Starting phenix.real_space_refine on Sun Jul 21 02:04:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx4_24724/07_2024/7rx4_24724.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx4_24724/07_2024/7rx4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx4_24724/07_2024/7rx4_24724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx4_24724/07_2024/7rx4_24724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx4_24724/07_2024/7rx4_24724.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx4_24724/07_2024/7rx4_24724.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 8460 2.51 5 N 2580 2.21 5 O 2520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13560 Number of models: 1 Model: "" Number of chains: 60 Chain: "B" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "C" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "D" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "F" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "G" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "H" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "K" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "L" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "M" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "N" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "O" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "P" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "Q" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "S" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "T" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "U" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "V" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "W" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "X" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "Y" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "Z" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "0" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "1" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "2" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "3" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "4" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "a" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "5" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "6" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "7" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "8" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "9" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "b" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "c" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "d" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "e" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "f" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "g" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "h" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "i" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "j" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "k" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "l" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "m" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "n" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "o" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "p" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "q" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "r" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "s" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "t" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "u" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "v" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "w" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "x" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Time building chain proxies: 7.94, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 5.78 Conformation dependent library (CDL) restraints added in 2.4 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3480 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 98.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU A 5 " --> pdb=" O GLN A 1 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU a 29 " --> pdb=" O ILE a 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU B 5 " --> pdb=" O GLN B 1 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 29 removed outlier: 3.935A pdb=" N GLU C 29 " --> pdb=" O ILE C 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU D 5 " --> pdb=" O GLN D 1 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU E 29 " --> pdb=" O ILE E 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 29 removed outlier: 3.778A pdb=" N LEU F 5 " --> pdb=" O GLN F 1 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU G 29 " --> pdb=" O ILE G 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU H 5 " --> pdb=" O GLN H 1 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU I 29 " --> pdb=" O ILE I 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 29 removed outlier: 3.776A pdb=" N LEU J 5 " --> pdb=" O GLN J 1 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU L 5 " --> pdb=" O GLN L 1 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU N 5 " --> pdb=" O GLN N 1 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 1 through 29 removed outlier: 3.778A pdb=" N LEU P 5 " --> pdb=" O GLN P 1 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU Q 29 " --> pdb=" O ILE Q 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 1 through 29 removed outlier: 3.776A pdb=" N LEU R 5 " --> pdb=" O GLN R 1 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 29 removed outlier: 