Starting phenix.real_space_refine on Sat Mar 16 11:23:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl1_21815/03_2024/6wl1_21815.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl1_21815/03_2024/6wl1_21815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl1_21815/03_2024/6wl1_21815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl1_21815/03_2024/6wl1_21815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl1_21815/03_2024/6wl1_21815.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl1_21815/03_2024/6wl1_21815.pdb" } resolution = 4.0 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= -0.000 sd= 0.000 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 9308 2.51 5 N 2600 2.21 5 O 2704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14612 Number of models: 1 Model: "" Number of chains: 52 Chain: "A" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "B" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "C" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "D" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "E" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "F" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "G" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "H" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "I" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "J" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "K" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "L" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "M" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "N" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "O" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "P" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "Q" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "R" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "S" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "T" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "U" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "V" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "W" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "X" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "Y" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "Z" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "a" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "b" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "c" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "d" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "e" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "f" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "g" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "h" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "i" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "j" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "k" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "l" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "m" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "n" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "o" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "p" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "q" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "r" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "s" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "t" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "u" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "v" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "w" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "x" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "y" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "z" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Time building chain proxies: 7.52, per 1000 atoms: 0.51 Number of scatterers: 14612 At special positions: 0 Unit cell: (94.34, 94.34, 160.06, 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 2704 8.00 N 2600 7.00 C 9308 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: 5.37 Conformation dependent library (CDL) restraints added in 2.4 seconds 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 97.3% 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 36 removed outlier: 3.810A pdb=" N LEU A 5 " --> pdb=" O GLN A 1 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN F 36 " --> pdb=" O ILE F 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN I 36 " --> pdb=" O ILE I 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN J 36 " --> pdb=" O ILE J 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN K 36 " --> pdb=" O ILE K 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN L 36 " --> pdb=" O ILE L 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN M 36 " --> pdb=" O ILE M 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN N 36 " --> pdb=" O ILE N 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN O 36 " --> pdb=" O ILE O 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN P 36 " --> pdb=" O ILE P 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN Q 36 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 36 removed outlier: 3.603A pdb=" N GLN S 36 " --> pdb=" O ILE S 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN T 36 " --> pdb=" O ILE T 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN U 36 " --> pdb=" O ILE U 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN V 36 " --> pdb=" O ILE V 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN W 36 " --> pdb=" O ILE W 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN X 36 " --> pdb=" O ILE X 