Starting phenix.real_space_refine on Wed Jun 11 14:42:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rx4_24724/06_2025/7rx4_24724.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rx4_24724/06_2025/7rx4_24724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rx4_24724/06_2025/7rx4_24724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rx4_24724/06_2025/7rx4_24724.map" model { file = "/net/cci-nas-00/data/ceres_data/7rx4_24724/06_2025/7rx4_24724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rx4_24724/06_2025/7rx4_24724.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.044 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: 3 Type Number sf(0) Gaussians C 8460 2.51 5 N 2580 2.21 5 O 2520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13560 Number of models: 1 Model: "" Number of chains: 60 Chain: "B" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "C" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "D" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "F" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "G" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "H" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "K" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "L" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "M" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "N" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "O" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "P" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "Q" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "S" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "T" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "U" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "V" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "W" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "X" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "Y" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "Z" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "0" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "1" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "2" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "3" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "4" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "a" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "5" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "6" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "7" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "8" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "9" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "b" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "c" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "d" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "e" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "f" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "g" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "h" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "i" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "j" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "k" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "l" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "m" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "n" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "o" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "p" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "q" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "r" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "s" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "t" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "u" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "v" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "w" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "x" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Time building chain proxies: 8.75, per 1000 atoms: 0.65 Number of scatterers: 13560 At special positions: 0 Unit cell: (119.88, 119.88, 92.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2520 8.00 N 2580 7.00 C 8460 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: 3.57 Conformation dependent library (CDL) restraints added in 1.8 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3480 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 98.