Starting phenix.real_space_refine on Wed Nov 20 03:20:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oko_12963/11_2024/7oko_12963_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oko_12963/11_2024/7oko_12963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oko_12963/11_2024/7oko_12963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oko_12963/11_2024/7oko_12963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oko_12963/11_2024/7oko_12963_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oko_12963/11_2024/7oko_12963_neut.cif" } resolution = 3.4 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.001 sd= 0.050 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: 4 Type Number sf(0) Gaussians S 182 5.16 5 C 34424 2.51 5 N 9763 2.21 5 O 10114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 272 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 54483 Number of models: 1 Model: "" Number of chains: 65 Chain: "AA" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "AB" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "AC" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "0" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "1" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "2" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "3" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "4" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "5" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "6" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "7" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "8" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "9" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "A" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "B" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "C" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "D" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "E" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "F" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "G" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "H" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "I" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "J" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "K" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "L" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "M" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "N" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "O" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "P" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "Q" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "R" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "S" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "T" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "U" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "V" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "W" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "X" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "Y" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "Z" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "a" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "b" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "c" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "d" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "e" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "f" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "g" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "h" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "i" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "j" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "k" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "l" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "m" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "n" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "o" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "p" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "q" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "r" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "s" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "t" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "u" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "v" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 467 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 53} Chain breaks: 1 Chain: "w" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 5, 'TRANS': 40} Chain: "x" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "y" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain: "z" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1639 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 14, 'TRANS': 201} Time building chain proxies: 30.39, per 1000 atoms: 0.56 Number of scatterers: 54483 At special positions: 0 Unit cell: (277.2, 278.3, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 182 16.00 O 10114 8.00 N 9763 7.00 C 34424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.42 Conformation dependent library (CDL) restraints added in 6.6 seconds 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12922 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 6.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain '3' and resid 125 through 133 Processing helix chain '3' and resid 136 through 149 Processing helix chain '4' and resid 137 through 147 Processing helix chain '4' and resid 149 through 149 No H-bonds generated for 'chain '4' and resid 149 through 149' Processing helix chain '9' and resid 137 through 147 Processing helix chain '9' and resid 149 through 149 No H-bonds generated for 'chain '9' and resid 149 through 149' Processing helix chain '8' and resid 125 through 133 Processing helix chain '8' and resid 136 through 149 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'B' and resid 137 through 147 Processing helix chain 'B' and resid 149 through 149 No H-bonds generated for 'chain 'B' and resid 149 through 149' Processing helix chain 'G' and resid 137 through 147 Processing helix chain 'G' and resid 149 through 149 No H-bonds generated for 'chain 'G' and resid 149 through 149' Processing helix chain 'F' and resid 125 through 133 Processing helix chain 'F' and resid 136 through 149 Processing helix chain 'K' and resid 125 through 133 Processing helix chain 'K' and resid 136 through 149 Processing helix chain 'L' and resid 137 through 147 Processing helix chain 'L' and resid 149 through 149 No H-bonds generated for 'chain 'L' and resid 149 through 149' Processing helix chain 'Q' and resid 137 through 147 Processing helix chain 'Q' and resid 149 through 149 No H-bonds generated for 'chain 'Q' and resid 149 through 149' Processing helix chain 'P' and resid 125 through 133 Processing helix chain 'P' and resid 136 through 149 Processing helix chain 'U' and resid 125 through 133 Processing helix chain 'U' and resid 136 through 149 Processing helix chain 'V' and resid 137 through 147 Processing helix chain 'V' and resid 149 through 149 No H-bonds generated for 'chain 'V' and resid 149 through 149' Processing helix chain 'Z' and resid 125 through 133 Processing helix chain 'Z' and resid 136 through 149 Processing helix chain 'a' and resid 137 through 147 Processing helix chain 'a' and resid 149 through 149 No H-bonds generated for 'chain 'a' and resid 149 through 149' Processing helix chain 'e' and resid 125 through 133 Processing helix chain 'e' and resid 136 through 149 Processing helix chain 'f' and resid 137 through 147 Processing helix chain 'f' and resid 149 through 149 No H-bonds generated for 'chain 'f' and resid 149 through 149' Processing helix chain 'k' and resid 137 through 147 Processing helix chain 'k' and resid 149 through 149 No H-bonds generated for 'chain 'k' and resid 149 through 149' Processing helix chain 'j' and resid 125 through 133 Processing helix chain 'j' and resid 136 through 149 Processing helix chain 'o' and resid 125 through 133 Processing helix chain 'o' and resid 136 through 149 Processing helix chain 'p' and resid 137 through 147 Processing helix chain 'p' and resid 149 through 149 No H-bonds generated for 'chain 'p' and resid 149 through 149' Processing helix chain 'u' and resid 137 through 147 Processing helix chain 'u' and resid 149 through 149 No H-bonds generated for 'chain 'u' and resid 149 through 149' Processing helix chain 't' and resid 125 through 133 Processing helix chain 't' and resid 136 through 149 Processing helix chain 'y' and resid 125 through 133 Processing helix chain 'y' and resid 136 through 149 Processing helix chain 'z' and resid 137 through 147 Processing helix chain 'z' and resid 149 through 149 No H-bonds generated for 'chain 'z' and resid 149 through 149' 286 hydrogen bonds defined for protein. 858 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: 9.11 Time building geometry restraints manager: 14.