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN Y 36 " --> pdb=" O ILE Y 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN Z 36 " --> pdb=" O ILE Z 32 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN a 36 " --> pdb=" O ILE a 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN b 36 " --> pdb=" O ILE b 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN c 36 " --> pdb=" O ILE c 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN d 36 " --> pdb=" O ILE d 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN f 36 " --> pdb=" O ILE f 32 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN g 36 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN i 36 " --> pdb=" O ILE i 32 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN j 36 " --> pdb=" O ILE j 32 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN k 36 " --> pdb=" O ILE k 32 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN l 36 " --> pdb=" O ILE l 32 " (cutoff:3.500A) Processing helix chain 'm' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN m 36 " --> pdb=" O ILE m 32 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN n 36 " --> pdb=" O ILE n 32 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN o 36 " --> pdb=" O ILE o 32 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN p 36 " --> pdb=" O ILE p 32 " (cutoff:3.500A) Processing helix chain 'q' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN q 36 " --> pdb=" O ILE q 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN r 36 " --> pdb=" O ILE r 32 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN s 36 " --> pdb=" O ILE s 32 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN t 36 " --> pdb=" O ILE t 32 " (cutoff:3.500A) Processing helix chain 'u' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN u 36 " --> pdb=" O ILE u 32 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 36 removed outlier: 3.601A pdb=" N GLN v 36 " --> pdb=" O ILE v 32 " (cutoff:3.500A) Processing helix chain 'w' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN w 36 " --> pdb=" O ILE w 32 " (cutoff:3.500A) Processing helix chain 'x' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN x 36 " --> pdb=" O ILE x 32 " (cutoff:3.500A) Processing helix chain 'y' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN y 36 " --> pdb=" O ILE y 32 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 36 removed outlier: 3.602A pdb=" N GLN z 36 " --> pdb=" O ILE z 32 " (cutoff:3.500A) 1560 hydrogen bonds defined for protein. 4680 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: 4.48 Time building geometry restraints manager: 5.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 2652 1.29 - 1.35: 2392 1.35 - 1.41: 520 1.41 - 1.48: 2028 1.48 - 1.54: 7072 Bond restraints: 14664 Sorted by residual: bond pdb=" CB ARG S 6 " pdb=" CG ARG S 6 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.83e+00 bond pdb=" CB ARG i 6 " pdb=" CG ARG i 6 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.82e+00 bond pdb=" CB ARG C 6 " pdb=" CG ARG C 6 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB ARG z 6 " pdb=" CG ARG z 6 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB ARG X 6 " pdb=" CG ARG X 6 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 ... (remaining 14659 not shown) Histogram of bond angle deviations from ideal: 106.12 - 111.21: 5478 111.21 - 116.29: 4454 116.29 - 121.37: 6916 121.37 - 126.46: 2756 126.46 - 131.54: 52 Bond angle restraints: 19656 Sorted by residual: angle pdb=" N LEU u 5 " pdb=" CA LEU u 5 " pdb=" CB LEU u 5 " ideal model delta sigma weight residual 110.16 107.46 2.70 1.48e+00 4.57e-01 3.32e+00 angle pdb=" N LEU F 5 " pdb=" CA LEU F 5 " pdb=" CB LEU F 5 " ideal model delta sigma weight residual 110.16 107.47 2.69 1.48e+00 4.57e-01 3.31e+00 angle pdb=" N LEU k 5 " pdb=" CA LEU k 5 " pdb=" CB LEU k 5 " ideal model delta sigma weight residual 110.16 107.49 2.67 1.48e+00 4.57e-01 3.26e+00 angle pdb=" N LEU D 5 " pdb=" CA LEU D 5 " pdb=" CB LEU D 5 " ideal model delta sigma weight residual 110.16 107.49 2.67 1.48e+00 4.57e-01 3.26e+00 angle pdb=" N LEU V 5 " pdb=" CA LEU V 5 " pdb=" CB LEU V 5 " ideal model delta sigma weight residual 110.16 107.49 2.67 1.48e+00 4.57e-01 3.24e+00 ... (remaining 19651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.52: 7015 5.52 - 11.04: 1617 11.04 - 16.56: 520 16.56 - 22.08: 52 22.08 - 27.60: 156 Dihedral angle restraints: 9360 sinusoidal: 3744 harmonic: 5616 Sorted by residual: dihedral pdb=" CA ALA P 28 " pdb=" C ALA P 28 " pdb=" N HIS P 29 " pdb=" CA HIS P 29 " ideal model delta harmonic sigma weight residual 180.00 169.45 10.55 0 5.00e+00 4.00e-02 4.45e+00 dihedral pdb=" CA ALA Y 28 " pdb=" C ALA Y 28 " pdb=" N HIS Y 29 " pdb=" CA HIS Y 29 " ideal model delta harmonic sigma weight residual 180.00 169.45 10.55 0 5.00e+00 4.00e-02 4.45e+00 dihedral pdb=" CA ALA X 28 " pdb=" C ALA X 28 " pdb=" N HIS X 29 " pdb=" CA HIS X 29 " ideal model delta harmonic sigma weight residual 180.00 169.46 10.54 0 5.00e+00 4.00e-02 4.45e+00 ... (remaining 9357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1341 0.031 - 0.062: 666 0.062 - 0.093: 273 0.093 - 0.124: 60 0.124 - 0.156: 52 Chirality restraints: 2392 Sorted by residual: chirality pdb=" CG LEU F 5 " pdb=" CB LEU F 5 " pdb=" CD1 LEU F 5 " pdb=" CD2 LEU F 5 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CG LEU q 5 " pdb=" CB LEU q 5 " pdb=" CD1 LEU q 5 " pdb=" CD2 LEU q 5 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CG LEU B 5 " pdb=" CB LEU B 5 " pdb=" CD1 LEU B 5 " pdb=" CD2 LEU B 5 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 