3.935A pdb=" N GLU S 29 " --> pdb=" O ILE S 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 1 through 29 removed outlier: 3.776A pdb=" N LEU T 5 " --> pdb=" O GLN T 1 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU U 29 " --> pdb=" O ILE U 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU V 5 " --> pdb=" O GLN V 1 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU W 29 " --> pdb=" O ILE W 25 " (cutoff:3.500A) Processing helix chain 'X' and resid 1 through 29 removed outlier: 3.778A pdb=" N LEU X 5 " --> pdb=" O GLN X 1 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU Y 29 " --> pdb=" O ILE Y 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU Z 5 " --> pdb=" O GLN Z 1 " (cutoff:3.500A) Processing helix chain '0' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU 0 29 " --> pdb=" O ILE 0 25 " (cutoff:3.500A) Processing helix chain '1' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU 1 5 " --> pdb=" O GLN 1 1 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU 2 29 " --> pdb=" O ILE 2 25 " (cutoff:3.500A) Processing helix chain '3' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU 3 5 " --> pdb=" O GLN 3 1 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU 4 29 " --> pdb=" O ILE 4 25 " (cutoff:3.500A) Processing helix chain '5' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU 5 5 " --> pdb=" O GLN 5 1 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 29 removed outlier: 3.935A pdb=" N GLU 6 29 " --> pdb=" O ILE 6 25 " (cutoff:3.500A) Processing helix chain '7' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU 7 5 " --> pdb=" O GLN 7 1 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU 8 29 " --> pdb=" O ILE 8 25 " (cutoff:3.500A) Processing helix chain '9' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU 9 5 " --> pdb=" O GLN 9 1 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU b 29 " --> pdb=" O ILE b 25 " (cutoff:3.500A) Processing helix chain 'c' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU c 5 " --> pdb=" O GLN c 1 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU d 29 " --> pdb=" O ILE d 25 " (cutoff:3.500A) Processing helix chain 'e' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU e 5 " --> pdb=" O GLN e 1 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU f 29 " --> pdb=" O ILE f 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU g 5 " --> pdb=" O GLN g 1 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 29 removed outlier: 3.937A pdb=" N GLU h 29 " --> pdb=" O ILE h 25 " (cutoff:3.500A) Processing helix chain 'i' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU i 5 " --> pdb=" O GLN i 1 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) Processing helix chain 'k' and resid 1 through 29 removed outlier: 3.778A pdb=" N LEU k 5 " --> pdb=" O GLN k 1 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU l 29 " --> pdb=" O ILE l 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU m 5 " --> pdb=" O GLN m 1 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU n 29 " --> pdb=" O ILE n 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU o 5 " --> pdb=" O GLN o 1 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU p 29 " --> pdb=" O ILE p 25 " (cutoff:3.500A) Processing helix chain 'q' and resid 1 through 29 removed outlier: 3.776A pdb=" N LEU q 5 " --> pdb=" O GLN q 1 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU r 29 " --> pdb=" O ILE r 25 " (cutoff:3.500A) Processing helix chain 's' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU s 5 " --> pdb=" O GLN s 1 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU t 29 " --> pdb=" O ILE t 25 " (cutoff:3.500A) Processing helix chain 'u' and resid 1 through 29 removed outlier: 3.776A pdb=" N LEU u 5 " --> pdb=" O GLN u 1 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU v 29 " --> pdb=" O ILE v 25 " (cutoff:3.500A) Processing helix chain 'w' and resid 1 through 29 removed outlier: 3.777A pdb=" N LEU w 5 " --> pdb=" O GLN w 1 " (cutoff:3.500A) Processing helix chain 'x' and resid 2 through 29 removed outlier: 3.936A pdb=" N GLU x 29 " --> pdb=" O ILE x 25 " (cutoff:3.500A) 1410 hydrogen bonds defined for protein. 4230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.61 Time building geometry restraints manager: 6.12 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: 106.05 - 111.10: 5578 111.10 - 116.15: 3182 116.15 - 121.20: 6715 121.20 - 126.25: 2825 126.25 - 131.30: 60 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 2.520 nonbonded pdb=" O GLU 3 29 " pdb=" N ALA o 2 " model vdw 1.929 2.520 nonbonded pdb=" O GLU J 29 " pdb=" N ALA A 2 " model vdw 1.929 2.520 nonbonded pdb=" O GLU T 29 " pdb=" N ALA e 2 " model vdw 1.929 2.520 nonbonded pdb=" O GLU H 29 " pdb=" N ALA 3 2 " model vdw 1.929 2.520 ... (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 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.490 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.520 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.550 ------------------------------------------------------------------------------- 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= 0.194 Angle : 0.492 3.771 18360 Z= 0.286 Chirality : 0.039 0.125 2220 Planarity : 0.003 0.018 2400 Dihedral : 13.385 38.781 5040 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.26 (0.16), residues: 1620 helix: 3.98 (0.10), residues: 1560 sheet: None (None), residues: 0 loop : 5.70 (0.70), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS e 22 TYR 0.002 0.001 TYR M 15 ARG 0.005 0.000 ARG O 3 *********************** 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 fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.777 Fit side-chains REVERT: C 20 SER cc_start: 0.8191 (p) cc_final: 0.7975 (p) REVERT: M 22 HIS cc_start: 0.6713 (m170) cc_final: 0.5934 (t-90) REVERT: 4 26 LEU cc_start: 0.7705 (tp) cc_final: 0.7491 (tt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.3036 time to fit residues: 71.0630 Evaluate side-chains 136 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13620 Z= 0.170 Angle : 0.464 11.604 18360 Z= 0.237 Chirality : 0.037 0.210 2220 Planarity : 0.003 0.018 2400 Dihedral : 3.677 18.622 1920 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.86 % Allowed : 7.38 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.14 (0.17), residues: 1620 helix: 3.94 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS o 22 TYR 0.006 0.001 TYR u 15 ARG 0.002 0.000 ARG t 3 *********************** 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 196 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 160 time to evaluate : 1.398 Fit side-chains REVERT: C 20 SER cc_start: 0.8313 (p) cc_final: 0.7987 (p) REVERT: E 22 HIS cc_start: 0.6752 (m170) cc_final: 0.6352 (t-90) REVERT: M 22 HIS cc_start: 0.7000 (OUTLIER) cc_final: 0.6240 (t-90) REVERT: Q 22 HIS cc_start: 0.6610 (m170) cc_final: 0.6175 (t-90) REVERT: S 22 HIS cc_start: 0.6748 (m170) cc_final: 0.6230 (t-90) REVERT: a 22 HIS cc_start: 0.6580 (m170) cc_final: 0.6192 (t-90) REVERT: 6 22 HIS cc_start: 0.7065 (m170) cc_final: 0.6272 (t-90) outliers start: 36 outliers final: 24 residues processed: 170 average time/residue: 0.3188 time to fit residues: 75.2984 Evaluate side-chains 177 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 152 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 R residue 25 ILE Chi-restraints excluded: chain S residue 20 SER Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain V 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 b residue 20 SER 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 t residue 20 SER 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 60 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 22 HIS O 22 HIS 2 22 HIS a 22 HIS b 22 HIS p 22 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13620 Z= 0.208 Angle : 0.464 9.073 18360 Z= 0.243 Chirality : 0.038 0.210 2220 Planarity : 0.003 0.018 2400 Dihedral : 3.665 19.261 1920 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.73 % Allowed : 18.33 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.15 (0.17), residues: 1620 helix: 3.94 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS 2 22 TYR 0.007 0.001 TYR u 15 ARG 0.003 0.000 ARG 8 3 *********************** 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 209 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 162 time to evaluate : 1.453 Fit side-chains REVERT: E 22 HIS cc_start: 0.6935 (m170) cc_final: 0.6521 (t-90) REVERT: I 24 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: M 24 GLU cc_start: 0.7305 (mp0) cc_final: 0.7103 (mp0) REVERT: O 26 LEU cc_start: 0.7906 (tp) cc_final: 0.7619 (tt) REVERT: Q 22 HIS cc_start: 0.6687 (m170) cc_final: 0.6135 (t-90) REVERT: S 22 HIS cc_start: 0.6990 (m170) cc_final: 0.6329 (t-90) REVERT: T 24 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7883 (tm-30) REVERT: X 29 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7210 (tm-30) REVERT: Z 29 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7215 (tm-30) REVERT: 6 22 HIS cc_start: 0.7091 (m170) cc_final: 0.6246 (t-90) REVERT: 9 29 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6916 (tm-30) outliers start: 47 outliers final: 32 residues processed: 180 average time/residue: 0.2952 time to fit residues: 74.0168 Evaluate side-chains 181 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE 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 S residue 20 SER 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 9 residue 29 GLU Chi-restraints excluded: chain b residue 22 HIS 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 j residue 20 SER Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain t residue 20 SER Chi-restraints excluded: chain u residue 25 ILE Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 20 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 22 HIS U 22 HIS f 22 HIS j 22 HIS l 22 HIS n 22 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13620 Z= 0.210 Angle : 0.460 10.341 18360 Z= 0.243 Chirality : 0.038 0.166 2220 Planarity : 0.002 0.018 2400 Dihedral : 3.694 19.815 1920 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.89 % Allowed : 23.65 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.18 (0.17), residues: 1620 helix: 3.96 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS b 22 TYR 0.007 0.001 TYR u 15 ARG 0.003 0.000 ARG 8 3 *********************** 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 206 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 157 time to evaluate : 1.487 Fit side-chains REVERT: B 29 GLU cc_start: 0.7841 (tt0) cc_final: 0.7486 (tm-30) REVERT: M 22 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6251 (t-90) REVERT: O 26 LEU cc_start: 0.7888 (tp) cc_final: 0.7676 (tt) REVERT: Q 22 HIS cc_start: 0.6738 (m170) cc_final: 0.6162 (t-90) REVERT: S 22 HIS cc_start: 0.7033 (m170) cc_final: 0.6356 (t-90) REVERT: T 24 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7857 (tm-30) REVERT: X 29 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7157 (tm-30) REVERT: Z 29 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7375 (tm-30) REVERT: 6 22 HIS cc_start: 0.7092 (m170) cc_final: 0.6288 (t-90) outliers start: 49 outliers final: 39 residues processed: 182 average time/residue: 