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 8994 1.31 - 1.44: 14823 1.44 - 1.57: 31563 1.57 - 1.69: 0 1.69 - 1.82: 364 Bond restraints: 55744 Sorted by residual: bond pdb=" C PRO c 185 " pdb=" O PRO c 185 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.19e-02 7.06e+03 1.35e+01 bond pdb=" C PRO I 185 " pdb=" O PRO I 185 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.19e-02 7.06e+03 1.34e+01 bond pdb=" C PRO X 185 " pdb=" O PRO X 185 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.23e-02 6.61e+03 1.28e+01 bond pdb=" N GLY c 186 " pdb=" CA GLY c 186 " ideal model delta sigma weight residual 1.447 1.480 -0.034 1.01e-02 9.80e+03 1.12e+01 bond pdb=" C VAL 4 212 " pdb=" O VAL 4 212 " ideal model delta sigma weight residual 1.237 1.206 0.031 9.80e-03 1.04e+04 1.02e+01 ... (remaining 55739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 75247 3.33 - 6.67: 609 6.67 - 10.00: 45 10.00 - 13.34: 5 13.34 - 16.67: 1 Bond angle restraints: 75907 Sorted by residual: angle pdb=" C PHE X 182 " pdb=" CA PHE X 182 " pdb=" CB PHE X 182 " ideal model delta sigma weight residual 110.77 94.10 16.67 1.67e+00 3.59e-01 9.97e+01 angle pdb=" C PHE I 182 " pdb=" CA PHE I 182 " pdb=" CB PHE I 182 " ideal model delta sigma weight residual 110.29 98.58 11.71 1.64e+00 3.72e-01 5.10e+01 angle pdb=" CA PHE X 182 " pdb=" C PHE X 182 " pdb=" O PHE X 182 " ideal model delta sigma weight residual 120.60 112.56 8.04 1.13e+00 7.83e-01 5.06e+01 angle pdb=" CA GLYAA 186 " pdb=" C GLYAA 186 " pdb=" O GLYAA 186 " ideal model delta sigma weight residual 121.38 115.46 5.92 9.40e-01 1.13e+00 3.97e+01 angle pdb=" CA GLY X 186 " pdb=" C GLY X 186 " pdb=" O GLY X 186 " ideal model delta sigma weight residual 121.38 115.50 5.88 9.40e-01 1.13e+00 3.92e+01 ... (remaining 75902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 30174 17.84 - 35.68: 2553 35.68 - 53.52: 326 53.52 - 71.36: 106 71.36 - 89.20: 43 Dihedral angle restraints: 33202 sinusoidal: 13130 harmonic: 20072 Sorted by residual: dihedral pdb=" C PHE X 182 " pdb=" N PHE X 182 " pdb=" CA PHE X 182 " pdb=" CB PHE X 182 " ideal model delta harmonic sigma weight residual -122.60 -100.46 -22.14 0 2.50e+00 1.60e-01 7.84e+01 dihedral pdb=" C PHE I 182 " pdb=" N PHE I 182 " pdb=" CA PHE I 182 " pdb=" CB PHE I 182 " ideal model delta harmonic sigma weight residual -122.60 -105.34 -17.26 0 2.50e+00 1.60e-01 4.77e+01 dihedral pdb=" C PHE m 182 " pdb=" N PHE m 182 " pdb=" CA PHE m 182 " pdb=" CB PHE m 182 " ideal model delta harmonic sigma weight residual -122.60 -110.06 -12.54 0 2.50e+00 1.60e-01 2.52e+01 ... (remaining 33199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 7926 0.094 - 0.187: 554 0.187 - 0.281: 13 0.281 - 0.374: 19 0.374 - 0.468: 3 Chirality restraints: 8515 Sorted by residual: chirality pdb=" CA PHE X 182 " pdb=" N PHE X 182 " pdb=" C PHE X 182 " pdb=" CB PHE X 182 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" CA PHE I 182 " pdb=" N PHE I 182 " pdb=" C PHE I 182 " pdb=" CB PHE I 182 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CA ASN r 180 " pdb=" N ASN r 180 " pdb=" C ASN r 180 " pdb=" CB ASN r 180 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.97e+00 ... (remaining 8512 not shown) Planarity restraints: 9919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP e 46 " 0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO e 47 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO e 47 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO e 47 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA k 62 " 0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO k 63 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO k 63 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO k 63 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP y 46 " 0.054 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO y 47 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO y 47 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO y 47 " 0.044 5.00e-02 4.00e+02 ... (remaining 9916 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 581 2.59 - 3.17: 46276 3.17 - 3.74: 77741 3.74 - 4.32: 104244 4.32 - 4.90: 180701 Nonbonded interactions: 409543 Sorted by model distance: nonbonded pdb=" OD1 ASN I 180 " pdb=" NE1 TRP S 197 " model vdw 2.010 3.120 nonbonded pdb=" OG1 THR L 149 " pdb=" OD1 ASP L 151 " model vdw 2.085 3.040 nonbonded pdb=" OG1 THR 4 149 " pdb=" OD1 ASP 4 151 " model vdw 2.087 3.040 nonbonded pdb=" OG1 THR u 149 " pdb=" OD1 ASP u 151 " model vdw 2.117 3.040 nonbonded pdb=" OD2 ASP A 218 " pdb=" OG1 THR A 231 " model vdw 2.126 3.040 ... (remaining 409538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '5' selection = chain 'AB' selection = chain 'C' selection = chain 'H' selection = chain 'M' selection = chain 'R' selection = chain 'W' selection = chain 'b' selection = chain 'g' selection = chain 'l' selection = chain 'q' selection = chain 'v' } ncs_group { reference = chain '1' selection = chain '6' selection = chain 'AA' selection = chain 'D' selection = chain 'I' selection = chain 'N' selection = chain 'S' selection = chain 'X' selection = chain 'c' selection = chain 'h' selection = chain 'm' selection = chain 'r' selection = chain 'w' } ncs_group { reference = chain '2' selection = chain '7' selection = chain 'AC' selection = chain 'E' selection = chain 'J' selection = chain 'O' selection = chain 'T' selection = chain 'Y' selection = chain 'd' selection = chain 'i' selection = chain 'n' selection = chain 's' selection = chain 'x' } ncs_group { reference = chain '3' selection = chain '4' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'B' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'L' selection = chain 'P' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'j' selection = chain 'k' selection = chain 'o' selection = chain 'p' selection = chain 't' selection = chain 'u' 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 individual isotropic 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: 5.550 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: 0.050 Extract box with map and model: 1.930 Check model and map are aligned: 0.360 Set scattering table: 0.440 Process input model: 95.450 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.810 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.006 0.070 55744 Z= 0.390 Angle : 0.835 16.674 75907 Z= 0.483 Chirality : 0.051 0.468 8515 Planarity : 0.007 0.086 9919 Dihedral : 13.642 89.202 20280 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.35 % Favored : 85.49 % Rotamer: Outliers : 0.92 % Allowed : 1.42 % Favored : 97.66 % Cbeta Deviations : 0.17 % 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: -3.66 (0.09), residues: 6968 helix: -1.28 (0.20), residues: 507 sheet: -2.13 (0.11), residues: 2028 loop : -2.86 (0.09), residues: 4433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 208 HIS 0.009 0.002 HIS I 183 PHE 0.027 0.002 PHE c 182 TYR 0.023 0.002 TYR L 136 ARG 0.016 0.001 ARG e 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1516 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 1463 time to evaluate : 4.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8454 (t0) cc_final: 0.8004 (t0) REVERT: 0 180 ASN cc_start: 0.8570 (t0) cc_final: 0.8132 (t0) REVERT: 4 66 MET cc_start: 0.5857 (mmt) cc_final: 0.5419 (mmt) REVERT: 4 85 THR cc_start: 0.8076 (p) cc_final: 0.7787 (t) REVERT: 4 166 ILE cc_start: 0.7269 (pt) cc_final: 0.6621 (pt) REVERT: 5 180 ASN cc_start: 0.8383 (t0) cc_final: 0.8144 (t0) REVERT: 8 128 ARG cc_start: 0.7903 (tpp80) cc_final: 0.7526 (tpp80) REVERT: 9 191 GLU cc_start: 0.5698 (tm-30) cc_final: 0.5469 (tm-30) REVERT: B 66 MET cc_start: 0.6722 (mmt) cc_final: 0.6142 (mmp) REVERT: C 180 ASN cc_start: 0.8514 (t0) cc_final: 0.7966 (t0) REVERT: F 128 ARG cc_start: 0.8109 (tpp80) cc_final: 0.7824 (tpp80) REVERT: H 177 ASP cc_start: 0.7580 (t0) cc_final: 0.7346 (t0) REVERT: K 151 ASP cc_start: 0.6995 (p0) cc_final: 0.6761 (p0) REVERT: L 58 THR cc_start: 0.8837 (m) cc_final: 0.8607 (p) REVERT: L 117 MET cc_start: 0.7108 (ptm) cc_final: 0.6854 (ptm) REVERT: M 180 ASN cc_start: 0.8130 (t0) cc_final: 0.7565 (t0) REVERT: Q 191 GLU cc_start: 0.6003 (tm-30) cc_final: 0.5780 (tm-30) REVERT: R 180 ASN cc_start: 0.8523 (t0) cc_final: 0.7969 (t0) REVERT: U 151 ASP cc_start: 0.7161 (p0) cc_final: 0.6775 (p0) REVERT: V 66 MET cc_start: 0.6292 (mmt) cc_final: 0.5792 (mmt) REVERT: V 85 THR cc_start: 0.8038 (p) cc_final: 0.7757 (t) REVERT: b 157 THR cc_start: 0.6591 (p) cc_final: 0.6216 (p) REVERT: f 85 THR cc_start: 0.7930 (p) cc_final: 0.7494 (t) REVERT: f 191 GLU cc_start: 0.5931 (tm-30) cc_final: 0.5610 (tm-30) REVERT: l 180 ASN cc_start: 0.8837 (t0) cc_final: 0.8515 (t0) REVERT: o 110 GLU cc_start: 0.6581 (tt0) cc_final: 0.6367 (tt0) REVERT: o 235 ILE cc_start: 0.9118 (mm) cc_final: 0.8880 (mm) REVERT: p 85 THR cc_start: 0.7782 (p) cc_final: 0.7472 (t) REVERT: r 179 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6369 (p0) REVERT: y 66 MET cc_start: 0.7808 (mmp) cc_final: 0.6982 (mmp) REVERT: y 163 SER cc_start: 0.8010 (p) cc_final: 0.7780 (t) outliers start: 53 outliers final: 35 residues processed: 1476 average time/residue: 0.5449 time to fit residues: 1351.8000 Evaluate side-chains 1221 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 1185 time to evaluate : 5.