2389 not shown) Planarity restraints: 2496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 5 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C LEU C 5 " 0.025 2.00e-02 2.50e+03 pdb=" O LEU C 5 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG C 6 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU f 5 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C LEU f 5 " 0.025 2.00e-02 2.50e+03 pdb=" O LEU f 5 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG f 6 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU N 5 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C LEU N 5 " 0.025 2.00e-02 2.50e+03 pdb=" O LEU N 5 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG N 6 " -0.008 2.00e-02 2.50e+03 ... (remaining 2493 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 4880 2.91 - 3.41: 14842 3.41 - 3.91: 23752 3.91 - 4.40: 26056 4.40 - 4.90: 43163 Nonbonded interactions: 112693 Sorted by model distance: nonbonded pdb=" NH2 ARG o 6 " pdb=" OE2 GLU u 3 " model vdw 2.413 2.520 nonbonded pdb=" NH2 ARG e 6 " pdb=" OE2 GLU k 3 " model vdw 2.413 2.520 nonbonded pdb=" OE2 GLU Z 3 " pdb=" NH2 ARG f 6 " model vdw 2.414 2.520 nonbonded pdb=" OE2 GLU t 3 " pdb=" NH2 ARG z 6 " model vdw 2.414 2.520 nonbonded pdb=" NH2 ARG O 6 " pdb=" OE2 GLU U 3 " model vdw 2.414 2.520 ... (remaining 112688 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.570 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: 0.020 Extract box with map and model: 2.610 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 37.930 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.240 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.007 0.041 14664 Z= 0.455 Angle : 0.811 4.525 19656 Z= 0.462 Chirality : 0.047 0.156 2392 Planarity : 0.005 0.014 2496 Dihedral : 7.850 27.597 5616 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.17 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: -1.08 (0.15), residues: 1768 helix: -0.52 (0.09), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS V 29 TYR 0.016 0.004 TYR j 8 ARG 0.008 0.003 ARG p 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.741 Fit side-chains REVERT: a 22 GLN cc_start: 0.8624 (mt0) cc_final: 0.8422 (mt0) REVERT: w 33 LEU cc_start: 0.8609 (mt) cc_final: 0.8390 (mp) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.3298 time to fit residues: 167.7018 Evaluate side-chains 152 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 22 GLN J 22 GLN K 22 GLN Q 36 GLN X 29 HIS Y 22 GLN k 22 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 14664 Z= 0.164 Angle : 0.406 2.255 19656 Z= 0.232 Chirality : 0.033 0.093 2392 Planarity : 0.002 0.011 2496 Dihedral : 3.475 8.242 1976 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.55 % Allowed : 13.98 % Favored : 84.47 % 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: 4.12 (0.15), residues: 1768 helix: 2.69 (0.09), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS S 29 TYR 0.008 0.002 TYR u 8 ARG 0.003 0.001 ARG U 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 319 time to evaluate : 1.647 Fit side-chains REVERT: B 22 GLN cc_start: 0.8243 (mt0) cc_final: 0.7922 (tt0) REVERT: E 19 LEU cc_start: 0.9417 (mt) cc_final: 0.9188 (mp) REVERT: G 31 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8360 (mm-30) REVERT: L 26 LEU cc_start: 0.8765 (mt) cc_final: 0.8490 (mm) REVERT: N 22 GLN cc_start: 0.8186 (mt0) cc_final: 0.7849 (tt0) REVERT: V 22 GLN cc_start: 0.8464 (mt0) cc_final: 0.8258 (mt0) outliers start: 21 outliers final: 3 residues processed: 336 average time/residue: 0.2630 time to fit residues: 130.3339 Evaluate side-chains 237 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain z residue 33 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 22 GLN n 36 GLN r 36 GLN t 36 GLN x 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14664 Z= 0.264 Angle : 0.504 5.210 19656 Z= 0.268 Chirality : 0.037 0.105 2392 Planarity : 0.002 0.010 2496 Dihedral : 3.265 7.731 1976 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.25 % Allowed : 16.72 % Favored : 80.03 % 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: 5.15 (0.14), residues: 1768 helix: 3.33 (0.09), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS d 29 TYR 0.004 0.000 TYR l 8 ARG 0.004 0.001 ARG K 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 255 time to evaluate : 1.619 Fit side-chains REVERT: G 31 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8327 (mm-30) REVERT: N 22 GLN cc_start: 0.8211 (mt0) cc_final: 0.7888 (tt0) REVERT: d 22 GLN cc_start: 0.8135 (mt0) cc_final: 0.7893 (tt0) outliers start: 44 outliers final: 19 residues processed: 276 average time/residue: 0.2608 time to fit residues: 105.4417 Evaluate side-chains 251 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 232 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain U residue 18 ILE Chi-restraints excluded: chain V residue 26 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain b residue 24 LYS Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain j residue 32 ILE Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain o residue 32 ILE Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain t residue 36 GLN Chi-restraints excluded: chain u residue 19 LEU Chi-restraints excluded: chain z residue 18 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 22 GLN r 36 GLN t 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14664 Z= 0.203 Angle : 0.409 4.041 19656 Z= 0.224 Chirality : 0.034 0.104 2392 Planarity : 0.001 0.010 2496 Dihedral : 3.231 7.873 1976 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.44 % Allowed : 17.97 % Favored : 79.59 % 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 (0.14), residues: 1768 helix: 3.94 (0.08), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Q 29 TYR 0.002 0.000 TYR l 8 ARG 0.003 0.001 ARG s 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 262 time to evaluate : 1.491 Fit side-chains REVERT: A 22 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: B 22 GLN cc_start: 0.8221 (mt0) cc_final: 0.8000 (tt0) REVERT: G 31 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8322 (mm-30) REVERT: N 22 GLN cc_start: 0.8170 (mt0) cc_final: 0.7925 (tt0) REVERT: o 22 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: z 31 GLU cc_start: 0.8735 (tp30) cc_final: 0.8486 (tp30) outliers start: 33 outliers final: 22 residues processed: 282 average time/residue: 0.2545 time to fit residues: 108.6443 Evaluate side-chains 269 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 245 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain U residue 18 ILE Chi-restraints excluded: chain V residue 26 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain b residue 24 LYS Chi-restraints excluded: chain c residue 22 GLN Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain o residue 22 GLN Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 36 GLN Chi-restraints excluded: chain u residue 19 LEU Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain x residue 22 GLN Chi-restraints excluded: chain z residue 18 ILE Chi-restraints excluded: chain z residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN K 22 GLN r 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14664 Z= 0.154 Angle : 0.342 2.764 19656 Z= 0.194 Chirality : 0.032 0.099 2392 Planarity : 0.001 0.007 2496 Dihedral : 3.243 11.171 1976 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.29 % Allowed : 15.46 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 6.73 (0.14), residues: 1768 helix: 4.30 (0.08), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 29 TYR 0.002 0.000 TYR j 8 ARG 0.003 0.001 ARG Y 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 285 time to evaluate : 1.675 Fit side-chains REVERT: G 31 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8318 (mm-30) REVERT: i 22 GLN cc_start: 0.8300 (tt0) cc_final: 0.8053 (tt0) REVERT: z 31 GLU cc_start: 0.8662 (tp30) cc_final: 0.8454 (tp30) outliers start: 85 outliers final: 29 residues processed: 346 average time/residue: 0.2265 time to fit residues: 118.2479 Evaluate side-chains 285 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 256 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain U residue 18 ILE Chi-restraints excluded: chain V residue 26 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 32 ILE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain b residue 24 LYS Chi-restraints excluded: chain c residue 22 GLN Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain h residue 22 GLN Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain o residue 32 ILE Chi-restraints excluded: chain r residue 22 GLN Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain t residue 36 GLN Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain x residue 22 GLN Chi-restraints excluded: chain z residue 18 ILE Chi-restraints excluded: chain z residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 22 GLN M 36 GLN c 36 GLN t 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14664 Z= 0.287 Angle : 0.511 6.107 19656 Z= 0.267 Chirality : 0.037 0.151 2392 Planarity : 0.002 0.015 2496 Dihedral : 3.234 8.436 1976 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.47 % Allowed : 15.61 % Favored : 78.92 % 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 (0.14), residues: 1768 helix: 3.83 (0.09), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS Q 29 TYR 0.006 0.001 TYR l 8 ARG 0.005 0.001 ARG P 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 228 time to evaluate : 1.265 Fit side-chains REVERT: A 22 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: F 22 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: G 31 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8218 (mm-30) REVERT: P 31 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8391 (mm-30) REVERT: i 22 GLN cc_start: 0.8394 (tt0) cc_final: 0.8110 (tt0) REVERT: o 22 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8018 (tt0) outliers start: 74 outliers final: 40 residues processed: 275 average time/residue: 0.2234 time to fit residues: 94.1484 Evaluate side-chains 264 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 221 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain U residue 18 ILE Chi-restraints excluded: chain V residue 26 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 18 ILE Chi-restraints excluded: chain Y residue 32 ILE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 24 LYS Chi-restraints excluded: chain c residue 22 GLN Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain h residue 22 GLN Chi-restraints excluded: chain j residue 32 ILE Chi-restraints excluded: chain k residue 18 ILE Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain o residue 22 GLN Chi-restraints excluded: chain o residue 32 ILE Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 32 ILE Chi-restraints excluded: chain q residue 18 ILE Chi-restraints excluded: chain q residue 22 GLN Chi-restraints excluded: chain r residue 22 GLN Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain s residue 26 LEU Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 36 GLN Chi-restraints excluded: chain x residue 