0.399 7500 Planarity : 0.003 0.030 8820 Dihedral : 4.257 30.180 6303 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.24 % Allowed : 19.50 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.10), residues: 5820 helix: 2.47 (0.08), residues: 3060 sheet: -0.16 (0.11), residues: 1440 loop : -0.65 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 24 HIS 0.004 0.001 HIS y 62 PHE 0.014 0.001 PHE z 96 TYR 0.011 0.001 TYR P 44 ARG 0.008 0.000 ARG R 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 878 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 697 time to evaluate : 4.385 Fit side-chains REVERT: H 9 ASP cc_start: 0.8030 (t0) cc_final: 0.7786 (t0) REVERT: L 9 ASP cc_start: 0.7491 (t0) cc_final: 0.7012 (t0) REVERT: R 9 ASP cc_start: 0.7976 (t0) cc_final: 0.7710 (t0) REVERT: V 36 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6490 (mt-10) REVERT: W 1 MET cc_start: 0.7241 (tmm) cc_final: 0.6631 (tpt) REVERT: Z 9 ASP cc_start: 0.7710 (t0) cc_final: 0.7452 (t0) REVERT: b 28 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7923 (mtpp) REVERT: c 36 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6346 (mt-10) REVERT: f 36 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6798 (mt-10) REVERT: g 9 ASP cc_start: 0.7718 (t0) cc_final: 0.7389 (t0) REVERT: h 36 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6219 (mp0) REVERT: l 9 ASP cc_start: 0.8005 (t0) cc_final: 0.7767 (t0) REVERT: p 36 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6449 (mt-10) REVERT: q 1 MET cc_start: 0.7171 (tmm) cc_final: 0.6660 (tpt) REVERT: s 36 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: t 9 ASP cc_start: 0.7687 (t0) cc_final: 0.7423 (t0) REVERT: y 28 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7726 (mtpt) REVERT: z 36 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6811 (mt-10) REVERT: 0 9 ASP cc_start: 0.7727 (t0) cc_final: 0.7392 (t0) REVERT: 1 36 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6274 (mp0) REVERT: 4 36 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6474 (mt-10) REVERT: 5 1 MET cc_start: 0.7102 (tmm) cc_final: 0.6619 (tpt) REVERT: 6 36 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6745 (mt-10) REVERT: 7 36 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6787 (mp0) outliers start: 181 outliers final: 121 residues processed: 763 average time/residue: 0.5626 time to fit residues: 683.3707 Evaluate side-chains 802 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 668 time to evaluate : 4.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 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 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 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 50 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 50 THR Chi-restraints excluded: chain V residue 88 VAL Chi-restraints excluded: chain W residue 4 VAL Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 88 VAL Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 50 THR Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain e residue 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 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 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 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 28 LYS Chi-restraints excluded: chain s residue 36 GLU Chi-restraints excluded: chain s residue 50 THR Chi-restraints excluded: chain t residue 50 THR Chi-restraints excluded: chain u residue 50 THR Chi-restraints excluded: chain v residue 4 VAL Chi-restraints excluded: chain v residue 50 THR Chi-restraints excluded: chain v residue 53 MET Chi-restraints excluded: chain v residue 88 VAL Chi-restraints excluded: chain w residue 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 53 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 36 GLU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 2 residue 88 VAL Chi-restraints excluded: chain 3 residue 88 VAL Chi-restraints excluded: chain 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 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: 0.0270 chunk 207 optimal weight: 0.3980 chunk 310 optimal weight: 0.0010 chunk 156 optimal weight: 0.1980 chunk 102 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 330 optimal weight: 2.9990 chunk 354 optimal weight: 0.9990 chunk 257 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 409 optimal weight: 0.9980 overall best weight: 0.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** m 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 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: 0.7303 moved from start: 0.1276 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= 0.148 Angle : 0.473 10.179 69720 Z= 0.255 Chirality : 0.045 0.451 7500 Planarity : 0.003 0.030 8820 Dihedral : 4.185 30.382 6303 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.44 % Allowed : 20.56 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.10), residues: 5820 helix: 2.73 (0.08), residues: 3060 sheet: -0.00 (0.11), residues: 1440 loop : -0.56 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP u 24 HIS 0.003 0.001 HIS W 62 PHE 0.013 0.001 PHE f 96 TYR 0.010 0.001 TYR P 44 ARG 0.008 0.000 ARG o 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 842 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 706 time to evaluate : 4.373 Fit side-chains REVERT: C 9 ASP cc_start: 0.7986 (t0) cc_final: 0.7751 (t0) REVERT: H 9 ASP cc_start: 0.8022 (t0) cc_final: 0.7805 (t0) REVERT: H 86 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7596 (ttt-90) REVERT: M 86 ARG cc_start: 0.7804 (ttp80) cc_final: 0.7583 (ttt-90) REVERT: R 9 ASP cc_start: 0.7839 (t0) cc_final: 0.7451 (t0) REVERT: S 86 ARG cc_start: 0.7729 (ttt-90) cc_final: 0.7293 (ttt-90) REVERT: V 36 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6545 (mt-10) REVERT: Y 36 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: Z 9 ASP cc_start: 0.7702 (t0) cc_final: 0.7417 (t0) REVERT: b 28 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7885 (mtpp) REVERT: g 9 ASP cc_start: 0.7666 (t0) cc_final: 0.7264 (t0) REVERT: h 36 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: k 9 ASP cc_start: 0.7652 (t0) cc_final: 0.7284 (t0) REVERT: l 86 ARG cc_start: 0.7796 (ttp80) cc_final: 0.7574 (ttt-90) REVERT: n 93 THR cc_start: 0.6820 (p) cc_final: 0.6482 (p) REVERT: p 36 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6541 (mt-10) REVERT: q 1 MET cc_start: 0.7101 (tmm) cc_final: 0.6561 (tpt) REVERT: s 36 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: t 9 ASP cc_start: 0.7685 (t0) cc_final: 0.7394 (t0) REVERT: w 28 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7879 (mtpt) REVERT: y 28 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7749 (mtpt) REVERT: z 36 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: 0 9 ASP cc_start: 0.7666 (t0) cc_final: 0.7263 (t0) REVERT: 0 86 ARG cc_start: 0.7639 (ttp80) cc_final: 0.7331 (ttt-90) REVERT: 1 36 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6387 (mp0) REVERT: 4 36 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6558 (mt-10) REVERT: 5 1 MET cc_start: 0.7082 (tmm) cc_final: 0.6550 (tpt) REVERT: 7 9 ASP cc_start: 0.7580 (t0) cc_final: 0.7200 (t0) outliers start: 136 outliers final: 99 residues processed: 746 average time/residue: 0.5722 time to fit residues: 674.2739 Evaluate side-chains 802 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 692 time to evaluate : 4.441 ------------------------------------------------------------------------------- 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 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 G residue 4 VAL Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain M residue 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 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 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 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 36 GLU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 50 THR 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 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 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 67 GLU Chi-restraints excluded: chain j residue 88 VAL Chi-restraints excluded: chain k 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 v residue 4 VAL 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 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 53 MET 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 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 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 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: 3.9990 chunk 498 optimal weight: 0.3980 chunk 454 optimal weight: 1.9990 chunk 485 optimal weight: 0.9980 chunk 291 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 380 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 438 optimal weight: 3.9990 chunk 458 optimal weight: 1.9990 chunk 483 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 51720 Z= 0.274 Angle : 0.535 6.507 69720 Z= 0.291 Chirality : 0.048 0.427 7500 Planarity : 0.004 0.043 8820 Dihedral : 4.363 28.644 6302 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.38 % Allowed : 20.66 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.10), residues: 5820 helix: 2.37 (0.08), residues: 3060 sheet: -0.26 (0.11), residues: 1440 loop : -0.60 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP r 65 HIS 0.004 0.001 HIS y 85 PHE 0.016 0.002 PHE b 96 TYR 0.010 0.001 TYR v 44 ARG 0.008 0.001 ARG f 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 863 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 730 time to evaluate : 4.474 Fit side-chains REVERT: S 86 ARG cc_start: 0.7758 (ttt-90) cc_final: 0.7312 (ttt-90) REVERT: V 36 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6444 (mt-10) REVERT: b 28 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.8014 (mtpp) REVERT: f 36 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6798 (mt-10) REVERT: g 9 ASP cc_start: 0.7715 (t0) cc_final: 0.7323 (t0) REVERT: h 36 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: p 36 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6439 (mt-10) REVERT: s 36 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: z 36 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6812 (mt-10) REVERT: 0 9 ASP cc_start: 0.7718 (t0) cc_final: 0.7317 (t0) REVERT: 1 36 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6069 (mp0) REVERT: 4 36 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6522 (mt-10) REVERT: 6 36 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6787 (mt-10) outliers start: 133 outliers final: 113 residues processed: 763 average time/residue: 0.5690 time to fit residues: 689.5849 Evaluate side-chains 843 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 720 time to evaluate : 4.389 ------------------------------------------------------------------------------- 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 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 G 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 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 1 MET Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 50 THR Chi-restraints excluded: chain T residue 50 THR Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain U residue 50 THR Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain V residue 4 VAL Chi-restraints excluded: chain V residue 36 GLU Chi-restraints excluded: chain V residue 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 28 LYS Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain f residue 4 VAL Chi-restraints excluded: chain f residue 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 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 28 LYS 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 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 x residue 50 THR Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain y residue 50 THR Chi-restraints excluded: chain y