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 179 ASP Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AA residue 199 LEU Chi-restraints excluded: chain 1 residue 166 GLN Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 1 residue 199 LEU Chi-restraints excluded: chain 4 residue 210 PRO Chi-restraints excluded: chain 6 residue 179 ASP Chi-restraints excluded: chain 6 residue 188 VAL Chi-restraints excluded: chain 6 residue 199 LEU Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain S residue 166 GLN Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain X residue 166 GLN Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain c residue 166 GLN Chi-restraints excluded: chain h residue 166 GLN Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain m residue 166 GLN Chi-restraints excluded: chain m residue 179 ASP Chi-restraints excluded: chain m residue 188 VAL Chi-restraints excluded: chain r residue 179 ASP Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain w residue 188 VAL Chi-restraints excluded: chain w residue 199 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 581 optimal weight: 2.9990 chunk 522 optimal weight: 5.9990 chunk 289 optimal weight: 0.7980 chunk 178 optimal weight: 6.9990 chunk 352 optimal weight: 2.9990 chunk 278 optimal weight: 0.8980 chunk 540 optimal weight: 0.9990 chunk 208 optimal weight: 0.0060 chunk 328 optimal weight: 2.9990 chunk 401 optimal weight: 6.9990 chunk 625 optimal weight: 2.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 238 ASN 8 37 GLN 8 134 GLN A 37 GLN A 134 GLN F 134 GLN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 GLN K 222 GLN N 184 GLN P 37 GLN W 159 HIS Z 37 GLN Z 144 ASN c 184 GLN e 37 GLN f 144 ASN h 184 GLN j 37 GLN j 184 GLN k 184 GLN o 37 GLN o 134 GLN p 184 GLN ** r 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 184 GLN y 37 GLN y 134 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 55744 Z= 0.226 Angle : 0.684 9.370 75907 Z= 0.344 Chirality : 0.046 0.244 8515 Planarity : 0.007 0.073 9919 Dihedral : 5.890 68.118 7768 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 2.60 % Allowed : 12.96 % Favored : 84.44 % 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: -3.47 (0.09), residues: 6968 helix: -1.60 (0.18), residues: 624 sheet: -2.06 (0.11), residues: 2132 loop : -2.64 (0.09), residues: 4212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 208 HIS 0.007 0.001 HIS r 159 PHE 0.018 0.002 PHE 3 38 TYR 0.014 0.001 TYR Q 136 ARG 0.008 0.000 ARG t 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1411 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 1261 time to evaluate : 6.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 199 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7664 (mm) REVERT: AB 180 ASN cc_start: 0.8573 (t0) cc_final: 0.8141 (t0) REVERT: 0 180 ASN cc_start: 0.8532 (t0) cc_final: 0.8146 (t0) REVERT: 0 196 ASP cc_start: 0.7599 (p0) cc_final: 0.7397 (p0) REVERT: 1 180 ASN cc_start: 0.7693 (m-40) cc_final: 0.7469 (t0) REVERT: 4 66 MET cc_start: 0.6271 (mmt) cc_final: 0.5512 (mmp) REVERT: 4 85 THR cc_start: 0.7996 (p) cc_final: 0.7709 (t) REVERT: 5 180 ASN cc_start: 0.8385 (t0) cc_final: 0.8108 (t0) REVERT: 6 199 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7472 (mm) REVERT: A 138 LYS cc_start: 0.8249 (ptmt) cc_final: 0.7990 (tttp) REVERT: B 66 MET cc_start: 0.6926 (mmt) cc_final: 0.6412 (mmp) REVERT: B 144 ASN cc_start: 0.8747 (t0) cc_final: 0.8502 (t0) REVERT: B 188 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7350 (m-30) REVERT: C 180 ASN cc_start: 0.8503 (t0) cc_final: 0.7941 (t0) REVERT: G 63 PRO cc_start: 0.8107 (Cg_exo) cc_final: 0.7431 (Cg_endo) REVERT: G 85 THR cc_start: 0.7797 (p) cc_final: 0.7509 (t) REVERT: I 199 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7791 (mm) REVERT: K 66 MET cc_start: 0.7202 (mmp) cc_final: 0.6936 (mmp) REVERT: K 151 ASP cc_start: 0.7014 (p0) cc_final: 0.6772 (p0) REVERT: L 85 THR cc_start: 0.7865 (p) cc_final: 0.7561 (t) REVERT: L 117 MET cc_start: 0.7068 (ptm) cc_final: 0.6853 (ptm) REVERT: L 144 ASN cc_start: 0.8468 (t0) cc_final: 0.8210 (t0) REVERT: M 180 ASN cc_start: 0.8185 (t0) cc_final: 0.7647 (t0) REVERT: N 199 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7211 (mm) REVERT: Q 66 MET cc_start: 0.7126 (mmt) cc_final: 0.6543 (mmp) REVERT: Q 191 GLU cc_start: 0.5867 (tm-30) cc_final: 0.5655 (tm-30) REVERT: R 180 ASN cc_start: 0.8501 (t0) cc_final: 0.7997 (t0) REVERT: U 151 ASP cc_start: 0.7039 (p0) cc_final: 0.6678 (p0) REVERT: V 85 THR cc_start: 0.7935 (p) cc_final: 0.7631 (t) REVERT: a 66 MET cc_start: 0.5970 (mmt) cc_final: 0.5662 (mmt) REVERT: b 157 THR cc_start: 0.6566 (p) cc_final: 0.6218 (p) REVERT: f 63 PRO cc_start: 0.7480 (Cg_endo) cc_final: 0.7165 (Cg_exo) REVERT: f 85 THR cc_start: 0.7854 (p) cc_final: 0.7472 (t) REVERT: h 177 ASP cc_start: 0.8010 (t0) cc_final: 0.7797 (t0) REVERT: l 180 ASN cc_start: 0.8764 (t0) cc_final: 0.8450 (t0) REVERT: o 235 ILE cc_start: 0.9046 (mm) cc_final: 0.8839 (mm) REVERT: r 177 ASP cc_start: 0.7840 (t0) cc_final: 0.7521 (t70) REVERT: r 179 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6860 (p0) REVERT: w 199 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7003 (mm) REVERT: y 66 MET cc_start: 0.7630 (mmp) cc_final: 0.6771 (mmp) REVERT: z 144 ASN cc_start: 0.8390 (t0) cc_final: 0.8184 (t0) outliers start: 150 outliers final: 71 residues processed: 1307 average time/residue: 0.6122 time to fit residues: 1365.6699 Evaluate side-chains 1253 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 1175 time to evaluate : 6.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AA residue 199 LEU Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain 0 residue 167 ILE Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 6 residue 179 ASP Chi-restraints excluded: chain 6 residue 199 LEU Chi-restraints excluded: chain 8 residue 163 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 138 LYS Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 163 SER Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 199 LEU Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Z residue 145 ARG Chi-restraints excluded: chain Z residue 163 SER Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 223 THR Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 SER Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 174 VAL Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain j residue 92 VAL Chi-restraints excluded: chain j residue 163 SER Chi-restraints excluded: chain j residue 188 ASP Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain m residue 179 ASP Chi-restraints excluded: chain o residue 141 ILE Chi-restraints excluded: chain o residue 163 SER Chi-restraints excluded: chain o residue 188 ASP Chi-restraints excluded: chain p residue 48 ASN Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain r residue 179 ASP Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain w residue 199 LEU Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 143 LEU Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 204 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 347 optimal weight: 4.9990 chunk 194 optimal weight: 0.4980 chunk 520 optimal weight: 3.9990 chunk 426 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 626 optimal weight: 7.9990 chunk 677 optimal weight: 4.9990 chunk 558 optimal weight: 6.9990 chunk 621 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 chunk 502 optimal weight: 8.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 180 ASN ** 4 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 48 ASN ** 8 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 48 ASN A 37 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 ASN L 184 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 48 ASN W 159 HIS ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 48 ASN h 180 ASN ** k 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 48 ASN o 37 GLN p 48 ASN q 159 HIS r 159 HIS ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 48 ASN ** y 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 48 ASN z 144 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 55744 Z= 0.491 Angle : 0.784 9.916 75907 Z= 0.402 Chirality : 0.048 0.224 8515 Planarity : 0.008 0.089 9919 Dihedral : 5.716 54.385 7730 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.70 % Favored : 84.30 % Rotamer: Outliers : 3.50 % Allowed : 17.98 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.79 (0.09), residues: 6968 helix: -1.53 (0.19), residues: 637 sheet: -2.12 (0.10), residues: 2548 loop : -3.05 (0.09), residues: 3783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 4 208 HIS 0.009 0.002 HIS r 159 PHE 0.022 0.003 PHE 7 185 TYR 0.033 0.003 TYR B 136 ARG 0.005 0.001 ARG m 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1451 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 1249 time to evaluate : 6.