22 GLN Chi-restraints excluded: chain z residue 18 ILE Chi-restraints excluded: chain z residue 32 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14664 Z= 0.236 Angle : 0.446 4.593 19656 Z= 0.236 Chirality : 0.034 0.116 2392 Planarity : 0.001 0.012 2496 Dihedral : 3.238 8.569 1976 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.51 % Allowed : 15.98 % Favored : 79.51 % 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: 6.22 (0.14), residues: 1768 helix: 3.99 (0.09), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS Q 29 TYR 0.005 0.001 TYR l 8 ARG 0.004 0.001 ARG l 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 232 time to evaluate : 1.497 Fit side-chains REVERT: A 22 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: F 22 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: G 31 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8270 (mm-30) REVERT: i 22 GLN cc_start: 0.8344 (tt0) cc_final: 0.8107 (tt0) REVERT: m 31 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8400 (mm-30) REVERT: o 22 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: t 36 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8618 (mt0) outliers start: 61 outliers final: 46 residues processed: 264 average time/residue: 0.2234 time to fit residues: 90.2810 Evaluate side-chains 280 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 230 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 22 GLN Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain U residue 18 ILE Chi-restraints excluded: chain V residue 26 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 18 ILE Chi-restraints excluded: chain Y residue 32 ILE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain b residue 22 GLN Chi-restraints excluded: chain b residue 24 LYS Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain c residue 22 GLN Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain h residue 22 GLN Chi-restraints excluded: chain k residue 18 ILE Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain o residue 22 GLN Chi-restraints excluded: chain o residue 32 ILE Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 32 ILE Chi-restraints excluded: chain q residue 18 ILE Chi-restraints excluded: chain q residue 22 GLN Chi-restraints excluded: chain r residue 22 GLN Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain t residue 36 GLN Chi-restraints excluded: chain u residue 18 ILE Chi-restraints excluded: chain u residue 19 LEU Chi-restraints excluded: chain x residue 22 GLN Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain z residue 18 ILE Chi-restraints excluded: chain z residue 32 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14664 Z= 0.172 Angle : 0.376 3.930 19656 Z= 0.205 Chirality : 0.033 0.119 2392 Planarity : 0.001 0.008 2496 Dihedral : 3.244 8.353 1976 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.81 % Allowed : 16.20 % Favored : 78.99 % 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: 6.67 (0.14), residues: 1768 helix: 4.27 (0.08), residues: 1768 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 29 TYR 0.003 0.000 TYR b 8 ARG 0.003 0.001 ARG P 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 252 time to evaluate : 1.731 Fit side-chains REVERT: A 22 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: G 31 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8303 (mm-30) REVERT: i 22 GLN cc_start: 0.8300 (tt0) cc_final: 0.8081 (tt0) REVERT: o 22 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8080 (tt0) outliers start: 65 outliers final: 55 residues processed: 283 average time/residue: 0.2435 time to fit residues: 103.4444 Evaluate side-chains 304 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 247 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain U residue 18 ILE Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 26 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 18 ILE Chi-restraints excluded: chain Y residue 32 ILE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain b residue 22 GLN Chi-restraints excluded: chain b residue 24 LYS Chi-restraints excluded: chain c residue 22 GLN Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain h residue 22 GLN Chi-restraints excluded: chain h residue 26 LEU Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain j residue 32 ILE Chi-restraints excluded: chain l residue 26 LEU Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain o residue 22 GLN Chi-restraints excluded: chain o residue 32 ILE Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 32 ILE Chi-restraints excluded: chain q residue 18 ILE Chi-restraints excluded: chain r residue 22 GLN Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 36 GLN Chi-restraints excluded: chain u residue 18 ILE Chi-restraints excluded: chain u residue 19 LEU Chi-restraints excluded: chain w residue 26 LEU Chi-restraints excluded: chain x residue 22 GLN Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain z residue 18 ILE Chi-restraints excluded: chain z residue 32 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14664 Z= 0.224 Angle : 0.438 4.473 19656 Z= 0.232 Chirality : 0.035 0.143 2392 Planarity : 0.001 0.011 2496 Dihedral : 3.229 8.747 1976 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.73 % Allowed : 16.35 % Favored : 78.92 % 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: 6.34 (0.14), residues: 1768 helix: 4.06 (0.09), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS Q 29 TYR 0.005 0.001 TYR c 8 ARG 0.003 0.001 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 230 time to evaluate : 1.357 Fit