Starting phenix.real_space_refine on Sun Dec 10 05:16:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx4_24724/12_2023/7rx4_24724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx4_24724/12_2023/7rx4_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_24724/12_2023/7rx4_24724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx4_24724/12_2023/7rx4_24724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx4_24724/12_2023/7rx4_24724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx4_24724/12_2023/7rx4_24724.pdb" } 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-1.21rc1-5172/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: 7.09, per 1000 atoms: 0.52 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: 6.15 Conformation dependent library (CDL) restraints added in 2.2 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: 0.96 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: 4.21 Time building geometry restraints manager: 6.45 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: 5576 111.10 - 116.15: 3184 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 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 g 24 " pdb=" CB GLU g 24 " pdb=" CG GLU g 24 " ideal model delta sigma weight residual 114.10 117.85 -3.75 2.00e+00 2.50e-01 3.51e+00 angle pdb=" CA GLU Z 24 " pdb=" CB GLU Z 24 " pdb=" CG GLU Z 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: 6489 7.76 - 15.51: 891 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: 1432 0.025 - 0.050: 376 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: 9823 3.12 - 3.71: 22954 3.71 - 4.31: 27236 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.240 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 37.840 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.260 ------------------------------------------------------------------------------- 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 : 1.518 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.3070 time to fit residues: 71.9729 Evaluate side-chains 135 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 22 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13620 Z= 0.163 Angle : 0.468 11.503 18360 Z= 0.237 Chirality : 0.037 0.191 2220 Planarity : 0.003 0.018 2400 Dihedral : 3.675 18.467 1920 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 7.86 % Favored : 89.37 % 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 0.002 0.000 HIS M 22 TYR 0.006 0.001 TYR u 15 ARG 0.003 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 189 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 154 time to evaluate : 1.613 Fit side-chains outliers start: 35 outliers final: 25 residues processed: 165 average time/residue: 0.3075 time to fit residues: 70.7709 Evaluate side-chains 167 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.566 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1257 time to fit residues: 8.1308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 22 HIS p 22 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1736 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= 0.211 Angle : 0.462 8.709 18360 Z= 0.246 Chirality : 0.039 0.212 2220 Planarity : 0.003 0.020 2400 Dihedral : 3.693 19.839 1920 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.67 % Allowed : 20.00 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 6.05 (0.17), residues: 1620 helix: 3.88 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Z 22 TYR 0.008 0.001 TYR u 15 ARG 0.004 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 189 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.516 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 175 average time/residue: 0.3068 time to fit residues: 74.3729 Evaluate side-chains 160 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.491 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1178 time to fit residues: 4.2055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 22 HIS b 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: 0.7665 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13620 Z= 0.175 Angle : 0.440 10.548 18360 Z= 0.231 Chirality : 0.036 0.152 2220 Planarity : 0.002 0.018 2400 Dihedral : 3.628 19.702 1920 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.62 % Allowed : 24.29 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.27 (0.17), residues: 1620 helix: 4.02 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS Z 22 TYR 0.006 0.001 TYR w 15 ARG 0.004 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 192 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 1.557 Fit side-chains outliers start: 33 outliers final: 27 residues processed: 177 average time/residue: 0.3089 time to fit residues: 76.2975 Evaluate side-chains 166 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1269 time to fit residues: 8.4091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 22 HIS n 22 HIS r 22 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13620 Z= 0.250 Angle : 0.507 9.318 18360 Z= 0.270 Chirality : 0.039 0.159 2220 Planarity : 0.003 0.021 2400 Dihedral : 3.801 20.874 1920 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.51 % Allowed : 27.06 % Favored : 71.43 % 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: 5.95 (0.17), residues: 1620 helix: 3.82 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS 3 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 177 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 1.464 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 165 average time/residue: 0.3141 time to fit residues: 71.5346 Evaluate side-chains 149 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.451 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1732 time to fit residues: 5.3143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 