Starting phenix.real_space_refine on Wed Mar 4 10:27:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rx4_24724/03_2026/7rx4_24724.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rx4_24724/03_2026/7rx4_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_24724/03_2026/7rx4_24724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rx4_24724/03_2026/7rx4_24724.map" model { file = "/net/cci-nas-00/data/ceres_data/7rx4_24724/03_2026/7rx4_24724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rx4_24724/03_2026/7rx4_24724.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.27, per 1000 atoms: 0.24 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: 1.18 Conformation dependent library (CDL) restraints added in 589.0 milliseconds 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: 0.33 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: 2.45 Time building geometry restraints manager: 1.56 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: 2.390 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.720 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.250 ------------------------------------------------------------------------------- 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 : 13.04 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG O 3 TYR 0.002 0.001 TYR M 15 HIS 0.000 0.000 HIS e 22 Details of bonding type rmsd covalent geometry : bond 0.00300 (13620) covalent geometry : angle 0.49155 (18360) hydrogen bonds : bond 0.08687 ( 1410) hydrogen bonds : angle 3.94701 ( 4230) *********************** 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 : 0.514 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: 0.7706 (tp) cc_final: 0.7492 (tt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1464 time to fit residues: 34.0716 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 : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4391 r_free = 0.4391 target = 0.199652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.179797 restraints weight = 18265.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.182613 restraints weight = 11290.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.184430 restraints weight = 8455.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.185359 restraints weight = 7065.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.186243 restraints weight = 6381.841| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13620 Z= 0.119 Angle : 0.471 11.717 18360 Z= 0.240 Chirality : 0.037 0.218 2220 Planarity : 0.003 0.019 2400 Dihedral : 3.698 18.610 1920 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.70 % Allowed : 7.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 6.08 (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 ARG 0.003 0.000 ARG v 3 TYR 0.006 0.001 TYR u 15 HIS 0.001 0.000 HIS q 22 Details of bonding type rmsd covalent geometry : bond 0.00258 (13620) covalent geometry : angle 0.47112 (18360) hydrogen bonds : bond 0.03475 ( 1410) hydrogen bonds : angle 3.48960 ( 4230) *********************** 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 202 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.586 Fit side-chains REVERT: C 20 SER cc_start: 0.8471 (p) cc_final: 0.8057 (p) REVERT: E 22 HIS cc_start: 0.6701 (m170) cc_final: 0.6388 (t-90) REVERT: M 22 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.6268 (t-90) REVERT: Q 22 HIS cc_start: 0.6568 (m170) cc_final: 0.6191 (t-90) REVERT: S 22 HIS cc_start: 0.6721 (m170) cc_final: 0.6277 (t-90) REVERT: a 22 HIS cc_start: 0.6547 (m170) cc_final: 0.6211 (t-90) REVERT: 6 22 HIS cc_start: 0.7039 (m170) cc_final: 0.6313 (t-90) outliers start: 34 outliers final: 24 residues processed: 179 average time/residue: 0.1450 time to fit residues: 36.2606 Evaluate side-chains 183 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 ILE 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 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 9 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 a 22 HIS b 22 HIS p 22 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.191616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.172276 restraints weight = 18153.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.173688 restraints weight = 12438.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.174593 restraints weight = 9757.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.175132 restraints weight = 8967.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.175299 restraints weight = 8300.545| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1811 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= 0.165 Angle : 0.509 9.570 18360 Z= 0.266 Chirality : 0.040 0.197 2220 Planarity : 0.003 0.018 2400 Dihedral : 3.771 19.264 1920 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.17 % Allowed : 20.71 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.90 (0.17), residues: 1620 helix: 3.79 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 8 3 TYR 0.009 0.001 TYR F 15 HIS 0.011 0.001 HIS 2 22 Details of bonding type rmsd covalent geometry : bond 0.00380 (13620) covalent geometry : angle 0.50873 (18360) hydrogen bonds : bond 0.04036 ( 1410) hydrogen bonds : angle 3.49165 ( 4230) *********************** 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 203 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.496 Fit side-chains REVERT: O 26 LEU cc_start: 0.7937 (tp) cc_final: 0.7634 (tt) REVERT: Q 22 HIS cc_start: 0.6578 (m170) cc_final: 0.6149 (t-90) REVERT: S 22 HIS cc_start: 0.7056 (m170) cc_final: 0.6397 (t-90) REVERT: T 24 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7822 (tm-30) REVERT: 6 22 HIS cc_start: 0.7074 (m170) cc_final: 0.6217 (t-90) outliers start: 40 outliers final: 26 residues processed: 182 average time/residue: 0.1389 time to fit residues: 35.3656 Evaluate side-chains 174 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain L residue 25 ILE 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 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 a residue 22 HIS 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 b residue 22 HIS Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain f residue 20 SER Chi-restraints excluded: chain g residue 25 ILE Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain o 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 46 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 22 HIS U 22 HIS 2 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 = 0.4273 r_free = 0.4273 target = 0.187829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.168858 restraints weight = 18205.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.169358 restraints weight = 14014.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.170513 restraints weight = 12338.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.170950 restraints weight = 10420.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.171018 restraints weight = 9485.579| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13620 Z= 0.207 Angle : 0.572 10.509 18360 Z= 0.300 Chirality : 0.042 0.168 2220 Planarity : 0.003 0.019 2400 Dihedral : 3.977 19.852 1920 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.65 % Allowed : 26.11 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.50 (0.17), residues: 1620 helix: 3.54 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 8 3 TYR 0.011 0.001 TYR u 15 HIS 0.008 0.001 HIS b 22 Details of bonding type rmsd covalent geometry : bond 0.00479 (13620) covalent geometry : angle 0.57195 (18360) hydrogen bonds : bond 0.04489 ( 1410) hydrogen bonds : angle 3.61708 ( 4230) *********************** 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 203 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.529 Fit side-chains REVERT: M 24 GLU cc_start: 0.7231 (mp0) cc_final: 0.7031 (mp0) REVERT: O 26 LEU cc_start: 0.8036 (tp) cc_final: 0.7794 (tt) REVERT: T 24 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7873 (tm-30) REVERT: 7 24 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7679 (tm-30) REVERT: 9 29 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7492 (tm-30) outliers start: 46 outliers final: 34 residues processed: 186 average time/residue: 0.1404 time to fit residues: 36.5767 Evaluate side-chains 174 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain J 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 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 0 residue 20 SER 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 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 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 22 HIS 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 t residue 11 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 59 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 a 22 HIS d 22 HIS j 22 HIS l 22 HIS n 22 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.193666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.173495 restraints weight = 18216.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.176018 restraints weight = 12138.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.177727 restraints weight = 9489.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.178481 restraints weight = 8094.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.179420 restraints weight = 7428.867| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2215 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= 0.136 Angle : 0.461 11.209 18360 Z= 0.245 Chirality : 0.038 0.224 2220 Planarity : 0.003 0.019 2400 Dihedral : 3.759 20.122 1920 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.89 % Allowed : 27.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.96 (0.17), residues: 1620 helix: 3.83 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 8 3 TYR 0.006 0.001 TYR w 15 HIS 0.003 0.001 HIS l 22 Details of bonding type rmsd covalent geometry : bond 0.00302 (13620) covalent geometry : angle 0.46117 (18360) hydrogen bonds : bond 0.03656 ( 1410) hydrogen bonds : angle 3.35409 ( 4230) *********************** 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 208 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 0.517 Fit side-chains REVERT: M 22 HIS cc_start: 0.6923 (OUTLIER) cc_final: 0.6197 (t-90) REVERT: O 26 LEU cc_start: 0.7955 (tp) cc_final: 0.7723 (tt) REVERT: Q 22 HIS cc_start: 0.6708 (m170) cc_final: 0.6283 (t-90) REVERT: S 22 HIS cc_start: 0.7027 (m170) cc_final: 0.6453 (t-90) REVERT: T 24 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7898 (tm-30) REVERT: W 24 GLU cc_start: 0.7576 (mp0) cc_final: 0.7348 (mp0) REVERT: 7 24 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7823 (tm-30) REVERT: 9 29 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7470 (tm-30) outliers start: 49 outliers final: 42 residues processed: 188 average time/residue: 0.1336 time to fit residues: 35.6258 Evaluate side-chains 186 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 HIS 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 25 ILE Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain X residue 25 ILE 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 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 a residue 22 HIS 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 45 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 22 HIS d 22 HIS j 22 HIS l 22 HIS r 22 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.192463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.172688 restraints weight = 18253.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.174154 restraints weight = 13298.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.175283 restraints weight = 10361.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.175743 restraints weight = 9046.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.176042 restraints weight = 8484.020| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13620 Z= 0.149 Angle : 0.503 11.330 18360 Z= 0.261 Chirality : 0.038 0.152 2220 Planarity : 0.003 0.019 2400 Dihedral : 3.775 20.586 1920 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.08 % Allowed : 26.67 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.93 (0.17), residues: 1620 helix: 3.81 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 8 3 TYR 0.007 0.001 TYR u 15 HIS 0.005 0.001 HIS j 22 Details of bonding type rmsd covalent geometry : bond 0.00339 (13620) covalent geometry : angle 0.50348 (18360) hydrogen bonds : bond 0.03790 ( 1410) hydrogen bonds : angle 3.38996 ( 4230) *********************** 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 220 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: O 26 LEU cc_start: 0.7962 (tp) cc_final: 0.7701 (tt) REVERT: S 22 HIS cc_start: 0.7078 (m170) cc_final: 0.6373 (t-90) REVERT: T 24 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: V 24 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7996 (tm-30) REVERT: 3 29 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7312 (tt0) REVERT: 9 29 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7479 (tm-30) REVERT: p 24 GLU cc_start: 0.7373 (mp0) cc_final: 0.7099 (mp0) outliers start: 64 outliers final: 49 residues processed: 195 average time/residue: 0.1349 time to fit residues: 37.2499 Evaluate side-chains 194 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 144 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 K residue 24 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 20 SER 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 12 LEU Chi-restraints excluded: chain T residue 24 GLU Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain X residue 25 ILE 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 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 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 11 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 o residue 25 ILE Chi-restraints excluded: chain p residue 22 HIS Chi-restraints excluded: chain q 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 Chi-restraints excluded: chain x residue 11 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 97 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 f 22 HIS j 22 HIS l 22 HIS n 22 HIS s 17 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.187845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.168682 restraints weight = 18048.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.169587 restraints weight = 12664.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.170399 restraints weight = 11004.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.170932 restraints weight = 9771.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.171040 restraints weight = 8854.471| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13620 Z= 0.136 Angle : 0.472 6.926 18360 Z= 0.251 Chirality : 0.037 0.153 2220 Planarity : 0.003 0.019 2400 Dihedral : 3.714 20.544 1920 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.03 % Allowed : 25.63 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG 8 3 TYR 0.007 0.001 TYR u 15 HIS 0.006 0.001 HIS d 22 Details of bonding type rmsd covalent geometry : bond 0.00303 (13620) covalent geometry : angle 0.47215 (18360) hydrogen bonds : bond 0.03618 ( 1410) hydrogen bonds : angle 3.33502 ( 4230) *********************** 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 234 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 158 time to evaluate : 0.543 Fit side-chains REVERT: B 29 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7742 (tt0) REVERT: E 24 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: M 22 HIS cc_start: 0.6840 (OUTLIER) cc_final: 0.6176 (t-90) REVERT: O 26 LEU cc_start: 0.7949 (tp) cc_final: 0.7648 (tt) REVERT: T 24 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: W 24 GLU cc_start: 0.7569 (mp0) cc_final: 0.7339 (mp0) REVERT: 8 26 LEU cc_start: 0.8184 (tp) cc_final: 0.7978 (tt) REVERT: 9 29 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7395 (tm-30) REVERT: c 12 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8222 (mm) REVERT: i 24 GLU cc_start: 0.8232 (tm-30) cc_final: 0.8029 (tm-30) REVERT: p 24 GLU cc_start: 0.7302 (mp0) cc_final: 0.7082 (mp0) outliers start: 76 outliers final: 55 residues processed: 205 average time/residue: 0.1277 time to fit residues: 37.4548 Evaluate side-chains 204 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 145 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 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 20 SER 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 12 LEU Chi-restraints excluded: chain T residue 24 GLU Chi-restraints excluded: chain U residue 20 SER 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 11 ILE Chi-restraints excluded: chain 0 residue 20 SER 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 18 ILE Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 9 residue 25 ILE Chi-restraints excluded: chain c residue 12 LEU 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 l residue 24 GLU 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 t residue 11 ILE Chi-restraints excluded: chain u residue 25 ILE Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 11 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 58 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 22 HIS U 22 HIS 0 22 HIS 2 22 HIS b 22 HIS d 22 HIS f 22 HIS j 22 HIS k 17 ASN l 22 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.193145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.172688 restraints weight = 17966.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.174453 restraints weight = 14373.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.175517 restraints weight = 10761.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.176133 restraints weight = 9595.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.176275 restraints weight = 8883.540| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13620 Z= 0.152 Angle : 0.522 10.968 18360 Z= 0.270 Chirality : 0.038 0.161 2220 Planarity : 0.003 0.020 2400 Dihedral : 3.763 21.274 1920 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.11 % Allowed : 25.32 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.93 (0.17), residues: 1620 helix: 3.81 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 8 3 TYR 0.008 0.001 TYR u 15 HIS 0.007 0.001 HIS n 22 Details of bonding type rmsd covalent geometry : bond 0.00344 (13620) covalent geometry : angle 0.52215 (18360) hydrogen bonds : bond 0.03789 ( 1410) hydrogen bonds : angle 3.38366 ( 4230) *********************** 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 233 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 156 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: D 29 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7470 (tm-30) REVERT: O 26 LEU cc_start: 0.7949 (tp) cc_final: 0.7653 (tt) REVERT: T 24 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: W 24 GLU cc_start: 0.7622 (mp0) cc_final: 0.7355 (mp0) REVERT: 3 29 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7246 (tt0) REVERT: 4 26 LEU cc_start: 0.8149 (tt) cc_final: 0.7819 (tp) REVERT: 9 29 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7317 (tm-30) REVERT: c 12 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8207 (mm) REVERT: w 19 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8623 (mt) outliers start: 77 outliers final: 56 residues processed: 204 average time/residue: 0.1281 time to fit residues: 37.1529 Evaluate side-chains 201 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 142 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain G residue 22 HIS 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 20 SER 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 12 LEU 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 0 residue 11 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 18 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 12 LEU 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 20 SER Chi-restraints excluded: chain g residue 25 ILE Chi-restraints excluded: chain h residue 11 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 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 v residue 11 ILE Chi-restraints excluded: chain w residue 19 LEU Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 11 ILE Chi-restraints excluded: chain x residue 18 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 n 22 HIS u 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.195066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.173895 restraints weight = 18284.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.176260 restraints weight = 11698.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.177307 restraints weight = 9007.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.178085 restraints weight = 8056.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.178109 restraints weight = 7383.605| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13620 Z= 0.135 Angle : 0.526 11.744 18360 Z= 0.269 Chirality : 0.038 0.187 2220 Planarity : 0.003 0.020 2400 Dihedral : 3.735 21.386 1920 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.16 % Allowed : 26.43 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.96 (0.17), residues: 1620 helix: 3.83 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 8 3 TYR 0.006 0.001 TYR u 15 HIS 0.008 0.001 HIS l 22 Details of bonding type rmsd covalent geometry : bond 0.00297 (13620) covalent geometry : angle 0.52622 (18360) hydrogen bonds : bond 0.03572 ( 1410) hydrogen bonds : angle 3.35727 ( 4230) *********************** 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 219 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 154 time to evaluate : 0.521 Fit side-chains REVERT: B 29 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7571 (tt0) REVERT: D 29 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7499 (tm-30) REVERT: E 24 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: M 22 HIS cc_start: 0.6922 (OUTLIER) cc_final: 0.6079 (t-90) REVERT: O 26 LEU cc_start: 0.7881 (tp) cc_final: 0.7601 (tt) REVERT: T 24 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: 3 29 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7154 (tt0) REVERT: 4 26 LEU cc_start: 0.7889 (tt) cc_final: 0.7659 (tp) REVERT: 9 29 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7272 (tm-30) REVERT: c 12 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8266 (mm) REVERT: k 12 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8325 (mm) REVERT: w 19 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8538 (mt) outliers start: 65 outliers final: 49 residues processed: 193 average time/residue: 0.1278 time to fit residues: 35.9717 Evaluate side-chains 200 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 N residue 25 ILE Chi-restraints excluded: chain O residue 20 SER 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 12 LEU Chi-restraints excluded: chain T residue 24 GLU Chi-restraints excluded: chain U residue 20 SER 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 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 18 ILE Chi-restraints excluded: chain 9 residue 25 ILE Chi-restraints excluded: chain c residue 12 LEU 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 12 LEU 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 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 19 LEU Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 11 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 22 HIS K 22 HIS d 22 HIS j 22 HIS l 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 = 0.4310 r_free = 0.4310 target = 0.191431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.169516 restraints weight = 18121.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.172190 restraints weight = 11849.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.173959 restraints weight = 9187.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.174761 restraints weight = 7859.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.175700 restraints weight = 7194.122| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2689 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= 0.173 Angle : 0.592 9.497 18360 Z= 0.301 Chirality : 0.041 0.228 2220 Planarity : 0.003 0.021 2400 Dihedral : 3.822 21.689 1920 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.92 % Allowed : 26.43 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.68 (0.17), residues: 1620 helix: 3.65 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 8 3 TYR 0.008 0.001 TYR u 15 HIS 0.011 0.001 HIS l 22 Details of bonding type rmsd covalent geometry : bond 0.00395 (13620) covalent geometry : angle 0.59224 (18360) hydrogen bonds : bond 0.04033 ( 1410) hydrogen bonds : angle 3.48937 ( 4230) ********************** 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 200 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 138 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 29 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7662 (tm-30) REVERT: O 26 LEU cc_start: 0.7896 (tp) cc_final: 0.7634 (tt) REVERT: T 24 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7875 (tm-30) REVERT: 4 26 LEU cc_start: 0.7934 (tt) cc_final: 0.7639 (tp) REVERT: 9 29 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7303 (tm-30) REVERT: c 12 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8285 (mm) REVERT: k 12 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8429 (mm) REVERT: p 24 GLU cc_start: 0.7209 (mp0) cc_final: 0.6793 (mp0) REVERT: w 19 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8678 (mt) outliers start: 62 outliers final: 51 residues processed: 179 average time/residue: 0.1326 time to fit residues: 33.6734 Evaluate side-chains 189 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 134 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain G residue 22 HIS 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 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 12 LEU Chi-restraints excluded: chain T residue 24 GLU Chi-restraints excluded: chain U residue 20 SER 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 11 ILE Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain 0 residue 11 ILE 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 18 ILE Chi-restraints excluded: chain 8 residue 24 GLU Chi-restraints excluded: chain 9 residue 25 ILE Chi-restraints excluded: chain c residue 12 LEU 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 12 LEU 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 o residue 25 ILE 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 19 LEU Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 11 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 22 HIS K 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 = 0.3775 r_free = 0.3775 target = 0.145665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124719 restraints weight = 17648.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125235 restraints weight = 16843.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125563 restraints weight = 14466.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125674 restraints weight = 13857.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125858 restraints weight = 13684.257| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13620 Z= 0.172 Angle : 0.602 12.100 18360 Z= 0.304 Chirality : 0.041 0.240 2220 Planarity : 0.003 0.021 2400 Dihedral : 3.842 21.637 1920 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.00 % Allowed : 26.43 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.61 (0.17), residues: 1620 helix: 3.61 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 8 3 TYR 0.008 0.001 TYR w 15 HIS 0.006 0.001 HIS G 22 Details of bonding type rmsd covalent geometry : bond 0.00392 (13620) covalent geometry : angle 0.60159 (18360) hydrogen bonds : bond 0.04065 ( 1410) hydrogen bonds : angle 3.50951 ( 4230) =============================================================================== Job complete usr+sys time: 1822.41 seconds wall clock time: 32 minutes 20.85 seconds (1940.85 seconds total)