side-chains REVERT: A 22 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: G 31 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8256 (mm-30) REVERT: i 22 GLN cc_start: 0.8336 (tt0) cc_final: 0.8128 (tt0) REVERT: o 22 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.8053 (tt0) outliers start: 64 outliers final: 52 residues processed: 268 average time/residue: 0.2321 time to fit residues: 95.6141 Evaluate side-chains 282 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 228 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain U residue 18 ILE Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 26 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 18 ILE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 22 GLN Chi-restraints excluded: chain b residue 24 LYS Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain c residue 22 GLN Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain h residue 22 GLN Chi-restraints excluded: chain h residue 26 LEU Chi-restraints excluded: chain j residue 32 ILE Chi-restraints excluded: chain k residue 18 ILE Chi-restraints excluded: chain l residue 26 LEU Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain o residue 22 GLN Chi-restraints excluded: chain o residue 32 ILE Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 32 ILE Chi-restraints excluded: chain q residue 18 ILE Chi-restraints excluded: chain r residue 22 GLN Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 36 GLN Chi-restraints excluded: chain u residue 18 ILE Chi-restraints excluded: chain x residue 22 GLN Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain z residue 18 ILE Chi-restraints excluded: chain z residue 32 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.8442 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14664 Z= 0.215 Angle : 0.430 4.452 19656 Z= 0.228 Chirality : 0.035 0.182 2392 Planarity : 0.001 0.011 2496 Dihedral : 3.232 8.842 1976 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.22 % Allowed : 16.94 % Favored : 78.85 % 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: 6.35 (0.14), residues: 1768 helix: 4.07 (0.09), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Q 29 TYR 0.004 0.001 TYR b 8 ARG 0.003 0.001 ARG P 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 233 time to evaluate : 1.619 Fit side-chains REVERT: A 22 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: G 31 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8256 (mm-30) REVERT: a 22 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: i 22 GLN cc_start: 0.8335 (tt0) cc_final: 0.8111 (tt0) REVERT: o 22 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8048 (tt0) outliers start: 57 outliers final: 51 residues processed: 266 average time/residue: 0.2358 time to fit residues: 97.5643 Evaluate side-chains 286 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 232 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain N residue 32 ILE Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain S residue 18 ILE Chi-restraints excluded: chain T residue 26 LEU Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain U residue 18 ILE Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 26 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain Y residue 18 ILE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 22 GLN Chi-restraints excluded: chain b residue 22 GLN Chi-restraints excluded: chain b residue 24 LYS Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain c residue 22 GLN Chi-restraints excluded: chain f residue 32 ILE Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain h residue 18 ILE Chi-restraints excluded: chain h residue 22 GLN Chi-restraints excluded: chain h residue 26 LEU Chi-restraints excluded: chain j residue 32 ILE Chi-restraints excluded: chain k residue 18 ILE Chi-restraints excluded: chain l residue 26 LEU Chi-restraints excluded: chain m residue 22 GLN Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 32 ILE Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain o residue 22 GLN Chi-restraints excluded: chain o residue 32 ILE Chi-restraints excluded: chain p residue 18 ILE Chi-restraints excluded: chain p residue 32 ILE Chi-restraints excluded: chain q residue 18 ILE Chi-restraints excluded: chain r residue 22 GLN Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain t residue 22 GLN Chi-restraints excluded: chain t residue 36 GLN Chi-restraints excluded: chain u residue 18 ILE Chi-restraints excluded: chain x residue 22 GLN Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain z residue 18 ILE Chi-restraints excluded: chain z residue 32 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.116659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.111801 restraints weight = 20364.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.112084 restraints weight = 16896.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.112156 restraints weight = 15591.976| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14664 Z= 0.214 Angle : 0.429 4.250 19656 Z= 0.227 Chirality : 0.034 0.184 2392 Planarity : 0.001 0.010 2496 Dihedral : 3.234 8.894 1976 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.73 % Allowed : 16.49 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.35 (0.14), residues: 1768 helix: 4.07 (0.09), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Q 29 TYR 0.004 0.001 TYR b 8 ARG 0.003 0.001 ARG P 10 =============================================================================== Job complete usr+sys time: 2560.69 seconds wall clock time: 47 minutes 2.53 seconds (2822.53 seconds total)