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 179 ASP cc_start: 0.7544 (p0) cc_final: 0.7324 (p0) REVERT: AB 180 ASN cc_start: 0.8704 (t0) cc_final: 0.8409 (t0) REVERT: 0 180 ASN cc_start: 0.8623 (t0) cc_final: 0.8294 (t0) REVERT: 0 196 ASP cc_start: 0.7752 (p0) cc_final: 0.7499 (p0) REVERT: 1 180 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7822 (m-40) REVERT: 3 141 ILE cc_start: 0.8614 (mm) cc_final: 0.8384 (mt) REVERT: 4 66 MET cc_start: 0.6534 (mmt) cc_final: 0.5673 (mmt) REVERT: 4 191 GLU cc_start: 0.6251 (tm-30) cc_final: 0.5981 (tm-30) REVERT: 8 49 MET cc_start: 0.7631 (ttt) cc_final: 0.7338 (ttt) REVERT: 9 144 ASN cc_start: 0.8845 (t0) cc_final: 0.8570 (t0) REVERT: B 66 MET cc_start: 0.6572 (mmt) cc_final: 0.5567 (mmp) REVERT: B 188 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7320 (m-30) REVERT: C 180 ASN cc_start: 0.8661 (t0) cc_final: 0.8267 (t0) REVERT: F 128 ARG cc_start: 0.8210 (tpp80) cc_final: 0.7719 (tpp80) REVERT: G 63 PRO cc_start: 0.8378 (Cg_exo) cc_final: 0.8011 (Cg_exo) REVERT: K 85 THR cc_start: 0.8150 (m) cc_final: 0.7946 (m) REVERT: K 151 ASP cc_start: 0.7075 (p0) cc_final: 0.6820 (p0) REVERT: L 108 LYS cc_start: 0.7261 (tptt) cc_final: 0.7038 (tptm) REVERT: L 191 GLU cc_start: 0.6463 (tm-30) cc_final: 0.5895 (tm-30) REVERT: L 192 LEU cc_start: 0.6963 (mp) cc_final: 0.6703 (tp) REVERT: M 180 ASN cc_start: 0.8480 (t0) cc_final: 0.8080 (t0) REVERT: Q 184 GLN cc_start: 0.7514 (mm-40) cc_final: 0.7295 (mm110) REVERT: Q 191 GLU cc_start: 0.6015 (tm-30) cc_final: 0.5583 (tm-30) REVERT: R 180 ASN cc_start: 0.8688 (t0) cc_final: 0.8224 (t0) REVERT: U 138 LYS cc_start: 0.8218 (ptmt) cc_final: 0.7972 (tttp) REVERT: U 151 ASP cc_start: 0.7068 (p0) cc_final: 0.6725 (p0) REVERT: V 191 GLU cc_start: 0.6111 (tm-30) cc_final: 0.5752 (tm-30) REVERT: Z 128 ARG cc_start: 0.7983 (tpp80) cc_final: 0.7753 (tpp80) REVERT: a 49 MET cc_start: 0.7570 (ttt) cc_final: 0.7269 (ttt) REVERT: b 157 THR cc_start: 0.6862 (OUTLIER) cc_final: 0.6497 (m) REVERT: e 235 ILE cc_start: 0.9010 (mm) cc_final: 0.8767 (mm) REVERT: f 63 PRO cc_start: 0.7768 (Cg_endo) cc_final: 0.7567 (Cg_exo) REVERT: f 144 ASN cc_start: 0.8611 (t0) cc_final: 0.8255 (t0) REVERT: j 138 LYS cc_start: 0.8376 (ptmt) cc_final: 0.8116 (tttp) REVERT: k 85 THR cc_start: 0.8030 (p) cc_final: 0.7799 (t) REVERT: k 191 GLU cc_start: 0.5884 (tm-30) cc_final: 0.5671 (tm-30) REVERT: l 180 ASN cc_start: 0.8710 (t0) cc_final: 0.8433 (t0) REVERT: o 235 ILE cc_start: 0.9111 (mm) cc_final: 0.8840 (mm) REVERT: r 177 ASP cc_start: 0.8017 (t0) cc_final: 0.7667 (t70) REVERT: r 179 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6599 (p0) REVERT: r 180 ASN cc_start: 0.8002 (t0) cc_final: 0.7796 (t0) REVERT: t 138 LYS cc_start: 0.8247 (ptmt) cc_final: 0.8041 (tttp) REVERT: t 141 ILE cc_start: 0.8702 (mm) cc_final: 0.8442 (mt) REVERT: u 71 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6557 (ttt180) REVERT: u 85 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7766 (t) REVERT: u 191 GLU cc_start: 0.6157 (tm-30) cc_final: 0.5863 (tm-30) REVERT: y 66 MET cc_start: 0.7876 (mmp) cc_final: 0.7116 (mmp) outliers start: 202 outliers final: 130 residues processed: 1342 average time/residue: 0.6292 time to fit residues: 1446.0479 Evaluate side-chains 1330 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1194 time to evaluate : 6.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AA residue 196 ASP Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain AC residue 181 ASP Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 179 ASP Chi-restraints excluded: chain 1 residue 180 ASN Chi-restraints excluded: chain 1 residue 198 VAL Chi-restraints excluded: chain 2 residue 181 ASP Chi-restraints excluded: chain 3 residue 30 ILE Chi-restraints excluded: chain 3 residue 46 ASP Chi-restraints excluded: chain 4 residue 230 MET Chi-restraints excluded: chain 5 residue 191 VAL Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 6 residue 178 SER Chi-restraints excluded: chain 6 residue 179 ASP Chi-restraints excluded: chain 6 residue 188 VAL Chi-restraints excluded: chain 7 residue 181 ASP Chi-restraints excluded: chain 8 residue 56 LYS Chi-restraints excluded: chain 8 residue 141 ILE Chi-restraints excluded: chain 8 residue 163 SER Chi-restraints excluded: chain 8 residue 188 ASP Chi-restraints excluded: chain 8 residue 216 MET Chi-restraints excluded: chain 9 residue 48 ASN Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 138 LYS Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 188 ASP Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 163 SER Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 159 HIS Chi-restraints excluded: chain S residue 179 ASP Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain V residue 26 SER Chi-restraints excluded: chain V residue 175 THR Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 167 ILE Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Z residue 141 ILE Chi-restraints excluded: chain Z residue 145 ARG Chi-restraints excluded: chain Z residue 163 SER Chi-restraints excluded: chain Z residue 216 MET Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain b residue 157 THR Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain e residue 116 LEU Chi-restraints excluded: chain e residue 117 MET Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 SER Chi-restraints excluded: chain e residue 216 MET Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 204 GLU Chi-restraints excluded: chain g residue 157 THR Chi-restraints excluded: chain g residue 191 VAL Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain j residue 92 VAL Chi-restraints excluded: chain j residue 117 MET Chi-restraints excluded: chain j residue 163 SER Chi-restraints excluded: chain j residue 188 ASP Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain m residue 179 ASP Chi-restraints excluded: chain n residue 181 ASP Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 117 MET Chi-restraints excluded: chain o residue 141 ILE Chi-restraints excluded: chain o residue 163 SER Chi-restraints excluded: chain p residue 48 ASN Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain r residue 159 HIS Chi-restraints excluded: chain r residue 179 ASP Chi-restraints excluded: chain t residue 46 ASP Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 163 SER Chi-restraints excluded: chain u residue 71 ARG Chi-restraints excluded: chain u residue 85 THR Chi-restraints excluded: chain u residue 147 VAL Chi-restraints excluded: chain u residue 162 LEU Chi-restraints excluded: chain v residue 73 VAL Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain w residue 188 VAL Chi-restraints excluded: chain y residue 117 MET Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 143 LEU Chi-restraints excluded: chain y residue 163 SER Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 116 LEU Chi-restraints excluded: chain z residue 173 SER Chi-restraints excluded: chain z residue 204 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 619 optimal weight: 2.9990 chunk 471 optimal weight: 8.9990 chunk 325 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 299 optimal weight: 0.8980 chunk 420 optimal weight: 7.9990 chunk 629 optimal weight: 3.9990 chunk 665 optimal weight: 0.7980 chunk 328 optimal weight: 0.9990 chunk 596 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 134 GLN 8 222 GLN 9 48 ASN A 134 GLN F 222 GLN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 HIS U 222 GLN ** V 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 144 ASN W 159 HIS X 159 HIS Z 222 GLN ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 ASN a 184 GLN e 222 GLN ** f 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 144 ASN k 184 GLN m 180 ASN ** r 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 222 GLN ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 134 GLN y 222 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 55744 Z= 0.239 Angle : 0.666 9.968 75907 Z= 0.335 Chirality : 0.045 0.236 8515 Planarity : 0.007 0.077 9919 Dihedral : 5.131 57.408 7716 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 3.57 % Allowed : 20.27 % Favored : 76.16 % 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: -3.50 (0.09), residues: 6968 helix: -1.19 (0.19), residues: 624 sheet: -2.00 (0.10), residues: 2327 loop : -2.80 (0.09), residues: 4017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP h 171 HIS 0.005 0.001 HIS r 159 PHE 0.016 0.002 PHE t 38 TYR 0.014 0.002 TYR 4 136 ARG 0.005 0.000 ARG P 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1436 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 1230 time to evaluate : 6.