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU A 5 " --> pdb=" O GLN A 1 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU a 29 " --> pdb=" O ILE a 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU B 5 " --> pdb=" O GLN B 1 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 29 removed outlier: 3.935A pdb=" N GLU C 29 " --> pdb=" O ILE C 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU D 5 " --> pdb=" O GLN D 1 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU E 29 " --> pdb=" O ILE E 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 29 removed outlier: 3.778A pdb=" N LEU F 5 " --> pdb=" O GLN F 1 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU G 29 " --> pdb=" O ILE G 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU H 5 " --> pdb=" O GLN H 1 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU I 29 " --> pdb=" O ILE I 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 29 removed outlier: 3.776A pdb=" N LEU J 5 " --> pdb=" O GLN J 1 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU L 5 " --> pdb=" O GLN L 1 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU N 5 " --> pdb=" O GLN N 1 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 29 removed outlier: 3.778A pdb=" N LEU P 5 " --> pdb=" O GLN P 1 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU Q 29 " --> pdb=" O ILE Q 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 1 through 29 removed outlier: 3.776A pdb=" N LEU R 5 " --> pdb=" O GLN R 1 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 29 removed outlier: 3.935A pdb=" N GLU S 29 " --> pdb=" O ILE S 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 1 through 29 removed outlier: 3.776A pdb=" N LEU T 5 " --> pdb=" O GLN T 1 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU U 29 " --> pdb=" O ILE U 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU V 5 " --> pdb=" O GLN V 1 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU W 29 " --> pdb=" O ILE W 25 " (cutoff:3.500A) Processing helix chain 'X' and resid 1 through 29 removed outlier: 3.778A pdb=" N LEU X 5 " --> pdb=" O GLN X 1 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU Y 29 " --> pdb=" O ILE Y 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU Z 5 " --> pdb=" O GLN Z 1 " (cutoff:3.500A) Processing helix chain '0' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU 0 29 " --> pdb=" O ILE 0 25 " (cutoff:3.500A) Processing helix chain '1' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU 1 5 " --> pdb=" O GLN 1 1 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU 2 29 " --> pdb=" O ILE 2 25 " (cutoff:3.500A) Processing helix chain '3' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU 3 5 " --> pdb=" O GLN 3 1 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU 4 29 " --> pdb=" O ILE 4 25 " (cutoff:3.500A) Processing helix chain '5' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU 5 5 " --> pdb=" O GLN 5 1 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 29 removed outlier: 3.935A pdb=" N GLU 6 29 " --> pdb=" O ILE 6 25 " (cutoff:3.500A) Processing helix chain '7' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU 7 5 " --> pdb=" O GLN 7 1 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU 8 29 " --> pdb=" O ILE 8 25 " (cutoff:3.500A) Processing helix chain '9' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU 9 5 " --> pdb=" O GLN 9 1 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU b 29 " --> pdb=" O ILE b 25 " (cutoff:3.500A) Processing helix chain 'c' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU c 5 " --> pdb=" O GLN c 1 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU d 29 " --> pdb=" O ILE d 25 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU e 5 " --> pdb=" O GLN e 1 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU f 29 " --> pdb=" O ILE f 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU g 5 " --> pdb=" O GLN g 1 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 29 removed outlier: 3.937A pdb=" N GLU h 29 " --> pdb=" O ILE h 25 " (cutoff:3.500A) Processing helix chain 'i' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU i 5 " --> pdb=" O GLN i 1 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 1 through 29 removed outlier: 3.778A pdb=" N LEU k 5 " --> pdb=" O GLN k 1 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU l 29 " --> pdb=" O ILE l 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU m 5 " --> pdb=" O GLN m 1 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU n 29 " --> pdb=" O ILE n 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU o 5 " --> pdb=" O GLN o 1 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU p 29 " --> pdb=" O ILE p 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 1 through 29 removed outlier: 3.776A pdb=" N LEU q 5 " --> pdb=" O GLN q 1 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU r 29 " --> pdb=" O ILE r 25 " (cutoff:3.500A) Processing helix chain 's' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU s 5 " --> pdb=" O GLN s 1 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU t 29 " --> pdb=" O ILE t 25 " (cutoff:3.500A) Processing helix chain 'u' and resid 1 through 29 removed outlier: 3.776A pdb=" N LEU u 5 " --> pdb=" O GLN u 1 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU v 29 " --> pdb=" O ILE v 25 " (cutoff:3.500A) Processing helix chain 'w' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU w 5 " --> pdb=" O GLN w 1 " (cutoff:3.500A) Processing helix chain 'x' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU x 29 " --> pdb=" O ILE x 25 " (cutoff:3.500A) 1410 hydrogen bonds defined for protein. 