0.2958 time to fit residues: 75.1110 Evaluate side-chains 182 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain E residue 22 HIS Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 24 GLU 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 S residue 20 SER Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain U residue 22 HIS Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain 1 residue 25 ILE Chi-restraints excluded: chain 2 residue 22 HIS Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 9 residue 25 ILE Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain e residue 25 ILE Chi-restraints excluded: chain g residue 25 ILE Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain j residue 22 HIS Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain l residue 22 HIS Chi-restraints excluded: chain m residue 25 ILE Chi-restraints excluded: chain n residue 22 HIS Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain p residue 22 HIS Chi-restraints excluded: chain q residue 25 ILE Chi-restraints excluded: chain u residue 25 ILE Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 20 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 22 HIS d 22 HIS j 22 HIS l 22 HIS n 22 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13620 Z= 0.233 Angle : 0.488 10.046 18360 Z= 0.257 Chirality : 0.039 0.248 2220 Planarity : 0.003 0.019 2400 Dihedral : 3.751 20.257 1920 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.29 % Allowed : 26.03 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.10 (0.17), residues: 1620 helix: 3.91 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS j 22 TYR 0.008 0.001 TYR u 15 ARG 0.004 0.000 ARG 8 3 *********************** 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 207 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 153 time to evaluate : 1.426 Fit side-chains REVERT: E 22 HIS cc_start: 0.6978 (m170) cc_final: 0.6430 (t-90) REVERT: M 22 HIS cc_start: 0.7022 (OUTLIER) cc_final: 0.6255 (t-90) REVERT: O 26 LEU cc_start: 0.7922 (tp) cc_final: 0.7683 (tt) REVERT: Q 22 HIS cc_start: 0.6791 (m170) cc_final: 0.6220 (t-90) REVERT: S 22 HIS cc_start: 0.7067 (m170) cc_final: 0.6353 (t-90) REVERT: T 24 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7878 (tm-30) REVERT: 3 29 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7338 (tt0) outliers start: 54 outliers final: 44 residues processed: 182 average time/residue: 0.2847 time to fit residues: 72.7240 Evaluate side-chains 186 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 141 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain J residue 25 ILE 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 22 HIS Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 20 SER Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain Z residue 25 ILE Chi-restraints excluded: chain 1 residue 25 ILE Chi-restraints excluded: chain 2 residue 22 HIS Chi-restraints excluded: chain 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 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 t residue 11 ILE Chi-restraints excluded: chain t residue 20 SER Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 20 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 22 HIS j 22 HIS l 22 HIS r 22 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13620 Z= 0.319 Angle : 0.590 10.396 18360 Z= 0.308 Chirality : 0.042 0.162 2220 Planarity : 0.003 0.020 2400 Dihedral : 3.972 20.435 1920 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.60 % Allowed : 26.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.64 (0.17), residues: 1620 helix: 3.63 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS a 22 TYR 0.010 0.001 TYR u 15 ARG 0.004 0.000 ARG 8 3 *********************** 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 204 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 146 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: B 29 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7747 (tt0) REVERT: O 26 LEU cc_start: 0.8024 (tp) cc_final: 0.7799 (tt) REVERT: Q 22 HIS cc_start: 0.6916 (m170) cc_final: 0.6264 (t-90) REVERT: T 24 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: V 24 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8135 (tm-30) REVERT: W 24 GLU cc_start: 0.7690 (mp0) cc_final: 0.7410 (mp0) REVERT: 3 29 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7616 (tm-30) outliers start: 58 outliers final: 45 residues processed: 181 average time/residue: 0.2800 time to fit residues: 71.0268 Evaluate side-chains 177 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 131 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain J residue 25 ILE 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 O residue 22 HIS Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 20 SER Chi-restraints excluded: chain T residue 24 GLU Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain 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 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 g residue 25 ILE Chi-restraints excluded: chain h residue 11 ILE Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 22 HIS Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 22 HIS Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain p residue 22 HIS Chi-restraints excluded: chain q residue 25 ILE Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 20 SER Chi-restraints excluded: chain v residue 11 ILE Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 18 ILE Chi-restraints excluded: chain x residue 20 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 22 HIS d 22 HIS j 22 HIS l 22 HIS n 22 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13620 Z= 0.173 Angle : 0.459 8.731 18360 Z= 0.241 Chirality : 0.036 0.147 2220 Planarity : 0.002 0.019 2400 Dihedral : 3.718 20.792 1920 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.05 % Allowed : 27.46 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.17 (0.17), residues: 1620 helix: 3.96 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS j 22 TYR 0.005 0.001 TYR g 15 ARG 0.004 0.000 ARG a 3 *********************** 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 221 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 170 time to evaluate : 1.503 Fit side-chains REVERT: B 29 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7625 (tt0) REVERT: D 29 GLU cc_start: 0.7605 (tt0) cc_final: 0.7197 (tm-30) REVERT: E 24 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: M 22 HIS cc_start: 0.6967 (OUTLIER) cc_final: 0.6201 (t-90) REVERT: O 26 LEU cc_start: 0.7970 (tp) cc_final: 0.7745 (tt) REVERT: Q 22 HIS cc_start: 0.6742 (m170) cc_final: 0.6172 (t-90) REVERT: T 24 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: V 24 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8073 (tm-30) REVERT: W 24 GLU cc_start: 0.7768 (mp0) cc_final: 0.7502 (mp0) REVERT: 3 29 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7485 (tm-30) REVERT: 4 26 LEU cc_start: 0.7928 (tt) cc_final: 0.7675 (tp) outliers start: 51 outliers final: 43 residues processed: 194 average time/residue: 0.2759 time to fit residues: 75.8171 Evaluate side-chains 198 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 152 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain J residue 25 ILE 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 O residue 22 HIS Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain T residue 24 GLU Chi-restraints excluded: chain U residue 22 HIS Chi-restraints excluded: chain V residue 25 ILE Chi-restraints excluded: chain W residue 20 SER Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain 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 A residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 9 residue 25 ILE Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain d residue 22 HIS Chi-restraints excluded: chain e residue 25 ILE Chi-restraints excluded: chain f residue 18 ILE Chi-restraints excluded: chain g residue 25 ILE Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 22 HIS Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 22 HIS Chi-restraints excluded: chain n residue 22 HIS Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain p residue 22 HIS Chi-restraints excluded: chain q residue 25 ILE Chi-restraints excluded: chain r residue 22 HIS Chi-restraints excluded: chain u residue 25 ILE Chi-restraints excluded: chain v residue 11 ILE Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 11 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 v 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13620 Z= 0.173 Angle : 0.482 12.028 18360 Z= 0.250 Chirality : 0.036 0.154 2220 Planarity : 0.002 0.019 2400 Dihedral : 3.686 21.215 1920 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.44 % Allowed : 28.33 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.19 (0.17), residues: 1620 helix: 3.97 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS l 22 TYR 0.005 0.001 TYR u 15 ARG 0.004 0.000 ARG 8 3 *********************** 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 222 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 166 time to evaluate : 1.428 Fit side-chains REVERT: E 24 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: M 22 HIS cc_start: 0.6994 (OUTLIER) cc_final: 0.6213 (t-90) REVERT: N 29 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7141 (tt0) REVERT: O 26 LEU cc_start: 0.7848 (tp) cc_final: 0.7623 (tt) REVERT: Q 22 HIS cc_start: 0.6790 (m170) cc_final: 0.6233 (t-90) REVERT: T 24 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: V 24 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8092 (tm-30) REVERT: c 12 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8242 (mm) REVERT: p 24 GLU cc_start: 0.7385 (mp0) cc_final: 0.6996 (mp0) outliers start: 56 outliers final: 46 residues processed: 193 average time/residue: 0.2700 time to fit residues: 73.9423 Evaluate side-chains 203 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 153 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain G residue 22 HIS Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain J residue 25 ILE 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 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 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 g residue 25 ILE Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 22 HIS Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 22 HIS Chi-restraints excluded: chain n residue 22 HIS Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain p residue 22 HIS Chi-restraints excluded: chain q residue 25 ILE Chi-restraints excluded: chain r residue 22 HIS Chi-restraints excluded: chain s residue 25 ILE Chi-restraints excluded: chain u residue 25 ILE Chi-restraints excluded: chain v residue 11 ILE Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 11 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13620 Z= 0.187 Angle : 0.518 11.986 18360 Z= 0.262 Chirality : 0.036 0.150 2220 Planarity : 0.002 0.019 2400 Dihedral : 3.677 20.967 1920 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.52 % Allowed : 28.02 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.16 (0.17), residues: 1620 helix: 3.95 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS n 22 TYR 0.006 0.001 TYR u 15 ARG 0.004 0.000 ARG 8 3 *********************** 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 216 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 159 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7574 (tt0) REVERT: E 24 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: M 22 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.6254 (t-90) REVERT: N 29 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7274 (tt0) REVERT: O 26 LEU cc_start: 0.7841 (tp) cc_final: 0.7606 (tt) REVERT: Q 22 HIS cc_start: 0.6718 (m170) cc_final: 0.6145 (t-90) REVERT: T 24 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: V 24 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8150 (tm-30) REVERT: W 24 GLU cc_start: 0.7479 (mp0) cc_final: 0.7224 (mp0) REVERT: 4 26 LEU cc_start: 0.7771 (tp) cc_final: 0.7552 (tt) REVERT: c 12 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8251 (mm) outliers start: 57 outliers final: 48 residues processed: 187 average time/residue: 0.2746 time to fit residues: 72.5805 Evaluate side-chains 204 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 152 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 20 SER Chi-restraints excluded: chain J residue 25 ILE 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 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 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 3 residue 25 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 8 residue 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 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 22 HIS Chi-restraints excluded: chain l residue 24 GLU 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 u residue 25 ILE Chi-restraints excluded: chain v residue 11 ILE Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 11 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.0010 chunk 79 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 22 HIS G 22 HIS O 22 HIS 0 22 HIS d 22 HIS j 22 HIS l 22 HIS u 17 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2420 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= 0.178 Angle : 0.515 11.706 18360 Z= 0.261 Chirality : 0.036 0.177 2220 Planarity : 0.002 0.020 2400 Dihedral : 3.653 21.466 1920 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.29 % Allowed : 28.17 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.18 (0.17), residues: 1620 helix: 3.96 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.000 HIS l 22 TYR 0.005 0.001 TYR u 15 ARG 0.005 0.000 ARG 8 3 ********************** 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 212 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 158 time to evaluate : 1.485 Fit side-chains revert: symmetry clash REVERT: B 29 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7586 (tt0) REVERT: E 24 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: G 24 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7636 (tp30) REVERT: M 22 HIS cc_start: 0.6990 (OUTLIER) cc_final: 0.6228 (t-90) REVERT: N 29 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7332 (tt0) REVERT: O 26 LEU cc_start: 0.7803 (tp) cc_final: 0.7560 (tt) REVERT: Q 22 HIS cc_start: 0.6714 (m170) cc_final: 0.6133 (t-90) REVERT: T 24 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: V 24 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8156 (tm-30) REVERT: W 24 GLU cc_start: 0.7634 (mp0) cc_final: 0.7359 (mp0) REVERT: 7 24 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7832 (tm-30) REVERT: c 12 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8242 (mm) REVERT: p 24 GLU cc_start: 0.7318 (mp0) cc_final: 0.6906 (mp0) outliers start: 54 outliers final: 46 residues processed: 184 average time/residue: 0.2840 time to fit residues: 73.9021 Evaluate side-chains 203 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 152 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 HIS 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 20 SER Chi-restraints excluded: chain J residue 25 ILE 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 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 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 3 residue 25 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain 5 residue 25 ILE Chi-restraints excluded: chain 7 residue 25 ILE Chi-restraints excluded: chain 8 residue 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 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 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 u residue 25 ILE Chi-restraints excluded: chain v residue 11 ILE Chi-restraints excluded: chain w residue 25 ILE Chi-restraints excluded: chain x residue 11 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.193090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.174855 restraints weight = 17885.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.176437 restraints weight = 13198.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.178585 restraints weight = 10832.333| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2474 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= 0.203 Angle : 0.545 11.619 18360 Z= 0.272 Chirality : 0.037 0.166 2220 Planarity : 0.003 0.021 2400 Dihedral : 3.670 21.489 1920 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.21 % Allowed : 28.41 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.16 (0.17), residues: 1620 helix: 3.95 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS j 22 TYR 0.006 0.001 TYR u 15 ARG 0.005 0.000 ARG 8 3 =============================================================================== Job complete usr+sys time: 2301.49 seconds wall clock time: 42 minutes 17.70 seconds (2537.70 seconds total)