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8699 (t0) cc_final: 0.8426 (t0) REVERT: 0 177 ASP cc_start: 0.6907 (t0) cc_final: 0.6498 (t0) REVERT: 0 180 ASN cc_start: 0.8531 (t0) cc_final: 0.8320 (t0) REVERT: 4 66 MET cc_start: 0.6559 (mmt) cc_final: 0.6007 (mmt) REVERT: C 180 ASN cc_start: 0.8638 (t0) cc_final: 0.8242 (t0) REVERT: G 63 PRO cc_start: 0.8178 (Cg_exo) cc_final: 0.7931 (Cg_endo) REVERT: G 67 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6302 (pp) REVERT: K 85 THR cc_start: 0.8052 (m) cc_final: 0.7793 (m) REVERT: L 108 LYS cc_start: 0.7221 (tptt) cc_final: 0.7015 (tptm) REVERT: L 191 GLU cc_start: 0.6046 (tm-30) cc_final: 0.5711 (tm-30) REVERT: M 180 ASN cc_start: 0.8437 (t0) cc_final: 0.8042 (t0) REVERT: Q 191 GLU cc_start: 0.5949 (tm-30) cc_final: 0.5668 (tm-30) REVERT: R 180 ASN cc_start: 0.8638 (t0) cc_final: 0.8216 (t0) REVERT: U 138 LYS cc_start: 0.8138 (ptmt) cc_final: 0.7858 (tttp) REVERT: U 151 ASP cc_start: 0.7004 (p0) cc_final: 0.6739 (p0) REVERT: U 164 ASP cc_start: 0.7834 (p0) cc_final: 0.7621 (p0) REVERT: V 191 GLU cc_start: 0.6067 (tm-30) cc_final: 0.5861 (tm-30) REVERT: Z 128 ARG cc_start: 0.7861 (tpp80) cc_final: 0.7636 (tpp80) REVERT: e 235 ILE cc_start: 0.9011 (mm) cc_final: 0.8743 (mm) REVERT: f 63 PRO cc_start: 0.7389 (Cg_endo) cc_final: 0.7147 (Cg_exo) REVERT: j 129 LYS cc_start: 0.8700 (ptpp) cc_final: 0.8441 (ptpp) REVERT: j 138 LYS cc_start: 0.8265 (ptmt) cc_final: 0.7997 (tttp) REVERT: k 66 MET cc_start: 0.7149 (mmt) cc_final: 0.6293 (mmp) REVERT: k 85 THR cc_start: 0.7800 (p) cc_final: 0.7569 (t) REVERT: k 90 ILE cc_start: 0.9052 (mm) cc_final: 0.8812 (mm) REVERT: l 180 ASN cc_start: 0.8626 (t0) cc_final: 0.8352 (t0) REVERT: o 120 GLU cc_start: 0.7984 (pm20) cc_final: 0.7697 (pm20) REVERT: o 235 ILE cc_start: 0.9054 (mm) cc_final: 0.8801 (mm) REVERT: r 159 HIS cc_start: 0.6574 (OUTLIER) cc_final: 0.5636 (t-90) REVERT: r 177 ASP cc_start: 0.8044 (t0) cc_final: 0.7628 (t70) REVERT: r 179 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6463 (p0) REVERT: t 138 LYS cc_start: 0.8153 (ptmt) cc_final: 0.7941 (tttp) REVERT: t 141 ILE cc_start: 0.8656 (mm) cc_final: 0.8416 (mt) REVERT: u 85 THR cc_start: 0.7743 (p) cc_final: 0.7476 (t) REVERT: u 191 GLU cc_start: 0.6084 (tm-30) cc_final: 0.5855 (tm-30) REVERT: y 66 MET cc_start: 0.7811 (mmp) cc_final: 0.7167 (mmp) outliers start: 206 outliers final: 144 residues processed: 1337 average time/residue: 0.6026 time to fit residues: 1376.9149 Evaluate side-chains 1336 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1189 time to evaluate : 6.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain AC residue 181 ASP Chi-restraints excluded: chain AC residue 182 SER Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 4 residue 127 THR Chi-restraints excluded: chain 4 residue 162 LEU Chi-restraints excluded: chain 4 residue 184 GLN Chi-restraints excluded: chain 5 residue 157 THR Chi-restraints excluded: chain 5 residue 191 VAL Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 6 residue 178 SER Chi-restraints excluded: chain 6 residue 188 VAL Chi-restraints excluded: chain 7 residue 184 GLU Chi-restraints excluded: chain 8 residue 143 LEU Chi-restraints excluded: chain 8 residue 168 LEU Chi-restraints excluded: chain 8 residue 216 MET Chi-restraints excluded: chain 9 residue 48 ASN Chi-restraints excluded: chain 9 residue 127 THR Chi-restraints excluded: chain 9 residue 149 THR Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 163 SER Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 216 MET Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 159 HIS Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 168 LEU Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain W residue 167 ILE Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 117 MET Chi-restraints excluded: chain Z residue 145 ARG Chi-restraints excluded: chain Z residue 163 SER Chi-restraints excluded: chain Z residue 216 MET Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 223 THR Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 117 MET Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 216 MET Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 204 GLU Chi-restraints excluded: chain g residue 157 THR Chi-restraints excluded: chain g residue 191 VAL Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain j residue 48 ASN Chi-restraints excluded: chain j residue 117 MET Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 216 MET Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 127 THR Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain m residue 179 ASP Chi-restraints excluded: chain m residue 196 ASP Chi-restraints excluded: chain o residue 117 MET Chi-restraints excluded: chain o residue 141 ILE Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain o residue 216 MET Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain r residue 159 HIS Chi-restraints excluded: chain r residue 179 ASP Chi-restraints excluded: chain t residue 48 ASN Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 224 LEU Chi-restraints excluded: chain u residue 127 THR Chi-restraints excluded: chain u residue 162 LEU Chi-restraints excluded: chain v residue 73 VAL Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain w residue 188 VAL Chi-restraints excluded: chain y residue 117 MET Chi-restraints excluded: chain y residue 134 GLN Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 143 LEU Chi-restraints excluded: chain z residue 116 LEU Chi-restraints excluded: chain z residue 127 THR Chi-restraints excluded: chain z residue 204 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 554 optimal weight: 0.9990 chunk 378 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 495 optimal weight: 0.9980 chunk 274 optimal weight: 3.9990 chunk 568 optimal weight: 1.9990 chunk 460 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 340 optimal weight: 4.9990 chunk 597 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 134 GLN ** 9 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN C 159 HIS F 222 GLN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN R 159 HIS U 222 GLN V 144 ASN a 238 ASN f 48 ASN f 144 ASN j 184 GLN r 159 HIS ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 55744 Z= 0.198 Angle : 0.644 10.585 75907 Z= 0.321 Chirality : 0.044 0.211 8515 Planarity : 0.006 0.074 9919 Dihedral : 4.759 57.822 7710 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 3.59 % Allowed : 21.22 % Favored : 75.19 % 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: -3.22 (0.10), residues: 6968 helix: -1.03 (0.19), residues: 624 sheet: -1.85 (0.11), residues: 2418 loop : -2.57 (0.09), residues: 3926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP k 180 HIS 0.003 0.001 HIS b 183 PHE 0.013 0.001 PHE t 38 TYR 0.014 0.001 TYR k 190 ARG 0.006 0.000 ARG U 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1412 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 1205 time to evaluate : 5.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8686 (t0) cc_final: 0.8384 (t0) REVERT: 0 180 ASN cc_start: 0.8562 (t0) cc_final: 0.8266 (t0) REVERT: 4 66 MET cc_start: 0.6727 (mmt) cc_final: 0.6027 (mmt) REVERT: 4 162 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6707 (tt) REVERT: C 180 ASN cc_start: 0.8646 (t0) cc_final: 0.8185 (t0) REVERT: G 66 MET cc_start: 0.7005 (mmt) cc_final: 0.6742 (mmp) REVERT: G 67 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6215 (pp) REVERT: I 199 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8073 (mm) REVERT: K 85 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7743 (m) REVERT: L 108 LYS cc_start: 0.7162 (tptt) cc_final: 0.6933 (tptm) REVERT: M 180 ASN cc_start: 0.8430 (t0) cc_final: 0.8008 (t0) REVERT: Q 191 GLU cc_start: 0.5746 (tm-30) cc_final: 0.5532 (tm-30) REVERT: R 180 ASN cc_start: 0.8614 (t0) cc_final: 0.8233 (t0) REVERT: U 138 LYS cc_start: 0.8119 (ptmt) cc_final: 0.7847 (tttp) REVERT: U 151 ASP cc_start: 0.6958 (p0) cc_final: 0.6703 (p0) REVERT: U 164 ASP cc_start: 0.7966 (p0) cc_final: 0.7684 (p0) REVERT: V 208 TRP cc_start: 0.7307 (t60) cc_final: 0.6892 (t-100) REVERT: Z 128 ARG cc_start: 0.7809 (tpp80) cc_final: 0.7597 (tpp80) REVERT: Z 138 LYS cc_start: 0.8230 (ptmt) cc_final: 0.7965 (tttp) REVERT: e 235 ILE cc_start: 0.8997 (mm) cc_final: 0.8737 (mm) REVERT: f 63 PRO cc_start: 0.7305 (Cg_endo) cc_final: 0.7006 (Cg_exo) REVERT: f 66 MET cc_start: 0.7104 (mmt) cc_final: 0.6761 (mmt) REVERT: j 129 LYS cc_start: 0.8754 (ptpp) cc_final: 0.8423 (ptpp) REVERT: j 138 LYS cc_start: 0.8235 (ptmt) cc_final: 0.7989 (tttp) REVERT: k 66 MET cc_start: 0.7248 (mmt) cc_final: 0.6428 (mmp) REVERT: k 85 THR cc_start: 0.7711 (p) cc_final: 0.7509 (t) REVERT: k 90 ILE cc_start: 0.9040 (mm) cc_final: 0.8792 (mm) REVERT: l 180 ASN cc_start: 0.8593 (t0) cc_final: 0.8302 (t0) REVERT: o 235 ILE cc_start: 0.9034 (mm) cc_final: 0.8773 (mm) REVERT: q 190 PHE cc_start: 0.7928 (p90) cc_final: 0.7531 (p90) REVERT: r 179 ASP cc_start: 0.7260 (p0) cc_final: 0.6941 (p0) REVERT: t 141 ILE cc_start: 0.8650 (mm) cc_final: 0.8394 (mt) REVERT: u 85 THR cc_start: 0.7683 (p) cc_final: 0.7430 (t) REVERT: u 191 GLU cc_start: 0.6175 (tm-30) cc_final: 0.5972 (tm-30) REVERT: w 177 ASP cc_start: 0.7903 (t0) cc_final: 0.7698 (t70) REVERT: y 61 THR cc_start: 0.7995 (p) cc_final: 0.7793 (p) REVERT: y 66 MET cc_start: 0.7695 (mmp) cc_final: 0.7049 (mmp) outliers start: 207 outliers final: 152 residues processed: 1322 average time/residue: 0.6682 time to fit residues: 1536.0494 Evaluate side-chains 1322 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 1166 time to evaluate : 5.