residue 53 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 71 CYS Chi-restraints excluded: chain z residue 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 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 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: 0.0770 chunk 512 optimal weight: 0.9980 chunk 313 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 356 optimal weight: 0.3980 chunk 537 optimal weight: 0.9990 chunk 495 optimal weight: 5.9990 chunk 428 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 330 optimal weight: 2.9990 chunk 262 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 51720 Z= 0.191 Angle : 0.501 7.697 69720 Z= 0.273 Chirality : 0.046 0.442 7500 Planarity : 0.003 0.040 8820 Dihedral : 4.301 29.289 6302 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.47 % Allowed : 20.63 % Favored : 76.90 % 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: 2.46 (0.08), residues: 3060 sheet: -0.23 (0.11), residues: 1440 loop : -0.62 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP r 65 HIS 0.004 0.001 HIS e 62 PHE 0.013 0.001 PHE b 96 TYR 0.010 0.001 TYR P 44 ARG 0.009 0.001 ARG r 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 838 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 700 time to evaluate : 4.247 Fit side-chains REVERT: H 86 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7601 (ttt-90) REVERT: S 12 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7704 (tm-30) REVERT: S 86 ARG cc_start: 0.7756 (ttt-90) cc_final: 0.7516 (ttt-90) REVERT: V 36 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6432 (mt-10) REVERT: b 28 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7931 (mtpp) REVERT: f 36 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6778 (mt-10) REVERT: g 9 ASP cc_start: 0.7711 (t0) cc_final: 0.7311 (t0) REVERT: h 36 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: l 86 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7585 (ttt-90) REVERT: p 36 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6543 (mt-10) REVERT: q 1 MET cc_start: 0.7130 (tmm) cc_final: 0.6661 (tpt) REVERT: s 36 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: z 36 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6796 (mt-10) REVERT: 0 9 ASP cc_start: 0.7711 (t0) cc_final: 0.7308 (t0) REVERT: 0 86 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7235 (ttt-90) REVERT: 1 36 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6274 (mp0) REVERT: 4 36 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6529 (mt-10) REVERT: 5 1 MET cc_start: 0.7105 (tmm) cc_final: 0.6651 (tpt) outliers start: 138 outliers final: 116 residues processed: 739 average time/residue: 0.5840 time to fit residues: 677.2180 Evaluate side-chains 809 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 684 time to evaluate : 4.306 ------------------------------------------------------------------------------- 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 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 G residue 4 VAL 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 53 MET Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 50 THR Chi-restraints excluded: chain Q residue 71 CYS Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 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 28 LYS Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain c residue 50 THR Chi-restraints excluded: chain d residue 50 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain f residue 4 VAL Chi-restraints excluded: chain f residue 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 l residue 1 MET 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 36 GLU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 88 VAL Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 50 THR Chi-restraints excluded: chain q residue 53 MET Chi-restraints excluded: chain q residue 71 CYS Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain r residue 88 VAL Chi-restraints excluded: chain s residue 28 LYS 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 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 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 y residue 53 MET Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 50 THR Chi-restraints excluded: chain z residue 88 VAL Chi-restraints excluded: chain 0 residue 50 THR Chi-restraints excluded: chain 1 residue 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 4 residue 4 VAL Chi-restraints excluded: chain 4 residue 36 GLU Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 5 residue 4 VAL Chi-restraints excluded: chain 5 residue 50 THR Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 50 THR Chi-restraints excluded: chain 6 residue 88 VAL Chi-restraints excluded: chain 7 residue 28 LYS 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: 0.0670 chunk 131 optimal weight: 0.8980 chunk 395 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 429 optimal weight: 0.9990 chunk 179 optimal weight: 0.0050 chunk 440 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.5534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.171817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150972 restraints weight = 56739.703| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.88 r_work: 0.3572 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 51720 Z= 0.179 Angle : 0.497 7.716 69720 Z= 0.269 Chirality : 0.046 0.436 7500 Planarity : 0.003 0.038 8820 Dihedral : 4.263 29.156 6302 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.58 % Allowed : 21.02 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.10), residues: 5820 helix: 2.56 (0.08), residues: 3060 sheet: -0.19 (0.11), residues: 1440 loop : -0.61 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP r 65 HIS 0.004 0.001 HIS W 62 PHE 0.013 0.001 PHE b 96 TYR 0.009 0.001 TYR v 44 ARG 0.008 0.001 ARG 6 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11370.91 seconds wall clock time: 197 minutes 55.76 seconds (11875.76 seconds total)