4230 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: 4.13 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 2400 1.29 - 1.35: 2580 1.35 - 1.42: 585 1.42 - 1.48: 1935 1.48 - 1.54: 6120 Bond restraints: 13620 Sorted by residual: bond pdb=" CG1 ILE N 25 " pdb=" CD1 ILE N 25 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.61e-01 bond pdb=" CG1 ILE D 25 " pdb=" CD1 ILE D 25 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.51e-01 bond pdb=" CG1 ILE V 25 " pdb=" CD1 ILE V 25 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.48e-01 bond pdb=" CG1 ILE 5 25 " pdb=" CD1 ILE 5 25 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.45e-01 bond pdb=" CG1 ILE w 25 " pdb=" CD1 ILE w 25 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.45e-01 ... (remaining 13615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.75: 17092 0.75 - 1.51: 835 1.51 - 2.26: 253 2.26 - 3.02: 82 3.02 - 3.77: 98 Bond angle restraints: 18360 Sorted by residual: angle pdb=" CA GLU 1 24 " pdb=" CB GLU 1 24 " pdb=" CG GLU 1 24 " ideal model delta sigma weight residual 114.10 117.87 -3.77 2.00e+00 2.50e-01 3.56e+00 angle pdb=" CA GLU g 24 " pdb=" CB GLU g 24 " pdb=" CG GLU g 24 " ideal model delta sigma weight residual 114.10 117.86 -3.76 2.00e+00 2.50e-01 3.54e+00 angle pdb=" CA GLU i 24 " pdb=" CB GLU i 24 " pdb=" CG GLU i 24 " ideal model delta sigma weight residual 114.10 117.86 -3.76 2.00e+00 2.50e-01 3.54e+00 angle pdb=" CA GLU o 24 " pdb=" CB GLU o 24 " pdb=" CG GLU o 24 " ideal model delta sigma weight residual 114.10 117.85 -3.75 2.00e+00 2.50e-01 3.52e+00 angle pdb=" CA GLU H 24 " pdb=" CB GLU H 24 " pdb=" CG GLU H 24 " ideal model delta sigma weight residual 114.10 117.85 -3.75 2.00e+00 2.50e-01 3.51e+00 ... (remaining 18355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.76: 6490 7.76 - 15.51: 890 15.51 - 23.27: 450 23.27 - 31.03: 480 31.03 - 38.78: 210 Dihedral angle restraints: 8520 sinusoidal: 3300 harmonic: 5220 Sorted by residual: dihedral pdb=" CA GLU T 24 " pdb=" C GLU T 24 " pdb=" N ILE T 25 " pdb=" CA ILE T 25 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA GLU q 24 " pdb=" C GLU q 24 " pdb=" N ILE q 25 " pdb=" CA ILE q 25 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA GLU 1 24 " pdb=" C GLU 1 24 " pdb=" N ILE 1 25 " pdb=" CA ILE 1 25 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 8517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1433 0.025 - 0.050: 375 0.050 - 0.075: 173 0.075 - 0.100: 154 0.100 - 0.125: 85 Chirality restraints: 2220 Sorted by residual: chirality pdb=" CA ILE D 18 " pdb=" N ILE D 18 " pdb=" C ILE D 18 " pdb=" CB ILE D 18 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA ILE N 18 " pdb=" N ILE N 18 " pdb=" C ILE N 18 " pdb=" CB ILE N 18 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE R 18 " pdb=" N ILE R 18 " pdb=" C ILE R 18 " pdb=" CB ILE R 18 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 2217 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU 9 24 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.26e+00 pdb=" C GLU 9 24 " -0.019 2.00e-02 2.50e+03 pdb=" O GLU 9 24 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE 9 25 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU J 24 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.26e+00 pdb=" C GLU J 24 " -0.019 2.00e-02 2.50e+03 pdb=" O GLU J 24 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE J 25 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU T 24 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" C GLU T 24 " -0.019 2.00e-02 2.50e+03 pdb=" O GLU T 24 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE T 25 " 0.006 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 68 2.52 - 3.12: 9824 3.12 - 3.71: 22955 3.71 - 4.31: 27234 4.31 - 4.90: 46534 Nonbonded interactions: 106615 Sorted by model distance: nonbonded pdb=" O GLU R 29 " pdb=" N ALA c 2 " model vdw 1.928 3.120 nonbonded pdb=" O GLU 3 29 " pdb=" N ALA o 2 " model vdw 1.929 3.120 nonbonded pdb=" O GLU J 29 " pdb=" N ALA A 2 " model vdw 1.929 3.120 nonbonded pdb=" O GLU T 29 " pdb=" N ALA e 2 " model vdw 1.929 3.120 nonbonded pdb=" O GLU H 29 " pdb=" N ALA 3 2 " model vdw 1.929 3.120 ... (remaining 106610 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 '8' selection = chain '9' 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.080 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 0.032 13620 Z= 0.129 Angle : 0.492 3.771 18360 Z= 0.286 Chirality : 0.039 0.125 2220 Planarity : 0.003 0.018 2400 Dihedral : 13.385 38.781 5040 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 6.26 (0.16), residues: 1620 helix: 3.98 (0.10), residues: 1560 sheet: None (None), residues: 0 loop : 5.70 (0.70), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS e 22 TYR 0.002 0.001 TYR M 15 ARG 0.005 0.000 ARG O 3 Details of bonding type rmsd hydrogen bonds : bond 0.08687 ( 1410) hydrogen bonds : angle 3.94701 ( 4230) covalent geometry : bond 0.00300 (13620) covalent geometry : angle 0.49155 (18360) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.392 Fit side-chains REVERT: C 20 SER cc_start: 0.8191 (p) cc_final: 0.7975 (p) REVERT: M 22 HIS cc_start: 0.6713 (m170) cc_final: 0.5934 (t-90) REVERT: 4 26 LEU cc_start: 0.7705 (tp) cc_final: 0.7491 (tt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2921 time to fit residues: 68.3066 Evaluate side-chains 136 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 22 HIS 2 22 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.199997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.180283 restraints weight = 18260.