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AB residue 73 VAL Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain AC residue 182 SER Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 3 residue 48 ASN Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 216 MET Chi-restraints excluded: chain 4 residue 127 THR Chi-restraints excluded: chain 4 residue 147 VAL Chi-restraints excluded: chain 4 residue 162 LEU Chi-restraints excluded: chain 4 residue 230 MET Chi-restraints excluded: chain 5 residue 191 VAL Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 6 residue 180 ASN Chi-restraints excluded: chain 6 residue 188 VAL Chi-restraints excluded: chain 7 residue 184 GLU Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 143 LEU Chi-restraints excluded: chain 8 residue 168 LEU Chi-restraints excluded: chain 8 residue 216 MET Chi-restraints excluded: chain 9 residue 48 ASN Chi-restraints excluded: chain 9 residue 127 THR Chi-restraints excluded: chain 9 residue 149 THR Chi-restraints excluded: chain 9 residue 204 GLU Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 143 LEU Chi-restraints excluded: chain P residue 163 SER Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 216 MET Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 159 HIS Chi-restraints excluded: chain U residue 48 ASN Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 168 LEU Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 167 ILE Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 60 ILE Chi-restraints excluded: chain Z residue 117 MET Chi-restraints excluded: chain Z residue 163 SER Chi-restraints excluded: chain Z residue 216 MET Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 223 THR Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain d residue 181 ASP Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 117 MET Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 SER Chi-restraints excluded: chain e residue 216 MET Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 174 VAL Chi-restraints excluded: chain f residue 204 GLU Chi-restraints excluded: chain g residue 157 THR Chi-restraints excluded: chain g residue 191 VAL Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain j residue 48 ASN Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 216 MET Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 127 THR Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain m residue 179 ASP Chi-restraints excluded: chain n residue 181 ASP Chi-restraints excluded: chain o residue 117 MET Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain o residue 216 MET Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 149 THR Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain t residue 48 ASN Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 216 MET Chi-restraints excluded: chain t residue 224 LEU Chi-restraints excluded: chain u residue 127 THR Chi-restraints excluded: chain u residue 147 VAL Chi-restraints excluded: chain u residue 149 THR Chi-restraints excluded: chain u residue 162 LEU Chi-restraints excluded: chain v residue 73 VAL Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain w residue 188 VAL Chi-restraints excluded: chain y residue 117 MET Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 143 LEU Chi-restraints excluded: chain z residue 116 LEU Chi-restraints excluded: chain z residue 127 THR Chi-restraints excluded: chain z residue 173 SER Chi-restraints excluded: chain z residue 204 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 224 optimal weight: 6.9990 chunk 599 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 391 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 666 optimal weight: 8.9990 chunk 553 optimal weight: 0.7980 chunk 308 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 349 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 134 GLN C 159 HIS ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 144 ASN a 238 ASN e 219 ASN g 180 ASN k 144 ASN k 184 GLN ** k 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 184 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 55744 Z= 0.188 Angle : 0.642 10.625 75907 Z= 0.320 Chirality : 0.044 0.360 8515 Planarity : 0.006 0.063 9919 Dihedral : 4.531 52.889 7708 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 3.71 % Allowed : 21.64 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.05 (0.10), residues: 6968 helix: -0.83 (0.20), residues: 624 sheet: -1.74 (0.11), residues: 2418 loop : -2.47 (0.09), residues: 3926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 4 208 HIS 0.002 0.001 HIS v 183 PHE 0.012 0.001 PHE K 38 TYR 0.022 0.001 TYR k 190 ARG 0.009 0.000 ARG e 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1404 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 1190 time to evaluate : 5.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8670 (t0) cc_final: 0.8354 (t0) REVERT: 0 180 ASN cc_start: 0.8601 (t0) cc_final: 0.8233 (t0) REVERT: 4 66 MET cc_start: 0.6633 (mmt) cc_final: 0.5948 (mmt) REVERT: 9 63 PRO cc_start: 0.6852 (Cg_endo) cc_final: 0.6651 (Cg_exo) REVERT: C 180 ASN cc_start: 0.8627 (t0) cc_final: 0.8200 (t0) REVERT: J 180 MET cc_start: 0.7070 (tpp) cc_final: 0.6414 (mmp) REVERT: K 85 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7793 (m) REVERT: K 151 ASP cc_start: 0.6952 (p0) cc_final: 0.6717 (p0) REVERT: L 108 LYS cc_start: 0.7138 (tptt) cc_final: 0.6926 (tptm) REVERT: M 180 ASN cc_start: 0.8469 (t0) cc_final: 0.8023 (t0) REVERT: Q 191 GLU cc_start: 0.5848 (tm-30) cc_final: 0.5584 (tm-30) REVERT: Q 208 TRP cc_start: 0.7315 (t60) cc_final: 0.6803 (t-100) REVERT: R 180 ASN cc_start: 0.8598 (t0) cc_final: 0.8212 (t0) REVERT: U 138 LYS cc_start: 0.8102 (ptmt) cc_final: 0.7840 (tttp) REVERT: U 151 ASP cc_start: 0.6931 (p0) cc_final: 0.6685 (p0) REVERT: U 164 ASP cc_start: 0.7938 (p0) cc_final: 0.7679 (p0) REVERT: V 208 TRP cc_start: 0.7216 (t60) cc_final: 0.6907 (t-100) REVERT: Z 138 LYS cc_start: 0.8203 (ptmt) cc_final: 0.7930 (tttp) REVERT: e 235 ILE cc_start: 0.8978 (mm) cc_final: 0.8707 (mm) REVERT: f 66 MET cc_start: 0.7156 (mmt) cc_final: 0.6800 (mmp) REVERT: h 177 ASP cc_start: 0.7694 (t0) cc_final: 0.7333 (t0) REVERT: h 179 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6739 (p0) REVERT: j 129 LYS cc_start: 0.8816 (ptpp) cc_final: 0.8488 (ptpp) REVERT: j 138 LYS cc_start: 0.8224 (ptmt) cc_final: 0.7984 (tttp) REVERT: k 90 ILE cc_start: 0.9027 (mm) cc_final: 0.8779 (mm) REVERT: l 180 ASN cc_start: 0.8601 (t0) cc_final: 0.8272 (t0) REVERT: o 235 ILE cc_start: 0.9025 (mm) cc_final: 0.8691 (mm) REVERT: t 141 ILE cc_start: 0.8643 (mm) cc_final: 0.8388 (mt) REVERT: y 66 MET cc_start: 0.7761 (mmp) cc_final: 0.7009 (mmp) REVERT: z 144 ASN cc_start: 0.8655 (t0) cc_final: 0.8065 (t0) outliers start: 214 outliers final: 162 residues processed: 1313 average time/residue: 0.6015 time to fit residues: 1347.0437 Evaluate side-chains 1322 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 1158 time to evaluate : 5.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain AC residue 180 MET Chi-restraints excluded: chain AC residue 182 SER Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 3 residue 48 ASN Chi-restraints excluded: chain 3 residue 163 SER Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 216 MET Chi-restraints excluded: chain 4 residue 127 THR Chi-restraints excluded: chain 4 residue 162 LEU Chi-restraints excluded: chain 4 residue 230 MET Chi-restraints excluded: chain 5 residue 157 THR Chi-restraints excluded: chain 5 residue 191 VAL Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 6 residue 180 ASN Chi-restraints excluded: chain 6 residue 188 VAL Chi-restraints excluded: chain 7 residue 184 GLU Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 168 LEU Chi-restraints excluded: chain 8 residue 216 MET Chi-restraints excluded: chain 9 residue 127 THR Chi-restraints excluded: chain 9 residue 149 THR Chi-restraints excluded: chain 9 residue 204 GLU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 196 ASP Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 184 GLN Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 163 SER Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 216 MET Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 159 HIS Chi-restraints excluded: chain U residue 48 ASN Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 168 