22 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13620 Z= 0.201 Angle : 0.478 10.608 18360 Z= 0.252 Chirality : 0.037 0.155 2220 Planarity : 0.002 0.019 2400 Dihedral : 3.735 20.451 1920 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.06 % Allowed : 27.54 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.12 (0.17), residues: 1620 helix: 3.92 (0.11), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS X 22 TYR 0.007 0.001 TYR u 15 ARG 0.004 0.000 ARG a 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 190 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 2.188 Fit side-chains outliers start: 26 outliers final: 23 residues processed: 172 average time/residue: 0.3173 time to fit residues: 76.9643 Evaluate side-chains 166 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.520 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1348 time to fit residues: 7.7753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 22 HIS f 22 HIS n 22 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13620 Z= 0.226 Angle : 0.507 10.832 18360 Z= 0.269 Chirality : 0.038 0.158 2220 Planarity : 0.003 0.020 2400 Dihedral : 3.811 21.226 1920 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.59 % Allowed : 27.86 % Favored : 70.56 % 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: 5.97 (0.17), residues: 1620 helix: 3.83 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS o 22 TYR 0.007 0.001 TYR u 15 ARG 0.004 0.000 ARG 8 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 183 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 1.475 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 173 average time/residue: 0.3129 time to fit residues: 76.0346 Evaluate side-chains 150 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.592 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1237 time to fit residues: 4.8818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 22 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13620 Z= 0.206 Angle : 0.509 11.176 18360 Z= 0.266 Chirality : 0.038 0.157 2220 Planarity : 0.003 0.020 2400 Dihedral : 3.771 21.075 1920 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.83 % Allowed : 28.89 % Favored : 69.29 % 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: 6.05 (0.17), residues: 1620 helix: 3.88 (0.10), residues: 1620 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS o 22 TYR 0.006 0.001 TYR w 15 ARG 0.004 0.000 ARG a 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 185 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.693 Fit side-chains outliers start: 23 outliers final: 17 residues processed: 168 average time/residue: 0.3255 time to fit residues: 77.1334 Evaluate side-chains 160 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1270 time to fit residues: 6.2395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 69 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2399 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= 0.193 Angle : 0.495 10.428 18360 Z= 0.261 Chirality : 0.037 0.156 2220 Planarity : 0.002 0.019 2400 Dihedral : 3.736 21.468 1920 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.56 % Allowed : 29.76 % 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: 6.07 (0.17), residues: 1620 helix: 3.89 (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 3 22 TYR 0.006 0.001 TYR w 15 ARG 0.004 0.000 ARG a 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 167 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 1.647 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 164 average time/residue: 0.3093 time to fit residues: 71.1378 Evaluate side-chains 152 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 1.640 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2210 time to fit residues: 4.1119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13620 Z= 0.206 Angle : 0.525 10.139 18360 Z= 0.273 Chirality : 0.038 0.159 2220 Planarity : 0.003 0.020 2400 Dihedral : 3.763 21.997 1920 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 30.48 % Favored : 68.73 % 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: 5.99 (0.17), residues: 1620 helix: 3.84 (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 3 22 TYR 0.007 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 168 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.505 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 162 average time/residue: 0.3114 time to fit residues: 70.2434 Evaluate side-chains 154 residues out of total 1260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 1.671 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1271 time to fit residues: 4.2126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 22 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.196426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.177208 restraints weight = 18085.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.178413 restraints weight = 12723.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.179000 restraints weight = 10484.758| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2497 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= 0.191 Angle : 0.508 9.978 18360 Z= 0.265 Chirality : 0.037 0.156 2220 Planarity : 0.002 0.020 2400 Dihedral : 3.721 21.583 1920 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.27 % Allowed : 30.00 % Favored : 68.73 % 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: 6.07 (0.17), residues: 1620 helix: 3.89 (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 5 22 TYR 0.006 0.001 TYR u 15 ARG 0.005 0.000 ARG 8 3 =============================================================================== Job complete usr+sys time: 2265.90 seconds wall clock time: 41 minutes 59.68 seconds (2519.68 seconds total)