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.183045 restraints weight = 11225.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.184810 restraints weight = 8390.831| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13620 Z= 0.118 Angle : 0.466 11.127 18360 Z= 0.239 Chirality : 0.037 0.222 2220 Planarity : 0.003 0.019 2400 Dihedral : 3.701 18.388 1920 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.38 % Allowed : 8.10 % Favored : 89.52 % 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: 6.09 (0.17), residues: 1620 helix: 3.90 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS q 22 TYR 0.005 0.001 TYR w 15 ARG 0.003 0.000 ARG 8 3 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 1410) hydrogen bonds : angle 3.47935 ( 4230) covalent geometry : bond 0.00253 (13620) covalent geometry : angle 0.46643 (18360) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.539 Fit side-chains REVERT: C 20 SER cc_start: 0.8482 (p) cc_final: 0.8080 (p) REVERT: E 22 HIS cc_start: 0.6702 (m170) cc_final: 0.6386 (t-90) REVERT: I 26 LEU cc_start: 0.7889 (tp) cc_final: 0.7684 (tt) REVERT: M 22 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.6243 (t-90) REVERT: Q 22 HIS cc_start: 0.6555 (m170) cc_final: 0.6171 (t-90) REVERT: S 22 HIS cc_start: 0.6712 (m170) cc_final: 0.6244 (t-90) REVERT: V 24 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7935 (tm-30) REVERT: a 22 HIS cc_start: 0.6562 (m170) cc_final: 0.6097 (t-90) REVERT: 6 22 HIS cc_start: 0.7029 (m170) cc_final: 0.6280 (t-90) outliers start: 30 outliers final: 20 residues processed: 178 average time/residue: 0.3011 time to fit residues: 74.7835 Evaluate side-chains 179 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 22 HIS Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain 1 residue 25 ILE Chi-restraints excluded: chain 2 residue 22 HIS Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain g residue 25 ILE Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain s residue 25 ILE Chi-restraints excluded: chain u residue 25 ILE Chi-restraints excluded: chain w residue 25 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 22 HIS O 22 HIS 2 22 HIS a 22 HIS b 22 HIS p 22 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.196475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.177535 restraints weight = 18027.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.179032 restraints weight = 13896.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.180570 restraints weight = 10707.506| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13620 Z= 0.117 Angle : 0.422 9.682 18360 Z= 0.223 Chirality : 0.037 0.184 2220 Planarity : 0.002 0.017 2400 Dihedral : 3.599 18.870 1920 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.33 % Allowed : 14.60 % Favored : 82.06 % 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: 6.19 (0.17), residues: 1620 helix: 3.97 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS 2 22 TYR 0.005 0.001 TYR w 15 ARG 0.003 0.000 ARG 8 3 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 1410) hydrogen bonds : angle 3.30347 ( 4230) covalent geometry : bond 0.00257 (13620) covalent geometry : angle 0.42238 (18360) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 1.378 Fit side-chains REVERT: E 22 HIS cc_start: 0.6705 (m170) cc_final: 0.6365 (t-90) REVERT: L 29 GLU cc_start: 0.7800 (tt0) cc_final: 0.7532 (tt0) REVERT: M 24 GLU cc_start: 0.7341 (mp0) cc_final: 0.7111 (mp0) REVERT: Q 22 HIS cc_start: 0.6763 (m170) cc_final: 0.6101 (t-90) REVERT: S 22 HIS cc_start: 0.6843 (m170) cc_final: 0.6225 (t-90) REVERT: T 24 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7860 (tm-30) REVERT: 6 22 HIS cc_start: 0.7051 (m170) cc_final: 0.6159 (t-90) outliers start: 42 outliers final: 33 residues processed: 187 average time/residue: 0.2875 time to fit residues: 75.2981 Evaluate side-chains 193 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 22 HIS Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 20 SER Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain 1 residue 25 ILE Chi-restraints excluded: chain 2 residue 22 HIS Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain a residue 22 HIS Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 9 residue 25 ILE Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain e residue 25 ILE Chi-restraints excluded: chain g residue 25 ILE Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain s residue 25 ILE Chi-restraints excluded: chain u residue 25 ILE Chi-restraints excluded: chain w residue 25 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 22 HIS M 22 HIS U 22 HIS f 22 HIS l 22 HIS n 22 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.195777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.176267 restraints weight = 17932.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.178676 restraints weight = 11797.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.180276 restraints weight = 9167.653| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13620 Z= 0.125 Angle : 0.457 11.081 18360 Z= 0.234 Chirality : 0.037 0.166 2220 Planarity : 0.002 0.017 2400 Dihedral : 3.604 19.535 1920 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.17 % Allowed : 22.22 % Favored : 74.60 % 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: 6.27 (0.17), residues: 1620 helix: 4.01 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS b 22 TYR 0.006 0.001 TYR w 15 ARG 0.004 0.000 ARG 8 3 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 1410) hydrogen bonds : angle 3.28355 ( 4230) covalent geometry : bond 0.00281 (13620) covalent geometry : angle 0.45747 (18360) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 1.767 Fit side-chains REVERT: B 29 GLU cc_start: 0.7780 (tt0) cc_final: 0.7516 (tm-30) REVERT: Q 22 HIS cc_start: 0.6695 (m170) cc_final: 0.6169 (t-90) REVERT: S 22 HIS cc_start: 0.6866 (m170) cc_final: 0.6268 (t-90) REVERT: T 24 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7790 (tm-30) REVERT: 6 22 HIS cc_start: 0.7007 (m170) cc_final: 0.6274 (t-90) outliers start: 40 outliers final: 34 residues processed: 185 average time/residue: 0.3195 time to fit residues: 82.8639 Evaluate side-chains 188 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 22 HIS Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 22 HIS Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain U residue 22 HIS Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain 1 residue 25 ILE Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 9 residue 25 ILE Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain e residue 25 ILE Chi-restraints excluded: chain g residue 25 ILE Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain l residue 22 HIS Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain n residue 22 HIS Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain p residue 22 HIS Chi-restraints excluded: chain q residue 25 ILE Chi-restraints excluded: chain u residue 25 ILE Chi-restraints excluded: chain w residue 25 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 80 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 22 HIS 2 22 HIS d 22 HIS j 22 HIS l 22 HIS n 22 HIS r 22 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.187117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.168203 restraints weight = 18033.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.169181 restraints weight = 13080.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.170215 restraints weight = 10488.508| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13620 Z= 0.192 Angle : 0.562 10.241 18360 Z= 0.291 Chirality : 0.041 0.249 2220 Planarity : 0.003 0.019 2400 Dihedral : 3.848 20.235 1920 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.57 % Allowed : 26.11 % Favored : 70.32 % 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: 5.85 (0.17), residues: 1620 helix: 3.76 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS M 22 TYR 0.010 0.001 TYR u 15 ARG 0.004 0.000 ARG 8 3 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 1410) hydrogen bonds : angle 3.52778 ( 4230) covalent geometry : bond 0.00444 (13620) covalent geometry : angle 0.56150 (18360) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 1.509 Fit side-chains REVERT: E 22 HIS cc_start: 0.6934 (m170) cc_final: 0.6414 (t-90) REVERT: Q 22 HIS cc_start: 0.6876 (m170) cc_final: 0.6230 (t-90) REVERT: T 24 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7878 (tm-30) outliers start: 45 outliers final: 30 residues processed: 181 average time/residue: 0.2911 time to fit residues: 73.6989 Evaluate side-chains 169 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain O residue 22 HIS Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain 1 residue 25 ILE Chi-restraints excluded: chain 2 residue 22 HIS Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 9 residue 25 ILE Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain d residue 22 HIS Chi-restraints excluded: chain g residue 25 ILE Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain j residue 22 HIS Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 22 HIS Chi-restraints excluded: chain n residue 22 HIS Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain p residue 22 HIS Chi-restraints excluded: chain q residue 25 ILE Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 18 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 22 HIS 2 22 HIS d 22 HIS j 22 HIS l 22 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.192386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.173137 restraints weight = 18264.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.175154 restraints weight = 13510.