LEU Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 167 ILE Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 60 ILE Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 117 MET Chi-restraints excluded: chain Z residue 145 ARG Chi-restraints excluded: chain Z residue 163 SER Chi-restraints excluded: chain Z residue 168 LEU Chi-restraints excluded: chain Z residue 188 ASP Chi-restraints excluded: chain Z residue 216 MET Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 117 MET Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 163 SER Chi-restraints excluded: chain e residue 216 MET Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 174 VAL Chi-restraints excluded: chain f residue 204 GLU Chi-restraints excluded: chain g residue 157 THR Chi-restraints excluded: chain g residue 180 ASN Chi-restraints excluded: chain g residue 191 VAL Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain j residue 48 ASN Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 216 MET Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 127 THR Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain n residue 181 ASP Chi-restraints excluded: chain o residue 117 MET Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain o residue 163 SER Chi-restraints excluded: chain o residue 168 LEU Chi-restraints excluded: chain o residue 216 MET Chi-restraints excluded: chain p residue 48 ASN Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 149 THR Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain t residue 48 ASN Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 163 SER Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 216 MET Chi-restraints excluded: chain t residue 224 LEU Chi-restraints excluded: chain u residue 127 THR Chi-restraints excluded: chain u residue 147 VAL Chi-restraints excluded: chain u residue 149 THR Chi-restraints excluded: chain v residue 73 VAL Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain w residue 188 VAL Chi-restraints excluded: chain y residue 60 ILE Chi-restraints excluded: chain y residue 81 THR Chi-restraints excluded: chain y residue 117 MET Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 143 LEU Chi-restraints excluded: chain y residue 216 MET Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 173 SER Chi-restraints excluded: chain z residue 204 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 642 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 379 optimal weight: 5.9990 chunk 486 optimal weight: 0.5980 chunk 377 optimal weight: 0.9990 chunk 561 optimal weight: 10.0000 chunk 372 optimal weight: 6.9990 chunk 664 optimal weight: 0.0970 chunk 415 optimal weight: 0.0870 chunk 404 optimal weight: 5.9990 chunk 306 optimal weight: 0.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 48 ASN A 222 GLN B 48 ASN C 159 HIS ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN R 159 HIS ** S 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 144 ASN W 180 ASN a 238 ASN b 166 GLN f 48 ASN j 184 GLN k 184 GLN ** k 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 184 GLN z 144 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 55744 Z= 0.175 Angle : 0.639 11.220 75907 Z= 0.316 Chirality : 0.044 0.250 8515 Planarity : 0.005 0.055 9919 Dihedral : 4.338 52.006 7704 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 3.57 % Allowed : 22.16 % Favored : 74.27 % 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: -2.88 (0.10), residues: 6968 helix: -0.66 (0.20), residues: 624 sheet: -1.56 (0.11), residues: 2483 loop : -2.40 (0.10), residues: 3861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 4 208 HIS 0.002 0.001 HIS v 183 PHE 0.013 0.001 PHE U 38 TYR 0.009 0.001 TYR V 136 ARG 0.009 0.000 ARG Z 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1370 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 1164 time to evaluate : 6.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8679 (t0) cc_final: 0.8364 (t0) REVERT: 0 180 ASN cc_start: 0.8545 (t0) cc_final: 0.8210 (t0) REVERT: 3 230 MET cc_start: 0.6799 (tpp) cc_final: 0.6457 (tpp) REVERT: C 180 ASN cc_start: 0.8592 (t0) cc_final: 0.8151 (t0) REVERT: I 199 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8036 (mm) REVERT: J 180 MET cc_start: 0.7473 (tpp) cc_final: 0.7194 (tpt) REVERT: K 85 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7768 (m) REVERT: K 151 ASP cc_start: 0.6936 (p0) cc_final: 0.6692 (p0) REVERT: M 180 ASN cc_start: 0.8433 (t0) cc_final: 0.7955 (t0) REVERT: Q 191 GLU cc_start: 0.5785 (tm-30) cc_final: 0.5537 (tm-30) REVERT: Q 208 TRP cc_start: 0.7208 (t60) cc_final: 0.6759 (t-100) REVERT: R 180 ASN cc_start: 0.8581 (t0) cc_final: 0.8173 (t0) REVERT: U 138 LYS cc_start: 0.8160 (ptmt) cc_final: 0.7879 (tttp) REVERT: U 151 ASP cc_start: 0.6930 (p0) cc_final: 0.6676 (p0) REVERT: U 164 ASP cc_start: 0.7887 (p0) cc_final: 0.7592 (p0) REVERT: V 208 TRP cc_start: 0.7184 (t60) cc_final: 0.6888 (t-100) REVERT: X 199 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7781 (mm) REVERT: Z 138 LYS cc_start: 0.8185 (ptmt) cc_final: 0.7825 (tttt) REVERT: a 208 TRP cc_start: 0.7348 (t60) cc_final: 0.6600 (t-100) REVERT: e 235 ILE cc_start: 0.8969 (mm) cc_final: 0.8691 (mm) REVERT: f 66 MET cc_start: 0.7564 (mmt) cc_final: 0.7212 (mmp) REVERT: h 177 ASP cc_start: 0.7700 (t0) cc_final: 0.7498 (t0) REVERT: j 138 LYS cc_start: 0.8212 (ptmt) cc_final: 0.7979 (tttp) REVERT: k 90 ILE cc_start: 0.9022 (mm) cc_final: 0.8786 (mm) REVERT: l 180 ASN cc_start: 0.8561 (t0) cc_final: 0.8194 (t0) REVERT: o 235 ILE cc_start: 0.9010 (mm) cc_final: 0.8677 (mm) REVERT: t 141 ILE cc_start: 0.8638 (mm) cc_final: 0.8386 (mt) REVERT: z 144 ASN cc_start: 0.8695 (t0) cc_final: 0.8238 (t0) outliers start: 206 outliers final: 147 residues processed: 1284 average time/residue: 0.6008 time to fit residues: 1312.4955 Evaluate side-chains 1287 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 1137 time to evaluate : 6.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AB residue 73 VAL Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain AC residue 182 SER Chi-restraints excluded: chain 0 residue 73 VAL Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 2 residue 184 GLU Chi-restraints excluded: chain 3 residue 48 ASN Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 216 MET Chi-restraints excluded: chain 4 residue 26 SER Chi-restraints excluded: chain 4 residue 127 THR Chi-restraints excluded: chain 4 residue 230 MET Chi-restraints excluded: chain 5 residue 157 THR Chi-restraints excluded: chain 5 residue 191 VAL Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 8 residue 60 ILE Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 163 SER Chi-restraints excluded: chain 8 residue 168 LEU Chi-restraints excluded: chain 9 residue 48 ASN Chi-restraints excluded: chain 9 residue 127 THR Chi-restraints excluded: chain 9 residue 204 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 184 GLN Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain P residue 108 LYS Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 216 MET Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 159 HIS Chi-restraints excluded: chain U residue 48 ASN Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 168 LEU Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 180 ASN Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 60 ILE Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 168 LEU Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 117 MET Chi-restraints excluded: chain e residue 141 ILE Chi-restraints excluded: chain e residue 216 MET Chi-restraints excluded: chain f residue 48 ASN Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 174 VAL Chi-restraints excluded: chain f residue 204 GLU Chi-restraints excluded: chain g residue 157 THR Chi-restraints excluded: chain g residue 191 VAL Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain j residue 48 ASN Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 216 MET Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 127 THR Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 117 MET Chi-restraints excluded: chain o residue 137 GLU Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain o residue 163 SER Chi-restraints excluded: chain p residue 48 ASN Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 149 THR Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain t residue 48 ASN Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 163 SER Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 216 MET Chi-restraints excluded: chain u residue 127 THR Chi-restraints excluded: chain u residue 147 VAL Chi-restraints excluded: chain u residue 149 THR Chi-restraints excluded: chain v residue 73 VAL Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain w residue 188 VAL Chi-restraints excluded: chain y residue 60 ILE Chi-restraints excluded: chain y residue 81 THR Chi-restraints excluded: chain y residue 117 MET Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 163 SER Chi-restraints excluded: chain y residue 216 MET Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 173 SER Chi-restraints excluded: chain z residue 204 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 410 optimal weight: 0.9980 chunk 265 optimal weight: 6.9990 chunk 396 optimal weight: 0.0010 chunk 200 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 422 optimal weight: 0.9980 chunk 452 optimal weight: 8.9990 chunk 328 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 521 optimal weight: 0.0370 overall best weight: 0.