Starting phenix.real_space_refine on Thu Nov 16 06:28:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl1_21815/11_2023/6wl1_21815.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl1_21815/11_2023/6wl1_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_21815/11_2023/6wl1_21815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl1_21815/11_2023/6wl1_21815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl1_21815/11_2023/6wl1_21815.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl1_21815/11_2023/6wl1_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 7.44, 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: 6.04 Conformation dependent library (CDL) restraints added in 2.7 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: 1.00 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: 4.68 Time building geometry restraints manager: 6.44 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: 0.870 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: 2.650 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 39.290 Find NCS groups from input model: 1.110 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.230 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.685 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.3307 time to fit residues: 167.5013 Evaluate side-chains 153 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9521 ------------------------------------------------------------------------------- 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: 0.8260 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 14664 Z= 0.170 Angle : 0.401 2.264 19656 Z= 0.231 Chirality : 0.032 0.092 2392 Planarity : 0.002 0.011 2496 Dihedral : 3.474 8.192 1976 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.63 % Allowed : 13.98 % Favored : 84.39 % 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: 4.14 (0.15), residues: 1768 helix: 2.70 (0.09), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 341 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 319 time to evaluate : 1.740 Fit side-chains outliers start: 22 outliers final: 3 residues processed: 337 average time/residue: 0.2582 time to fit residues: 128.0479 Evaluate side-chains 236 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 233 time to evaluate : 1.699 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1401 time to fit residues: 2.9458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 22 GLN n 36 GLN r 36 GLN x 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14664 Z= 0.336 Angle : 0.581 6.536 19656 Z= 0.305 Chirality : 0.039 0.111 2392 Planarity : 0.002 0.009 2496 Dihedral : 3.312 7.959 1976 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.70 % Allowed : 16.12 % Favored : 80.18 % 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: 4.69 (0.14), residues: 1768 helix: 3.04 (0.09), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 273 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 223 time to evaluate : 1.466 Fit side-chains outliers start: 50 outliers final: 23 residues processed: 253 average time/residue: 0.2424 time to fit residues: 92.1308 Evaluate side-chains 227 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 204 time to evaluate : 1.652 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1483 time to fit residues: 8.3539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14664 Z= 0.162 Angle : 0.360 3.191 19656 Z= 0.202 Chirality : 0.032 0.099 2392 Planarity : 0.001 0.007 2496 Dihedral : 3.240 8.019 1976 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.63 % Allowed : 17.83 % Favored : 80.55 % 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 (0.08), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 305 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 283 time to evaluate : 1.669 Fit side-chains outliers start: 22 outliers final: 5 residues processed: 298 average time/residue: 0.2580 time to fit residues: 113.4715 Evaluate side-chains 266 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 261 time to evaluate : 1.671 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1465 time to fit residues: 3.5813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 2 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14664 Z= 0.163 Angle : 0.364 3.451 19656 Z= 0.201 Chirality : 0.033 0.100 2392 Planarity : 0.001 0.006 2496 Dihedral : 3.220 7.419 1976 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.77 % Allowed : 15.90 % 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: 6.67 (0.14), residues: 1768 helix: 4.26 (0.08), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 342 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 264 time to evaluate : 1.717 Fit side-chains outliers start: 78 outliers final: 21 residues processed: 315 average time/residue: 0.2364 time to fit residues: 113.0365 Evaluate side-chains 270 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 249 time to evaluate : 1.633 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1352 time to fit residues: 7.4896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 22 GLN c 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3983 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= 0.170 Angle : 0.375 3.781 19656 Z= 0.204 Chirality : 0.033 0.104 2392 Planarity : 0.001 0.006 2496 Dihedral : 3.214 7.983 1976 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.29 % Allowed : 16.35 % Favored : 81.36 % 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: 6.78 (0.14), residues: 1768 helix: 4.33 (0.08), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 289 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 258 time to evaluate : 1.723 Fit side-chains outliers start: 31 outliers final: 13 residues processed: 270 average time/residue: 0.2494 time to fit residues: 101.2909 Evaluate side-chains 260 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 247 time to evaluate : 1.716 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1381 time to fit residues: 5.7220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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: 0.8430 moved from start: 0.3980 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= 0.210 Angle : 0.427 4.174 19656 Z= 0.227 Chirality : 0.034 0.126 2392 Planarity : 0.001 0.008 2496 Dihedral : 3.216 8.388 1976 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.78 % Allowed : 17.46 % Favored : 80.77 % 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: 6.50 (0.14), residues: 1768 helix: 4.16 (0.08), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 266 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 242 time to evaluate : 1.750 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 249 average time/residue: 0.2406 time to fit residues: 91.4781 Evaluate side-chains 253 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 237 time to evaluate : 1.577 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1360 time to fit residues: 6.5042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 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: 0.8432 moved from start: 0.4025 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 : 0.428 4.155 19656 Z= 0.227 Chirality : 0.034 0.139 2392 Planarity : 0.001 0.006 2496 Dihedral : 3.224 8.468 1976 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.18 % Allowed : 17.16 % Favored : 81.66 % 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: 6.48 (0.14), residues: 1768 helix: 4.15 (0.08), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 253 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 237 time to evaluate : 1.647 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 244 average time/residue: 0.2367 time to fit residues: 88.3486 Evaluate side-chains 240 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 232 time to evaluate : 1.793 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1453 time to fit residues: 4.3279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8466 moved from start: 0.4009 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= 0.248 Angle : 0.469 4.920 19656 Z= 0.246 Chirality : 0.036 0.163 2392 Planarity : 0.002 0.008 2496 Dihedral : 3.242 8.624 1976 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.11 % Allowed : 17.46 % Favored : 81.43 % 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: 6.24 (0.14), residues: 1768 helix: 4.00 (0.09), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 255 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 240 time to evaluate : 1.586 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 245 average time/residue: 0.2386 time to fit residues: 89.1802 Evaluate side-chains 245 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 236 time to evaluate : 1.769 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1359 time to fit residues: 4.5065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.8386 moved from start: 0.4179 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= 0.176 Angle : 0.386 4.084 19656 Z= 0.209 Chirality : 0.033 0.143 2392 Planarity : 0.001 0.006 2496 Dihedral : 3.258 8.371 1976 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.59 % Allowed : 17.31 % Favored : 82.10 % 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: 6.67 (0.14), residues: 1768 helix: 4.27 (0.08), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 ********************** 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 258 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 250 time to evaluate : 1.798 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 253 average time/residue: 0.2464 time to fit residues: 93.7572 Evaluate side-chains 249 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 245 time to evaluate : 1.721 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1269 time to fit residues: 3.3643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.114965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.109968 restraints weight = 20453.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.110332 restraints weight = 17784.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.110332 restraints weight = 15991.040| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4057 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= 0.248 Angle : 0.472 4.867 19656 Z= 0.246 Chirality : 0.036 0.186 2392 Planarity : 0.002 0.008 2496 Dihedral : 3.250 8.788 1976 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.74 % Allowed : 17.75 % Favored : 81.51 % 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: 6.23 (0.14), residues: 1768 helix: 3.99 (0.09), residues: 1768 sheet: None (None), residues: 0 loop : None (None), residues: 0 =============================================================================== Job complete usr+sys time: 2494.41 seconds wall clock time: 46 minutes 23.14 seconds (2783.14 seconds total)