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.176371 restraints weight = 10621.604| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13620 Z= 0.161 Angle : 0.524 10.496 18360 Z= 0.272 Chirality : 0.039 0.159 2220 Planarity : 0.003 0.019 2400 Dihedral : 3.849 20.838 1920 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.13 % Allowed : 26.11 % Favored : 69.76 % 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: 5.89 (0.17), residues: 1620 helix: 3.78 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS l 22 TYR 0.008 0.001 TYR u 15 ARG 0.004 0.000 ARG 8 3 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 1410) hydrogen bonds : angle 3.43311 ( 4230) covalent geometry : bond 0.00366 (13620) covalent geometry : angle 0.52404 (18360) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: E 24 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: Q 22 HIS cc_start: 0.6819 (m170) cc_final: 0.6181 (t-90) REVERT: T 24 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: W 24 GLU cc_start: 0.7708 (mp0) cc_final: 0.7467 (mp0) REVERT: i 24 GLU cc_start: 0.8247 (tm-30) cc_final: 0.8041 (tm-30) outliers start: 52 outliers final: 46 residues processed: 176 average time/residue: 0.2961 time to fit residues: 73.8070 Evaluate side-chains 183 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 22 HIS Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 22 HIS Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain T residue 24 GLU Chi-restraints excluded: chain U residue 22 HIS Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain 1 residue 25 ILE Chi-restraints excluded: chain 2 residue 22 HIS Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 8 residue 24 GLU Chi-restraints excluded: chain 9 residue 25 ILE Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 22 HIS Chi-restraints excluded: chain e residue 25 ILE Chi-restraints excluded: chain g residue 25 ILE Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 22 HIS Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 22 HIS Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain p residue 22 HIS Chi-restraints excluded: chain q residue 25 ILE Chi-restraints excluded: chain r residue 22 HIS Chi-restraints excluded: chain s residue 25 ILE Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain u residue 25 ILE Chi-restraints excluded: chain v residue 11 ILE Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 18 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 22 HIS j 22 HIS l 22 HIS n 22 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.191724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.172873 restraints weight = 18292.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.173878 restraints weight = 12608.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.174798 restraints weight = 10939.656| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13620 Z= 0.160 Angle : 0.520 9.391 18360 Z= 0.271 Chirality : 0.039 0.159 2220 Planarity : 0.003 0.020 2400 Dihedral : 3.836 20.889 1920 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.05 % Allowed : 27.06 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.88 (0.17), residues: 1620 helix: 3.77 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS l 22 TYR 0.008 0.001 TYR u 15 ARG 0.004 0.000 ARG 8 3 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 1410) hydrogen bonds : angle 3.43148 ( 4230) covalent geometry : bond 0.00365 (13620) covalent geometry : angle 0.51966 (18360) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: E 24 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: Q 22 HIS cc_start: 0.6784 (m170) cc_final: 0.6209 (t-90) REVERT: T 24 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: 3 29 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7520 (tt0) REVERT: p 24 GLU cc_start: 0.7335 (mp0) cc_final: 0.7070 (mp0) outliers start: 51 outliers final: 45 residues processed: 178 average time/residue: 0.2853 time to fit residues: 71.5806 Evaluate side-chains 183 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 22 HIS Chi-restraints excluded: chain O residue 22 HIS Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain T residue 24 GLU Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain 0 residue 20 SER Chi-restraints excluded: chain 1 residue 25 ILE Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 4 residue 20 SER Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 24 GLU Chi-restraints excluded: chain 9 residue 25 ILE Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain d residue 22 HIS Chi-restraints excluded: chain e residue 25 ILE Chi-restraints excluded: chain g residue 25 ILE Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 22 HIS Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 22 HIS Chi-restraints excluded: chain n residue 22 HIS Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain p residue 22 HIS Chi-restraints excluded: chain q residue 25 ILE Chi-restraints excluded: chain r residue 22 HIS Chi-restraints excluded: chain s residue 25 ILE Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain u residue 25 ILE Chi-restraints excluded: chain v residue 11 ILE Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 18 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 45 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 22 HIS 2 22 HIS d 22 HIS j 22 HIS l 22 HIS n 22 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.195483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.177167 restraints weight = 18274.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.177901 restraints weight = 12864.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.178350 restraints weight = 11780.801| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13620 Z= 0.130 Angle : 0.495 11.675 18360 Z= 0.257 Chirality : 0.037 0.156 2220 Planarity : 0.003 0.019 2400 Dihedral : 3.758 21.563 1920 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.81 % Allowed : 28.33 % Favored : 67.86 % 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: 6.12 (0.17), residues: 1620 helix: 3.92 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS l 22 TYR 0.005 0.001 TYR u 15 ARG 0.004 0.000 ARG a 3 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 1410) hydrogen bonds : angle 3.33190 ( 4230) covalent geometry : bond 0.00284 (13620) covalent geometry : angle 0.49454 (18360) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 1.426 Fit side-chains REVERT: E 24 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: M 22 HIS cc_start: 0.6937 (OUTLIER) cc_final: 0.6242 (t-90) REVERT: Q 22 HIS cc_start: 0.6715 (m170) cc_final: 0.6162 (t-90) REVERT: T 24 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: U 24 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6489 (mp0) REVERT: 3 29 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7303 (tt0) outliers start: 48 outliers final: 42 residues processed: 182 average time/residue: 0.2833 time to fit residues: 73.5010 Evaluate side-chains 195 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain G residue 22 HIS Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 22 HIS Chi-restraints excluded: chain O residue 22 HIS Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain T residue 24 GLU Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain 1 residue 25 ILE Chi-restraints excluded: chain 2 residue 22 HIS Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 9 residue 25 ILE Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain d residue 22 HIS Chi-restraints excluded: chain e residue 25 ILE Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 20 SER Chi-restraints excluded: chain g residue 25 ILE Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 22 HIS Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 22 HIS Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain n residue 22 HIS Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain p residue 22 HIS Chi-restraints excluded: chain q residue 25 ILE Chi-restraints excluded: chain r residue 22 HIS Chi-restraints excluded: chain s residue 25 ILE Chi-restraints excluded: chain u residue 25 ILE Chi-restraints excluded: chain w residue 25 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 66 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 22 HIS 2 22 HIS d 22 HIS j 22 HIS l 22 HIS n 22 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.193425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.174124 restraints weight = 18122.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.175825 restraints weight = 12504.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.177026 restraints weight = 9623.525| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13620 Z= 0.150 Angle : 0.529 8.481 18360 Z= 0.274 Chirality : 0.038 0.159 2220 Planarity : 0.003 0.020 2400 Dihedral : 3.794 21.539 1920 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.05 % Allowed : 28.49 % Favored : 67.46 % 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: 6.01 (0.17), residues: 1620 helix: 3.86 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS l 22 TYR 0.007 0.001 TYR w 15 ARG 0.004 0.000 ARG 8 3 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 1410) hydrogen bonds : angle 3.38765 ( 4230) covalent geometry : bond 0.00336 (13620) covalent geometry : angle 0.52895 (18360) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: E 24 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: M 22 HIS cc_start: 0.7001 (OUTLIER) cc_final: 0.6225 (t-90) REVERT: Q 22 HIS cc_start: 0.6744 (m170) cc_final: 0.6099 (t-90) REVERT: T 24 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: U 24 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6665 (mp0) REVERT: 3 29 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7466 (tm-30) REVERT: p 24 GLU cc_start: 0.7481 (mp0) cc_final: 0.7083 (mp0) outliers start: 51 outliers final: 42 residues processed: 176 average time/residue: 0.2812 time to fit residues: 70.4335 Evaluate side-chains 189 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain G residue 22 HIS Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 22 HIS Chi-restraints excluded: chain O residue 22 HIS Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain T residue 24 GLU Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain 1 residue 25 ILE Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 8 residue 24 GLU Chi-restraints excluded: chain 9 residue 25 ILE Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 22 HIS Chi-restraints excluded: chain e residue 25 ILE Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 20 SER Chi-restraints excluded: chain g residue 25 ILE Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 22 HIS Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 22 HIS Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain n residue 22 HIS Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain p residue 22 HIS Chi-restraints excluded: chain q residue 25 ILE Chi-restraints excluded: chain r residue 22 HIS Chi-restraints excluded: chain s residue 25 ILE Chi-restraints excluded: chain u residue 25 ILE Chi-restraints excluded: chain w residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 72 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 22 HIS d 22 HIS j 22 HIS l 22 HIS r 22 HIS s 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.192852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.174567 restraints weight = 18028.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.175262 restraints weight = 11799.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.175937 restraints weight = 9817.213| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13620 Z= 0.183 Angle : 0.592 12.252 18360 Z= 0.304 Chirality : 0.040 0.164 2220 Planarity : 0.003 0.021 2400 Dihedral : 3.908 21.651 1920 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.73 % Allowed : 28.97 % Favored : 67.30 % 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: 5.77 (0.17), residues: 1620 helix: 3.71 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS l 22 TYR 0.008 0.001 TYR u 15 ARG 0.005 0.000 ARG 8 3 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 1410) hydrogen bonds : angle 3.50218 ( 4230) covalent geometry : bond 0.00417 (13620) covalent geometry : angle 0.59160 (18360) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: E 24 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: Q 22 HIS cc_start: 0.6778 (m170) cc_final: 0.6206 (t-90) REVERT: T 24 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: U 24 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: W 24 GLU cc_start: 0.7371 (mp0) cc_final: 0.7083 (mp0) REVERT: p 24 GLU cc_start: 0.7434 (mp0) cc_final: 0.7001 (mp0) outliers start: 47 outliers final: 39 residues processed: 168 average time/residue: 0.2993 time to fit residues: 71.0913 Evaluate side-chains 177 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain G residue 22 HIS Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain M residue 22 HIS Chi-restraints excluded: chain O residue 22 HIS Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain T residue 24 GLU Chi-restraints excluded: chain U residue 24 GLU Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain 0 residue 20 SER Chi-restraints excluded: chain 1 residue 25 ILE Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 8 residue 24 GLU Chi-restraints excluded: chain 9 residue 25 ILE Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain d residue 22 HIS Chi-restraints excluded: chain e residue 25 ILE Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain f residue 20 SER Chi-restraints excluded: chain g residue 25 ILE Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 22 HIS Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 22 HIS Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain p residue 22 HIS Chi-restraints excluded: chain q residue 25 ILE Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain u residue 25 ILE Chi-restraints excluded: chain w residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 22 HIS I 22 HIS d 22 HIS j 22 HIS l 22 HIS n 22 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.190762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.172054 restraints weight = 18391.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.172800 restraints weight = 12197.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.174046 restraints weight = 10054.300| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13620 Z= 0.169 Angle : 0.582 12.186 18360 Z= 0.298 Chirality : 0.039 0.166 2220 Planarity : 0.003 0.021 2400 Dihedral : 3.895 22.004 1920 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.81 % Allowed : 29.44 % Favored : 66.75 % 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: 5.75 (0.17), residues: 1620 helix: 3.70 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS l 22 TYR 0.009 0.001 TYR u 15 ARG 0.005 0.000 ARG 8 3 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 1410) hydrogen bonds : angle 3.47071 ( 4230) covalent geometry : bond 0.00383 (13620) covalent geometry : angle 0.58153 (18360) =============================================================================== Job complete usr+sys time: 3664.19 seconds wall clock time: 64 minutes 23.53 seconds (3863.53 seconds total)