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 180 ASN 6 180 ASN C 159 HIS ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 GLN R 159 HIS ** S 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 144 ASN W 180 ASN Z 184 GLN a 238 ASN e 219 ASN ** g 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 184 GLN y 134 GLN z 144 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 55744 Z= 0.175 Angle : 0.642 10.980 75907 Z= 0.317 Chirality : 0.044 0.389 8515 Planarity : 0.005 0.054 9919 Dihedral : 4.236 47.979 7704 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.45 % Allowed : 22.38 % Favored : 74.17 % 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: -2.76 (0.10), residues: 6968 helix: -0.59 (0.20), residues: 624 sheet: -1.24 (0.11), residues: 2405 loop : -2.50 (0.09), residues: 3939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 4 208 HIS 0.003 0.001 HIS W 183 PHE 0.011 0.001 PHE K 38 TYR 0.013 0.001 TYR k 190 ARG 0.009 0.000 ARG e 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13936 Ramachandran restraints generated. 6968 Oldfield, 0 Emsley, 6968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 5772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 1145 time to evaluate : 6.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 180 ASN cc_start: 0.8666 (t0) cc_final: 0.8348 (t0) REVERT: 0 180 ASN cc_start: 0.8533 (t0) cc_final: 0.8190 (t0) REVERT: 6 199 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7887 (mm) REVERT: C 180 ASN cc_start: 0.8515 (t0) cc_final: 0.8056 (t0) REVERT: I 199 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8025 (mm) REVERT: J 180 MET cc_start: 0.7559 (tpp) cc_final: 0.7304 (tpt) REVERT: K 85 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7759 (m) REVERT: K 151 ASP cc_start: 0.6929 (p0) cc_final: 0.6693 (p0) REVERT: L 190 TYR cc_start: 0.7307 (m-80) cc_final: 0.6896 (m-80) REVERT: M 180 ASN cc_start: 0.8471 (t0) cc_final: 0.8016 (t0) REVERT: Q 191 GLU cc_start: 0.5779 (tm-30) cc_final: 0.5523 (tm-30) REVERT: Q 208 TRP cc_start: 0.7210 (t60) cc_final: 0.6797 (t-100) REVERT: R 180 ASN cc_start: 0.8552 (t0) cc_final: 0.8125 (t0) REVERT: U 138 LYS cc_start: 0.8159 (ptmt) cc_final: 0.7881 (tttp) REVERT: U 151 ASP cc_start: 0.6909 (p0) cc_final: 0.6674 (p0) REVERT: U 164 ASP cc_start: 0.7842 (p0) cc_final: 0.7516 (p0) REVERT: V 208 TRP cc_start: 0.7170 (t60) cc_final: 0.6898 (t-100) REVERT: X 199 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7777 (mm) REVERT: Z 128 ARG cc_start: 0.8202 (tpp80) cc_final: 0.7931 (tpp80) REVERT: Z 138 LYS cc_start: 0.8202 (ptmt) cc_final: 0.7865 (tttt) REVERT: Z 184 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7966 (mm-40) REVERT: a 208 TRP cc_start: 0.7385 (t------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 188 VAL Chi-restraints excluded: chain AB residue 73 VAL Chi-restraints excluded: chain AB residue 191 VAL Chi-restraints excluded: chain AB residue 192 VAL Chi-restraints excluded: chain AC residue 180 MET Chi-restraints excluded: chain AC residue 182 SER Chi-restraints excluded: chain 0 residue 73 VAL Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 3 residue 48 ASN Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 3 residue 216 MET Chi-restraints excluded: chain 4 residue 26 SER Chi-restraints excluded: chain 4 residue 127 THR Chi-restraints excluded: chain 4 residue 147 VAL Chi-restraints excluded: chain 4 residue 230 MET Chi-restraints excluded: chain 5 residue 157 THR Chi-restraints excluded: chain 5 residue 191 VAL Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 6 residue 180 ASN Chi-restraints excluded: chain 6 residue 199 LEU Chi-restraints excluded: chain 8 residue 60 ILE Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 168 LEU Chi-restraints excluded: chain 9 residue 127 THR Chi-restraints excluded: chain 9 residue 204 GLU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain F residue 48 ASN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 117 MET Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 168 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 184 GLN Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain P residue 44 ASN Chi-restraints excluded: chain P residue 48 ASN Chi-restraints excluded: chain P residue 81 THR Chi-restraints excluded: chain P residue 117 MET Chi-restraints excluded: chain P residue 163 SER Chi-restraints excluded: chain P residue 216 MET Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain Q residue 149 THR Chi-restraints excluded: chain Q residue 204 GLU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 159 HIS Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain U residue 48 ASN Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 180 ASN Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain X residue 199 LEU Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 60 ILE Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 168 LEU Chi-restraints excluded: chain Z residue 184 GLN Chi-restraints excluded: chain a residue 74 THR Chi-restraints excluded: chain a residue 127 THR Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 184 GLN Chi-restraints excluded: chain a residue 204 GLU Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 117 MET Chi-restraints excluded: chain e residue 163 SER Chi-restraints excluded: chain e residue 216 MET Chi-restraints excluded: chain f residue 127 THR Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 174 VAL Chi-restraints excluded: chain f residue 204 GLU Chi-restraints excluded: chain g residue 191 VAL Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain h residue 179 ASP Chi-restraints excluded: chain j residue 48 ASN Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 81 THR Chi-restraints excluded: chain j residue 92 VAL Chi-restraints excluded: chain j residue 117 MET Chi-restraints excluded: chain j residue 168 LEU Chi-restraints excluded: chain j residue 216 MET Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 102 VAL Chi-restraints excluded: chain k residue 127 THR Chi-restraints excluded: chain k residue 173 SER Chi-restraints excluded: chain k residue 178 LYS Chi-restraints excluded: chain l residue 188 VAL Chi-restraints excluded: chain o residue 40 LEU Chi-restraints excluded: chain o residue 44 ASN Chi-restraints excluded: chain o residue 81 THR Chi-restraints excluded: chain o residue 117 MET Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain o residue 163 SER Chi-restraints excluded: chain o residue 168 LEU Chi-restraints excluded: chain p residue 48 ASN Chi-restraints excluded: chain p residue 127 THR Chi-restraints excluded: chain p residue 149 THR Chi-restraints excluded: chain p residue 173 SER Chi-restraints excluded: chain q residue 73 VAL Chi-restraints excluded: chain q residue 188 VAL Chi-restraints excluded: chain q residue 191 VAL Chi-restraints excluded: chain t residue 48 ASN Chi-restraints excluded: chain t residue 92 VAL Chi-restraints excluded: chain t residue 143 LEU Chi-restraints excluded: chain t residue 163 SER Chi-restraints excluded: chain t residue 168 LEU Chi-restraints excluded: chain t residue 216 MET Chi-restraints excluded: chain u residue 127 THR Chi-restraints excluded: chain u residue 147 VAL Chi-restraints excluded: chain u residue 149 THR Chi-restraints excluded: chain u residue 162 LEU Chi-restraints excluded: chain v residue 157 THR Chi-restraints excluded: chain v residue 191 VAL Chi-restraints excluded: chain w residue 179 ASP Chi-restraints excluded: chain w residue 188 VAL Chi-restraints excluded: chain y residue 60 ILE Chi-restraints excluded: chain y residue 81 THR Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 163 SER Chi-restraints excluded: chain y residue 168 LEU Chi-restraints excluded: chain y residue 216 MET Chi-restraints excluded: chain z residue 48 ASN Chi-restraints excluded: chain z residue 173 SER Chi-restraints excluded: chain z residue 204 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 689 random chunks: chunk 604 optimal weight: 3.9990 chunk 636 optimal weight: 0.0010 chunk 580 optimal weight: 5.9990 chunk 618 optimal weight: 0.7980 chunk 372 optimal weight: 6.9990 chunk 269 optimal weight: 0.0470 chunk 485 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 559 optimal weight: 3.9990 chunk 585 optimal weight: 3.9990 chunk 616 optimal weight: 5.9990 overall best weight: 1.1686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: