Starting phenix.real_space_refine on Fri Mar 15 22:16:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/03_2024/6wkx_21812.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/03_2024/6wkx_21812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/03_2024/6wkx_21812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/03_2024/6wkx_21812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/03_2024/6wkx_21812.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/03_2024/6wkx_21812.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 8085 2.51 5 N 2415 2.21 5 O 2415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "V ARG 110": "NH1" <-> "NH2" Residue "W ARG 210": "NH1" <-> "NH2" Residue "X ARG 310": "NH1" <-> "NH2" Residue "X GLU 313": "OE1" <-> "OE2" Residue "Y ARG 410": "NH1" <-> "NH2" Residue "Y GLU 413": "OE1" <-> "OE2" Residue "B ARG 10": "NH1" <-> "NH2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "Z ARG 110": "NH1" <-> "NH2" Residue "a ARG 210": "NH1" <-> "NH2" Residue "b ARG 310": "NH1" <-> "NH2" Residue "b GLU 313": "OE1" <-> "OE2" Residue "c ARG 410": "NH1" <-> "NH2" Residue "c GLU 413": "OE1" <-> "OE2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "d ARG 110": "NH1" <-> "NH2" Residue "e ARG 210": "NH1" <-> "NH2" Residue "f ARG 310": "NH1" <-> "NH2" Residue "f GLU 313": "OE1" <-> "OE2" Residue "g ARG 410": "NH1" <-> "NH2" Residue "g GLU 413": "OE1" <-> "OE2" Residue "D ARG 10": "NH1" <-> "NH2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "h ARG 110": "NH1" <-> "NH2" Residue "i ARG 210": "NH1" <-> "NH2" Residue "j ARG 310": "NH1" <-> "NH2" Residue "j GLU 313": "OE1" <-> "OE2" Residue "k ARG 410": "NH1" <-> "NH2" Residue "k GLU 413": "OE1" <-> "OE2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E GLU 13": "OE1" <-> "OE2" Residue "l ARG 110": "NH1" <-> "NH2" Residue "m ARG 210": "NH1" <-> "NH2" Residue "n ARG 310": "NH1" <-> "NH2" Residue "n GLU 313": "OE1" <-> "OE2" Residue "o ARG 410": "NH1" <-> "NH2" Residue "o GLU 413": "OE1" <-> "OE2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F GLU 13": "OE1" <-> "OE2" Residue "p ARG 110": "NH1" <-> "NH2" Residue "q ARG 210": "NH1" <-> "NH2" Residue "r ARG 310": "NH1" <-> "NH2" Residue "r GLU 313": "OE1" <-> "OE2" Residue "s ARG 410": "NH1" <-> "NH2" Residue "s GLU 413": "OE1" <-> "OE2" Residue "G ARG 10": "NH1" <-> "NH2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "t ARG 110": "NH1" <-> "NH2" Residue "u ARG 210": "NH1" <-> "NH2" Residue "v ARG 310": "NH1" <-> "NH2" Residue "v GLU 313": "OE1" <-> "OE2" Residue "w ARG 410": "NH1" <-> "NH2" Residue "w GLU 413": "OE1" <-> "OE2" Residue "H ARG 10": "NH1" <-> "NH2" Residue "H GLU 13": "OE1" <-> "OE2" Residue "x ARG 110": "NH1" <-> "NH2" Residue "y ARG 210": "NH1" <-> "NH2" Residue "z ARG 310": "NH1" <-> "NH2" Residue "z GLU 313": "OE1" <-> "OE2" Residue "0 ARG 410": "NH1" <-> "NH2" Residue "0 GLU 413": "OE1" <-> "OE2" Residue "I ARG 10": "NH1" <-> "NH2" Residue "I GLU 13": "OE1" <-> "OE2" Residue "1 ARG 110": "NH1" <-> "NH2" Residue "2 ARG 210": "NH1" <-> "NH2" Residue "3 ARG 310": "NH1" <-> "NH2" Residue "3 GLU 313": "OE1" <-> "OE2" Residue "4 ARG 410": "NH1" <-> "NH2" Residue "4 GLU 413": "OE1" <-> "OE2" Residue "J ARG 10": "NH1" <-> "NH2" Residue "J GLU 13": "OE1" <-> "OE2" Residue "5 ARG 110": "NH1" <-> "NH2" Residue "6 ARG 210": "NH1" <-> "NH2" Residue "7 ARG 310": "NH1" <-> "NH2" Residue "7 GLU 313": "OE1" <-> "OE2" Residue "8 ARG 410": "NH1" <-> "NH2" Residue "8 GLU 413": "OE1" <-> "OE2" Residue "K ARG 10": "NH1" <-> "NH2" Residue "K GLU 13": "OE1" <-> "OE2" Residue "9 ARG 110": "NH1" <-> "NH2" Residue "AA ARG 210": "NH1" <-> "NH2" Residue "BA ARG 310": "NH1" <-> "NH2" Residue "BA GLU 313": "OE1" <-> "OE2" Residue "CA ARG 410": "NH1" <-> "NH2" Residue "CA GLU 413": "OE1" <-> "OE2" Residue "L ARG 10": "NH1" <-> "NH2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "DA ARG 110": "NH1" <-> "NH2" Residue "EA ARG 210": "NH1" <-> "NH2" Residue "FA ARG 310": "NH1" <-> "NH2" Residue "FA GLU 313": "OE1" <-> "OE2" Residue "GA ARG 410": "NH1" <-> "NH2" Residue "GA GLU 413": "OE1" <-> "OE2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M GLU 13": "OE1" <-> "OE2" Residue "HA ARG 110": "NH1" <-> "NH2" Residue "IA ARG 210": "NH1" <-> "NH2" Residue "JA ARG 310": "NH1" <-> "NH2" Residue "JA GLU 313": "OE1" <-> "OE2" Residue "KA ARG 410": "NH1" <-> "NH2" Residue "KA GLU 413": "OE1" <-> "OE2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N GLU 13": "OE1" <-> "OE2" Residue "LA ARG 110": "NH1" <-> "NH2" Residue "MA ARG 210": "NH1" <-> "NH2" Residue "NA ARG 310": "NH1" <-> "NH2" Residue "NA GLU 313": "OE1" <-> "OE2" Residue "OA ARG 410": "NH1" <-> "NH2" Residue "OA GLU 413": "OE1" <-> "OE2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O GLU 13": "OE1" <-> "OE2" Residue "PA ARG 110": "NH1" <-> "NH2" Residue "QA ARG 210": "NH1" <-> "NH2" Residue "RA ARG 310": "NH1" <-> "NH2" Residue "RA GLU 313": "OE1" <-> "OE2" Residue "SA ARG 410": "NH1" <-> "NH2" Residue "SA GLU 413": "OE1" <-> "OE2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P GLU 13": "OE1" <-> "OE2" Residue "TA ARG 110": "NH1" <-> "NH2" Residue "UA ARG 210": "NH1" <-> "NH2" Residue "VA ARG 310": "NH1" <-> "NH2" Residue "VA GLU 313": "OE1" <-> "OE2" Residue "WA ARG 410": "NH1" <-> "NH2" Residue "WA GLU 413": "OE1" <-> "OE2" Residue "Q ARG 10": "NH1" <-> "NH2" Residue "Q GLU 13": "OE1" <-> "OE2" Residue "XA ARG 110": "NH1" <-> "NH2" Residue "YA ARG 210": "NH1" <-> "NH2" Residue "ZA ARG 310": "NH1" <-> "NH2" Residue "ZA GLU 313": "OE1" <-> "OE2" Residue "aA ARG 410": "NH1" <-> "NH2" Residue "aA GLU 413": "OE1" <-> "OE2" Residue "R ARG 10": "NH1" <-> "NH2" Residue "R GLU 13": "OE1" <-> "OE2" Residue "bA ARG 110": "NH1" <-> "NH2" Residue "cA ARG 210": "NH1" <-> "NH2" Residue "dA ARG 310": "NH1" <-> "NH2" Residue "dA GLU 313": "OE1" <-> "OE2" Residue "eA ARG 410": "NH1" <-> "NH2" Residue "eA GLU 413": "OE1" <-> "OE2" Residue "S ARG 10": "NH1" <-> "NH2" Residue "S GLU 13": "OE1" <-> "OE2" Residue "fA ARG 110": "NH1" <-> "NH2" Residue "gA ARG 210": "NH1" <-> "NH2" Residue "hA ARG 310": "NH1" <-> "NH2" Residue "hA GLU 313": "OE1" <-> "OE2" Residue "iA ARG 410": "NH1" <-> "NH2" Residue "iA GLU 413": "OE1" <-> "OE2" Residue "T ARG 10": "NH1" <-> "NH2" Residue "T GLU 13": "OE1" <-> "OE2" Residue "jA ARG 110": "NH1" <-> "NH2" Residue "kA ARG 210": "NH1" <-> "NH2" Residue "lA ARG 310": "NH1" <-> "NH2" Residue "lA GLU 313": "OE1" <-> "OE2" Residue "mA ARG 410": "NH1" <-> "NH2" Residue "mA GLU 413": "OE1" <-> "OE2" Residue "U ARG 10": "NH1" <-> "NH2" Residue "U GLU 13": "OE1" <-> "OE2" Residue "nA ARG 110": "NH1" <-> "NH2" Residue "oA ARG 210": "NH1" <-> "NH2" Residue "pA ARG 310": "NH1" <-> "NH2" Residue "pA GLU 313": "OE1" <-> "OE2" Residue "qA ARG 410": "NH1" <-> "NH2" Residue "qA GLU 413": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12915 Number of models: 1 Model: "" Number of chains: 105 Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "V" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "W" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "X" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "Y" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "Z" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "a" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "b" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "c" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "C" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "d" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "e" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "f" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "g" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "D" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "h" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "i" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "j" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "k" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "E" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "l" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "m" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "n" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "o" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "F" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "p" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "q" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "r" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "s" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "G" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "t" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "u" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "v" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "w" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "H" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "x" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "y" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "z" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "0" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "I" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "1" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "2" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "3" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "4" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "J" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "5" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "6" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "7" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "8" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "K" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "9" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "AA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "BA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "CA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "L" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "DA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "EA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "FA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "GA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "M" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "HA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "IA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "JA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "KA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "N" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "LA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "MA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "NA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "OA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "O" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "PA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "QA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "RA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "SA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "P" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "TA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "UA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "VA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "WA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "Q" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "XA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "YA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "ZA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "aA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "R" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "bA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "cA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "dA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "eA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "S" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "fA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "gA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "hA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "iA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "T" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "jA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "kA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "lA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "mA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "U" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "nA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "oA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "pA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "qA" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Time building chain proxies: 6.55, per 1000 atoms: 0.51 Number of scatterers: 12915 At special positions: 0 Unit cell: (62.4, 63.44, 211.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2415 8.00 N 2415 7.00 C 8085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.02 Conformation dependent library (CDL) restraints added in 2.0 seconds 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3150 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 0 sheets defined 93.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 removed outlier: 3.649A pdb=" N LEU A 5 " --> pdb=" O GLN A 1 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 115 Processing helix chain 'W' and resid 202 through 215 Processing helix chain 'X' and resid 302 through 315 Processing helix chain 'Y' and resid 402 through 415 Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'Z' and resid 102 through 115 Processing helix chain 'a' and resid 202 through 215 Processing helix chain 'b' and resid 302 through 315 Processing helix chain 'c' and resid 402 through 415 Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'd' and resid 102 through 115 Processing helix chain 'e' and resid 202 through 215 Processing helix chain 'f' and resid 302 through 315 Processing helix chain 'g' and resid 402 through 415 Processing helix chain 'D' and resid 2 through 15 Processing helix chain 'h' and resid 102 through 115 Processing helix chain 'i' and resid 202 through 215 Processing helix chain 'j' and resid 302 through 315 Processing helix chain 'k' and resid 402 through 415 Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'l' and resid 102 through 115 Processing helix chain 'm' and resid 202 through 215 Processing helix chain 'n' and resid 302 through 315 Processing helix chain 'o' and resid 402 through 415 Processing helix chain 'F' and resid 2 through 15 Processing helix chain 'p' and resid 102 through 115 Processing helix chain 'q' and resid 202 through 215 Processing helix chain 'r' and resid 302 through 315 Processing helix chain 's' and resid 402 through 415 Processing helix chain 'G' and resid 2 through 15 Processing helix chain 't' and resid 102 through 115 Processing helix chain 'u' and resid 202 through 215 Processing helix chain 'v' and resid 302 through 315 Processing helix chain 'w' and resid 402 through 415 Processing helix chain 'H' and resid 2 through 15 Processing helix chain 'x' and resid 102 through 115 Processing helix chain 'y' and resid 202 through 215 Processing helix chain 'z' and resid 302 through 315 Processing helix chain '0' and resid 402 through 415 Processing helix chain 'I' and resid 2 through 15 Processing helix chain '1' and resid 102 through 115 Processing helix chain '2' and resid 202 through 215 Processing helix chain '3' and resid 302 through 315 Processing helix chain '4' and resid 402 through 415 Processing helix chain 'J' and resid 2 through 15 Processing helix chain '5' and resid 102 through 115 Processing helix chain '6' and resid 202 through 215 Processing helix chain '7' and resid 302 through 315 Processing helix chain '8' and resid 402 through 415 Processing helix chain 'K' and resid 2 through 15 Processing helix chain '9' and resid 102 through 115 Processing helix chain 'AA' and resid 202 through 215 Processing helix chain 'BA' and resid 302 through 315 Processing helix chain 'CA' and resid 402 through 415 Processing helix chain 'L' and resid 2 through 15 Processing helix chain 'DA' and resid 102 through 115 Processing helix chain 'EA' and resid 202 through 215 Processing helix chain 'FA' and resid 302 through 315 Processing helix chain 'GA' and resid 402 through 415 Processing helix chain 'M' and resid 2 through 15 Processing helix chain 'HA' and resid 102 through 115 Processing helix chain 'IA' and resid 202 through 215 Processing helix chain 'JA' and resid 302 through 315 Processing helix chain 'KA' and resid 402 through 415 Processing helix chain 'N' and resid 2 through 15 Processing helix chain 'LA' and resid 102 through 115 Processing helix chain 'MA' and resid 202 through 215 Processing helix chain 'NA' and resid 302 through 315 Processing helix chain 'OA' and resid 402 through 415 Processing helix chain 'O' and resid 2 through 15 Processing helix chain 'PA' and resid 102 through 115 Processing helix chain 'QA' and resid 202 through 215 Processing helix chain 'RA' and resid 302 through 315 Processing helix chain 'SA' and resid 402 through 415 Processing helix chain 'P' and resid 2 through 15 Processing helix chain 'TA' and resid 102 through 115 Processing helix chain 'UA' and resid 202 through 215 Processing helix chain 'VA' and resid 302 through 315 Processing helix chain 'WA' and resid 402 through 415 Processing helix chain 'Q' and resid 2 through 15 Processing helix chain 'XA' and resid 102 through 115 Processing helix chain 'YA' and resid 202 through 215 Processing helix chain 'ZA' and resid 302 through 315 Processing helix chain 'aA' and resid 402 through 415 Processing helix chain 'R' and resid 2 through 15 Processing helix chain 'bA' and resid 102 through 115 Processing helix chain 'cA' and resid 202 through 215 Processing helix chain 'dA' and resid 302 through 315 Processing helix chain 'eA' and resid 402 through 415 Processing helix chain 'S' and resid 2 through 15 Processing helix chain 'fA' and resid 102 through 115 Processing helix chain 'gA' and resid 202 through 215 Processing helix chain 'hA' and resid 302 through 315 Processing helix chain 'iA' and resid 402 through 415 Processing helix chain 'T' and resid 2 through 15 Processing helix chain 'jA' and resid 102 through 115 Processing helix chain 'kA' and resid 202 through 215 Processing helix chain 'lA' and resid 302 through 315 Processing helix chain 'mA' and resid 402 through 415 Processing helix chain 'U' and resid 2 through 15 Processing helix chain 'nA' and resid 102 through 115 Processing helix chain 'oA' and resid 202 through 215 Processing helix chain 'pA' and resid 302 through 315 Processing helix chain 'qA' and resid 402 through 415 1050 hydrogen bonds defined for protein. 3150 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: 3.74 Time building geometry restraints manager: 6.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 2310 1.29 - 1.35: 2310 1.35 - 1.41: 735 1.41 - 1.47: 1785 1.47 - 1.54: 5775 Bond restraints: 12915 Sorted by residual: bond pdb=" CA ILEgA 211 " pdb=" C ILEgA 211 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.18e-02 7.18e+03 4.90e-01 bond pdb=" CA GLUoA 213 " pdb=" C GLUoA 213 " ideal model delta sigma weight residual 1.527 1.518 0.008 1.21e-02 6.83e+03 4.73e-01 bond pdb=" CA ILEYA 211 " pdb=" C ILEYA 211 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.18e-02 7.18e+03 4.69e-01 bond pdb=" CA ILE a 211 " pdb=" C ILE a 211 " ideal model delta sigma weight residual 1.524 1.516 0.008 1.18e-02 7.18e+03 4.58e-01 bond pdb=" CA GLU a 213 " pdb=" C GLU a 213 " ideal model delta sigma weight residual 1.527 1.519 0.008 1.21e-02 6.83e+03 4.57e-01 ... (remaining 12910 not shown) Histogram of bond angle deviations from ideal: 108.65 - 111.76: 5810 111.76 - 114.87: 2037 114.87 - 117.98: 1627 117.98 - 121.09: 5143 121.09 - 124.20: 2708 Bond angle restraints: 17325 Sorted by residual: angle pdb=" NE ARGWA 406 " pdb=" CZ ARGWA 406 " pdb=" NH1 ARGWA 406 " ideal model delta sigma weight residual 121.50 119.78 1.72 1.00e+00 1.00e+00 2.96e+00 angle pdb=" NE ARG G 6 " pdb=" CZ ARG G 6 " pdb=" NH1 ARG G 6 " ideal model delta sigma weight residual 121.50 119.79 1.71 1.00e+00 1.00e+00 2.93e+00 angle pdb=" NE ARG R 6 " pdb=" CZ ARG R 6 " pdb=" NH1 ARG R 6 " ideal model delta sigma weight residual 121.50 119.79 1.71 1.00e+00 1.00e+00 2.91e+00 angle pdb=" NE ARG w 406 " pdb=" CZ ARG w 406 " pdb=" NH1 ARG w 406 " ideal model delta sigma weight residual 121.50 119.79 1.71 1.00e+00 1.00e+00 2.91e+00 angle pdb=" NE ARGOA 406 " pdb=" CZ ARGOA 406 " pdb=" NH1 ARGOA 406 " ideal model delta sigma weight residual 121.50 119.81 1.69 1.00e+00 1.00e+00 2.87e+00 ... (remaining 17320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.02: 5691 8.02 - 16.05: 1232 16.05 - 24.07: 574 24.07 - 32.09: 399 32.09 - 40.11: 294 Dihedral angle restraints: 8190 sinusoidal: 3465 harmonic: 4725 Sorted by residual: dihedral pdb=" CA ILE 6 204 " pdb=" CB ILE 6 204 " pdb=" CG1 ILE 6 204 " pdb=" CD1 ILE 6 204 " ideal model delta sinusoidal sigma weight residual 60.00 100.11 -40.11 3 1.50e+01 4.44e-03 7.14e+00 dihedral pdb=" CA ILEgA 204 " pdb=" CB ILEgA 204 " pdb=" CG1 ILEgA 204 " pdb=" CD1 ILEgA 204 " ideal model delta sinusoidal sigma weight residual 60.00 100.11 -40.11 3 1.50e+01 4.44e-03 7.14e+00 dihedral pdb=" CA ILEIA 204 " pdb=" CB ILEIA 204 " pdb=" CG1 ILEIA 204 " pdb=" CD1 ILEIA 204 " ideal model delta sinusoidal sigma weight residual 60.00 100.11 -40.11 3 1.50e+01 4.44e-03 7.13e+00 ... (remaining 8187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.017: 612 0.017 - 0.033: 449 0.033 - 0.050: 532 0.050 - 0.066: 205 0.066 - 0.083: 197 Chirality restraints: 1995 Sorted by residual: chirality pdb=" CA ILE 3 311 " pdb=" N ILE 3 311 " pdb=" C ILE 3 311 " pdb=" CB ILE 3 311 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.08 2.00e-01 2.50e+01 1.71e-01 chirality pdb=" CA ILEBA 311 " pdb=" N ILEBA 311 " pdb=" C ILEBA 311 " pdb=" CB ILEBA 311 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.08 2.00e-01 2.50e+01 1.69e-01 chirality pdb=" CA ILE j 311 " pdb=" N ILE j 311 " pdb=" C ILE j 311 " pdb=" CB ILE j 311 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.08 2.00e-01 2.50e+01 1.68e-01 ... (remaining 1992 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR v 308 " -0.008 2.00e-02 2.50e+03 5.84e-03 6.83e-01 pdb=" CG TYR v 308 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR v 308 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR v 308 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR v 308 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR v 308 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR v 308 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR v 308 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRdA 308 " -0.008 2.00e-02 2.50e+03 5.83e-03 6.80e-01 pdb=" CG TYRdA 308 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYRdA 308 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYRdA 308 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYRdA 308 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYRdA 308 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYRdA 308 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYRdA 308 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRRA 308 " 0.008 2.00e-02 2.50e+03 5.79e-03 6.71e-01 pdb=" CG TYRRA 308 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYRRA 308 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYRRA 308 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYRRA 308 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYRRA 308 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYRRA 308 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYRRA 308 " -0.000 2.00e-02 2.50e+03 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4158 2.82 - 3.34: 15647 3.34 - 3.86: 21033 3.86 - 4.38: 25256 4.38 - 4.90: 38427 Nonbonded interactions: 104521 Sorted by model distance: nonbonded pdb=" O GLU I 13 " pdb=" NH2 ARG 9 110 " model vdw 2.298 2.520 nonbonded pdb=" NH2 ARG 0 410 " pdb=" O GLU 7 313 " model vdw 2.311 2.520 nonbonded pdb=" O GLU M 13 " pdb=" NH2 ARGPA 110 " model vdw 2.329 2.520 nonbonded pdb=" O GLU C 13 " pdb=" NH2 ARG l 110 " model vdw 2.335 2.520 nonbonded pdb=" O GLU f 313 " pdb=" NH2 ARG o 410 " model vdw 2.341 2.520 ... (remaining 104516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain 'CA' selection = chain 'D' selection = chain 'DA' selection = chain 'E' selection = chain 'EA' selection = chain 'F' selection = chain 'FA' selection = chain 'G' selection = chain 'GA' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'IA' selection = chain 'J' selection = chain 'JA' selection = chain 'K' selection = chain 'KA' selection = chain 'L' selection = chain 'LA' selection = chain 'M' selection = chain 'MA' selection = chain 'N' selection = chain 'NA' selection = chain 'O' selection = chain 'OA' selection = chain 'P' selection = chain 'PA' selection = chain 'Q' selection = chain 'QA' selection = chain 'R' selection = chain 'RA' selection = chain 'S' selection = chain 'SA' selection = chain 'T' selection = chain 'TA' selection = chain 'U' selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'XA' selection = chain 'Y' selection = chain 'YA' selection = chain 'Z' selection = chain 'ZA' selection = chain 'a' selection = chain 'aA' selection = chain 'b' selection = chain 'bA' selection = chain 'c' selection = chain 'cA' selection = chain 'd' selection = chain 'dA' selection = chain 'e' selection = chain 'eA' selection = chain 'f' selection = chain 'fA' selection = chain 'g' selection = chain 'gA' selection = chain 'h' selection = chain 'hA' selection = chain 'i' selection = chain 'iA' selection = chain 'j' selection = chain 'jA' selection = chain 'k' selection = chain 'kA' selection = chain 'l' selection = chain 'lA' selection = chain 'm' selection = chain 'mA' selection = chain 'n' selection = chain 'nA' selection = chain 'o' selection = chain 'oA' selection = chain 'p' selection = chain 'pA' selection = chain 'q' selection = chain 'qA' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.310 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 35.920 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 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 0.018 12915 Z= 0.403 Angle : 0.595 3.415 17325 Z= 0.381 Chirality : 0.038 0.083 1995 Planarity : 0.002 0.006 2310 Dihedral : 15.107 40.115 5040 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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: -3.67 (0.20), residues: 1365 helix: -2.12 (0.12), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.004 TYR X 308 ARG 0.001 0.000 ARGHA 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 650 time to evaluate : 1.231 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TYR cc_start: 0.9301 (t80) cc_final: 0.8977 (t80) REVERT: A 15 GLN cc_start: 0.8855 (mt0) cc_final: 0.8508 (mt0) REVERT: V 108 TYR cc_start: 0.9316 (t80) cc_final: 0.8838 (t80) REVERT: V 112 LEU cc_start: 0.9478 (mm) cc_final: 0.9173 (mm) REVERT: V 115 GLN cc_start: 0.8958 (mt0) cc_final: 0.8521 (mt0) REVERT: W 208 TYR cc_start: 0.9317 (t80) cc_final: 0.8870 (t80) REVERT: W 212 LEU cc_start: 0.9437 (mm) cc_final: 0.9146 (mm) REVERT: W 215 GLN cc_start: 0.9125 (mt0) cc_final: 0.8751 (tt0) REVERT: X 308 TYR cc_start: 0.9317 (t80) cc_final: 0.8898 (t80) REVERT: X 315 GLN cc_start: 0.8967 (mt0) cc_final: 0.8416 (mt0) REVERT: Y 408 TYR cc_start: 0.9316 (t80) cc_final: 0.8688 (t80) REVERT: Y 412 LEU cc_start: 0.9460 (mm) cc_final: 0.9096 (mm) REVERT: Y 415 GLN cc_start: 0.8911 (mt0) cc_final: 0.8250 (mt0) REVERT: B 15 GLN cc_start: 0.8857 (mt0) cc_final: 0.8425 (mt0) REVERT: Z 112 LEU cc_start: 0.9439 (mm) cc_final: 0.9152 (mm) REVERT: a 215 GLN cc_start: 0.9140 (mt0) cc_final: 0.8883 (mt0) REVERT: b 315 GLN cc_start: 0.8833 (mt0) cc_final: 0.8454 (mt0) REVERT: C 8 TYR cc_start: 0.9253 (t80) cc_final: 0.8106 (t80) REVERT: C 12 LEU cc_start: 0.9380 (mm) cc_final: 0.9010 (mm) REVERT: C 15 GLN cc_start: 0.8860 (mt0) cc_final: 0.8430 (mt0) REVERT: d 108 TYR cc_start: 0.9308 (t80) cc_final: 0.9104 (t80) REVERT: d 112 LEU cc_start: 0.9542 (mm) cc_final: 0.9288 (mm) REVERT: e 215 GLN cc_start: 0.9083 (mt0) cc_final: 0.8766 (mt0) REVERT: f 308 TYR cc_start: 0.9370 (t80) cc_final: 0.9133 (t80) REVERT: f 312 LEU cc_start: 0.9416 (mm) cc_final: 0.9172 (mm) REVERT: g 415 GLN cc_start: 0.8880 (mt0) cc_final: 0.8616 (mt0) REVERT: i 208 TYR cc_start: 0.9339 (t80) cc_final: 0.8901 (t80) REVERT: j 308 TYR cc_start: 0.9340 (t80) cc_final: 0.8973 (t80) REVERT: j 312 LEU cc_start: 0.9414 (mm) cc_final: 0.9059 (mm) REVERT: k 408 TYR cc_start: 0.9414 (t80) cc_final: 0.9148 (t80) REVERT: E 8 TYR cc_start: 0.9334 (t80) cc_final: 0.9047 (t80) REVERT: E 12 LEU cc_start: 0.9403 (mm) cc_final: 0.9178 (mm) REVERT: m 208 TYR cc_start: 0.9274 (t80) cc_final: 0.8254 (t80) REVERT: m 212 LEU cc_start: 0.9446 (mm) cc_final: 0.9140 (mm) REVERT: m 215 GLN cc_start: 0.9203 (mt0) cc_final: 0.8845 (mt0) REVERT: n 308 TYR cc_start: 0.9366 (t80) cc_final: 0.9145 (t80) REVERT: o 413 GLU cc_start: 0.9352 (pp20) cc_final: 0.9145 (pp20) REVERT: p 108 TYR cc_start: 0.9429 (t80) cc_final: 0.8689 (t80) REVERT: p 112 LEU cc_start: 0.9433 (mm) cc_final: 0.9041 (mm) REVERT: r 308 TYR cc_start: 0.9412 (t80) cc_final: 0.8847 (t80) REVERT: t 108 TYR cc_start: 0.9392 (t80) cc_final: 0.9160 (t80) REVERT: t 112 LEU cc_start: 0.9447 (mm) cc_final: 0.9194 (mm) REVERT: t 115 GLN cc_start: 0.8925 (mt0) cc_final: 0.8633 (mt0) REVERT: u 215 GLN cc_start: 0.9162 (mt0) cc_final: 0.8775 (mt0) REVERT: v 308 TYR cc_start: 0.9309 (t80) cc_final: 0.8839 (t80) REVERT: v 315 GLN cc_start: 0.8904 (mt0) cc_final: 0.8646 (mt0) REVERT: w 413 GLU cc_start: 0.9409 (pp20) cc_final: 0.9162 (pp20) REVERT: H 3 GLU cc_start: 0.8739 (tp30) cc_final: 0.8538 (tp30) REVERT: x 108 TYR cc_start: 0.9340 (t80) cc_final: 0.8687 (t80) REVERT: x 112 LEU cc_start: 0.9524 (mm) cc_final: 0.9106 (mm) REVERT: y 215 GLN cc_start: 0.9194 (mt0) cc_final: 0.8825 (mt0) REVERT: I 8 TYR cc_start: 0.9397 (t80) cc_final: 0.9113 (t80) REVERT: 1 108 TYR cc_start: 0.9398 (t80) cc_final: 0.8828 (t80) REVERT: 1 112 LEU cc_start: 0.9462 (mm) cc_final: 0.9177 (mm) REVERT: 2 215 GLN cc_start: 0.9159 (mt0) cc_final: 0.8703 (mt0) REVERT: 3 312 LEU cc_start: 0.9268 (mm) cc_final: 0.9010 (mm) REVERT: 6 215 GLN cc_start: 0.9140 (mt0) cc_final: 0.8815 (mt0) REVERT: 8 408 TYR cc_start: 0.9287 (t80) cc_final: 0.9034 (t80) REVERT: K 8 TYR cc_start: 0.9365 (t80) cc_final: 0.8388 (t80) REVERT: K 12 LEU cc_start: 0.9349 (mm) cc_final: 0.8917 (mm) REVERT: K 15 GLN cc_start: 0.8849 (mt0) cc_final: 0.8012 (mt0) REVERT: 9 112 LEU cc_start: 0.9486 (mm) cc_final: 0.9247 (mm) REVERT: AA 215 GLN cc_start: 0.9078 (mt0) cc_final: 0.8697 (mt0) REVERT: BA 315 GLN cc_start: 0.8934 (mt0) cc_final: 0.8533 (mt0) REVERT: CA 412 LEU cc_start: 0.9442 (mm) cc_final: 0.9237 (mm) REVERT: L 3 GLU cc_start: 0.8857 (tp30) cc_final: 0.8422 (tp30) REVERT: L 8 TYR cc_start: 0.9277 (t80) cc_final: 0.8394 (t80) REVERT: L 12 LEU cc_start: 0.9439 (mm) cc_final: 0.9059 (mm) REVERT: L 15 GLN cc_start: 0.8947 (mt0) cc_final: 0.8671 (mt0) REVERT: DA 108 TYR cc_start: 0.9266 (t80) cc_final: 0.8421 (t80) REVERT: DA 112 LEU cc_start: 0.9460 (mm) cc_final: 0.9101 (mm) REVERT: EA 208 TYR cc_start: 0.9321 (t80) cc_final: 0.8532 (t80) REVERT: EA 215 GLN cc_start: 0.9060 (mt0) cc_final: 0.8701 (mt0) REVERT: FA 308 TYR cc_start: 0.9266 (t80) cc_final: 0.8365 (t80) REVERT: FA 312 LEU cc_start: 0.9429 (mm) cc_final: 0.9130 (mm) REVERT: FA 315 GLN cc_start: 0.8866 (mt0) cc_final: 0.8401 (mt0) REVERT: GA 408 TYR cc_start: 0.9219 (t80) cc_final: 0.8244 (t80) REVERT: GA 412 LEU cc_start: 0.9426 (mm) cc_final: 0.9095 (mm) REVERT: GA 415 GLN cc_start: 0.8856 (mt0) cc_final: 0.8405 (mt0) REVERT: M 8 TYR cc_start: 0.9289 (t80) cc_final: 0.9081 (t80) REVERT: M 12 LEU cc_start: 0.9418 (mm) cc_final: 0.9184 (mm) REVERT: M 15 GLN cc_start: 0.8877 (mt0) cc_final: 0.8300 (mt0) REVERT: HA 112 LEU cc_start: 0.9506 (mm) cc_final: 0.9247 (mm) REVERT: IA 215 GLN cc_start: 0.9101 (mt0) cc_final: 0.8762 (mt0) REVERT: JA 315 GLN cc_start: 0.8890 (mt0) cc_final: 0.8389 (mt0) REVERT: KA 415 GLN cc_start: 0.8946 (mt0) cc_final: 0.8445 (mt0) REVERT: N 8 TYR cc_start: 0.9353 (t80) cc_final: 0.8993 (t80) REVERT: N 12 LEU cc_start: 0.9388 (mm) cc_final: 0.9136 (mm) REVERT: N 15 GLN cc_start: 0.8823 (mt0) cc_final: 0.8245 (mt0) REVERT: LA 115 GLN cc_start: 0.8895 (mt0) cc_final: 0.8550 (mt0) REVERT: MA 208 TYR cc_start: 0.9314 (t80) cc_final: 0.8966 (t80) REVERT: MA 215 GLN cc_start: 0.9136 (mt0) cc_final: 0.8792 (mt0) REVERT: NA 308 TYR cc_start: 0.9375 (t80) cc_final: 0.9087 (t80) REVERT: NA 315 GLN cc_start: 0.8891 (mt0) cc_final: 0.8450 (mt0) REVERT: OA 408 TYR cc_start: 0.9310 (t80) cc_final: 0.9042 (t80) REVERT: OA 415 GLN cc_start: 0.8988 (mt0) cc_final: 0.8660 (mt0) REVERT: O 8 TYR cc_start: 0.9239 (t80) cc_final: 0.8609 (t80) REVERT: O 12 LEU cc_start: 0.9357 (mm) cc_final: 0.9052 (mm) REVERT: PA 108 TYR cc_start: 0.9372 (t80) cc_final: 0.9050 (t80) REVERT: PA 115 GLN cc_start: 0.8934 (mt0) cc_final: 0.8493 (mt0) REVERT: QA 208 TYR cc_start: 0.9295 (t80) cc_final: 0.8625 (t80) REVERT: QA 215 GLN cc_start: 0.9127 (mt0) cc_final: 0.8760 (mt0) REVERT: RA 308 TYR cc_start: 0.9308 (t80) cc_final: 0.8649 (t80) REVERT: RA 312 LEU cc_start: 0.9411 (mm) cc_final: 0.9067 (mm) REVERT: RA 315 GLN cc_start: 0.8872 (mt0) cc_final: 0.8310 (mt0) REVERT: SA 408 TYR cc_start: 0.9299 (t80) cc_final: 0.8749 (t80) REVERT: SA 412 LEU cc_start: 0.9430 (mm) cc_final: 0.9189 (mm) REVERT: SA 415 GLN cc_start: 0.9023 (mt0) cc_final: 0.8502 (mt0) REVERT: P 15 GLN cc_start: 0.8875 (mt0) cc_final: 0.8407 (mt0) REVERT: UA 212 LEU cc_start: 0.9389 (mm) cc_final: 0.9171 (mm) REVERT: UA 215 GLN cc_start: 0.9123 (mt0) cc_final: 0.8732 (tt0) REVERT: VA 315 GLN cc_start: 0.8730 (mt0) cc_final: 0.8232 (mt0) REVERT: WA 412 LEU cc_start: 0.9403 (mm) cc_final: 0.9120 (mm) REVERT: Q 15 GLN cc_start: 0.8818 (mt0) cc_final: 0.8459 (mt0) REVERT: XA 115 GLN cc_start: 0.8856 (mt0) cc_final: 0.8356 (mt0) REVERT: YA 215 GLN cc_start: 0.9069 (mt0) cc_final: 0.8830 (tt0) REVERT: ZA 315 GLN cc_start: 0.8854 (mt0) cc_final: 0.8322 (mt0) REVERT: aA 415 GLN cc_start: 0.8953 (mt0) cc_final: 0.8536 (mt0) REVERT: R 8 TYR cc_start: 0.9383 (t80) cc_final: 0.9118 (t80) REVERT: R 12 LEU cc_start: 0.9428 (mm) cc_final: 0.9206 (mm) REVERT: cA 211 ILE cc_start: 0.9706 (mt) cc_final: 0.9491 (mm) REVERT: cA 212 LEU cc_start: 0.9387 (mm) cc_final: 0.9173 (mm) REVERT: dA 312 LEU cc_start: 0.9332 (mm) cc_final: 0.9118 (mm) REVERT: eA 408 TYR cc_start: 0.9407 (t80) cc_final: 0.9021 (t80) REVERT: S 8 TYR cc_start: 0.9333 (t80) cc_final: 0.8509 (t80) REVERT: S 12 LEU cc_start: 0.9448 (mm) cc_final: 0.8945 (mm) REVERT: iA 408 TYR cc_start: 0.9292 (t80) cc_final: 0.9024 (t80) REVERT: T 3 GLU cc_start: 0.8810 (tp30) cc_final: 0.8535 (tp30) REVERT: T 11 ILE cc_start: 0.9429 (mt) cc_final: 0.9184 (mm) REVERT: jA 112 LEU cc_start: 0.9202 (mm) cc_final: 0.8963 (mm) REVERT: mA 408 TYR cc_start: 0.9373 (t80) cc_final: 0.8892 (t80) REVERT: mA 412 LEU cc_start: 0.9163 (mm) cc_final: 0.8782 (mm) REVERT: U 8 TYR cc_start: 0.9152 (t80) cc_final: 0.8858 (t80) REVERT: nA 108 TYR cc_start: 0.9235 (t80) cc_final: 0.8887 (t80) REVERT: nA 112 LEU cc_start: 0.9549 (mm) cc_final: 0.9344 (mm) REVERT: oA 215 GLN cc_start: 0.8867 (mt0) cc_final: 0.8630 (mt0) outliers start: 0 outliers final: 0 residues processed: 650 average time/residue: 0.1936 time to fit residues: 191.1627 Evaluate side-chains 623 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 623 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 0.0060 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12915 Z= 0.137 Angle : 0.445 3.964 17325 Z= 0.245 Chirality : 0.036 0.144 1995 Planarity : 0.003 0.015 2310 Dihedral : 3.474 10.765 1890 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.43 % Allowed : 2.51 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1365 helix: 1.19 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYRgA 208 ARG 0.002 0.000 ARG 2 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 658 time to evaluate : 1.426 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8702 (tp30) cc_final: 0.8491 (mm-30) REVERT: A 15 GLN cc_start: 0.8799 (mt0) cc_final: 0.8596 (mt0) REVERT: V 108 TYR cc_start: 0.9171 (t80) cc_final: 0.8800 (t80) REVERT: W 208 TYR cc_start: 0.9163 (t80) cc_final: 0.8879 (t80) REVERT: W 212 LEU cc_start: 0.9402 (mm) cc_final: 0.9189 (mm) REVERT: Y 408 TYR cc_start: 0.9125 (t80) cc_final: 0.8708 (t80) REVERT: Y 412 LEU cc_start: 0.9341 (mm) cc_final: 0.9083 (mm) REVERT: B 15 GLN cc_start: 0.8831 (mt0) cc_final: 0.8525 (tt0) REVERT: b 315 GLN cc_start: 0.8722 (mt0) cc_final: 0.8222 (tt0) REVERT: c 411 ILE cc_start: 0.9380 (mm) cc_final: 0.9175 (mt) REVERT: C 15 GLN cc_start: 0.8901 (mt0) cc_final: 0.8684 (tt0) REVERT: d 108 TYR cc_start: 0.9234 (t80) cc_final: 0.8359 (t80) REVERT: d 112 LEU cc_start: 0.9495 (mm) cc_final: 0.9162 (mm) REVERT: e 208 TYR cc_start: 0.8940 (t80) cc_final: 0.8082 (t80) REVERT: e 212 LEU cc_start: 0.9250 (mm) cc_final: 0.9034 (mm) REVERT: f 308 TYR cc_start: 0.9133 (t80) cc_final: 0.8540 (t80) REVERT: D 3 GLU cc_start: 0.8736 (tp30) cc_final: 0.8487 (mm-30) REVERT: h 115 GLN cc_start: 0.8935 (mt0) cc_final: 0.8716 (mt0) REVERT: i 208 TYR cc_start: 0.9104 (t80) cc_final: 0.8668 (t80) REVERT: i 212 LEU cc_start: 0.9088 (mm) cc_final: 0.8863 (mm) REVERT: j 308 TYR cc_start: 0.9149 (t80) cc_final: 0.8624 (t80) REVERT: j 312 LEU cc_start: 0.9341 (mm) cc_final: 0.9136 (mm) REVERT: k 408 TYR cc_start: 0.9226 (t80) cc_final: 0.8943 (t80) REVERT: l 115 GLN cc_start: 0.8934 (mt0) cc_final: 0.8691 (mt0) REVERT: F 11 ILE cc_start: 0.9408 (mt) cc_final: 0.9166 (mt) REVERT: r 311 ILE cc_start: 0.9323 (mt) cc_final: 0.9068 (mt) REVERT: t 108 TYR cc_start: 0.9173 (t80) cc_final: 0.8779 (t80) REVERT: u 208 TYR cc_start: 0.9034 (t80) cc_final: 0.8749 (t80) REVERT: u 212 LEU cc_start: 0.9435 (mm) cc_final: 0.9196 (mm) REVERT: v 311 ILE cc_start: 0.9357 (mt) cc_final: 0.9105 (mt) REVERT: v 315 GLN cc_start: 0.8734 (mt0) cc_final: 0.8272 (mt0) REVERT: x 111 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8944 (mt) REVERT: x 112 LEU cc_start: 0.9551 (mm) cc_final: 0.8994 (mm) REVERT: x 115 GLN cc_start: 0.8719 (mt0) cc_final: 0.8259 (mt0) REVERT: y 208 TYR cc_start: 0.9021 (t80) cc_final: 0.8390 (t80) REVERT: y 212 LEU cc_start: 0.9318 (mm) cc_final: 0.9033 (mm) REVERT: I 3 GLU cc_start: 0.8786 (tp30) cc_final: 0.8021 (mm-30) REVERT: I 8 TYR cc_start: 0.9289 (t80) cc_final: 0.8906 (t80) REVERT: 1 112 LEU cc_start: 0.9545 (mm) cc_final: 0.9246 (mm) REVERT: 2 211 ILE cc_start: 0.9461 (mt) cc_final: 0.9179 (mt) REVERT: 4 415 GLN cc_start: 0.8815 (mt0) cc_final: 0.7894 (mt0) REVERT: J 15 GLN cc_start: 0.8777 (mt0) cc_final: 0.8571 (tt0) REVERT: 5 115 GLN cc_start: 0.8787 (mt0) cc_final: 0.8547 (mt0) REVERT: K 3 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8261 (tp30) REVERT: K 8 TYR cc_start: 0.9199 (t80) cc_final: 0.8609 (t80) REVERT: K 12 LEU cc_start: 0.9266 (mm) cc_final: 0.9009 (mm) REVERT: 9 112 LEU cc_start: 0.9483 (mm) cc_final: 0.9205 (mm) REVERT: BA 315 GLN cc_start: 0.8838 (mt0) cc_final: 0.8561 (tt0) REVERT: L 8 TYR cc_start: 0.9102 (t80) cc_final: 0.8495 (t80) REVERT: DA 108 TYR cc_start: 0.9145 (t80) cc_final: 0.8500 (t80) REVERT: DA 115 GLN cc_start: 0.8903 (mt0) cc_final: 0.8696 (tt0) REVERT: EA 208 TYR cc_start: 0.9161 (t80) cc_final: 0.8657 (t80) REVERT: FA 308 TYR cc_start: 0.9048 (t80) cc_final: 0.8364 (t80) REVERT: FA 315 GLN cc_start: 0.8749 (mt0) cc_final: 0.8418 (tt0) REVERT: GA 408 TYR cc_start: 0.9129 (t80) cc_final: 0.8465 (t80) REVERT: GA 415 GLN cc_start: 0.8897 (mt0) cc_final: 0.8508 (tt0) REVERT: HA 115 GLN cc_start: 0.8841 (mt0) cc_final: 0.8631 (mt0) REVERT: KA 415 GLN cc_start: 0.8757 (mt0) cc_final: 0.8476 (mt0) REVERT: N 8 TYR cc_start: 0.9129 (t80) cc_final: 0.8893 (t80) REVERT: N 15 GLN cc_start: 0.8764 (mt0) cc_final: 0.8559 (tt0) REVERT: LA 115 GLN cc_start: 0.8902 (mt0) cc_final: 0.8700 (tt0) REVERT: OA 408 TYR cc_start: 0.9125 (t80) cc_final: 0.8916 (t80) REVERT: O 8 TYR cc_start: 0.9085 (t80) cc_final: 0.8658 (t80) REVERT: O 15 GLN cc_start: 0.8778 (mt0) cc_final: 0.8420 (mt0) REVERT: PA 115 GLN cc_start: 0.8933 (mt0) cc_final: 0.8686 (tt0) REVERT: QA 208 TYR cc_start: 0.9048 (t80) cc_final: 0.8793 (t80) REVERT: RA 308 TYR cc_start: 0.9115 (t80) cc_final: 0.8672 (t80) REVERT: RA 312 LEU cc_start: 0.9354 (mm) cc_final: 0.9121 (mm) REVERT: SA 408 TYR cc_start: 0.9075 (t80) cc_final: 0.8669 (t80) REVERT: P 15 GLN cc_start: 0.8813 (mt0) cc_final: 0.8516 (tt0) REVERT: UA 212 LEU cc_start: 0.9416 (mm) cc_final: 0.9095 (mm) REVERT: WA 412 LEU cc_start: 0.9172 (mm) cc_final: 0.8922 (mm) REVERT: XA 108 TYR cc_start: 0.9111 (t80) cc_final: 0.8195 (t80) REVERT: XA 115 GLN cc_start: 0.8818 (mt0) cc_final: 0.8602 (tt0) REVERT: YA 208 TYR cc_start: 0.9137 (t80) cc_final: 0.8287 (t80) REVERT: YA 212 LEU cc_start: 0.9374 (mm) cc_final: 0.9089 (mm) REVERT: ZA 315 GLN cc_start: 0.8772 (mt0) cc_final: 0.8456 (mt0) REVERT: R 8 TYR cc_start: 0.9227 (t80) cc_final: 0.8637 (t80) REVERT: R 12 LEU cc_start: 0.9323 (mm) cc_final: 0.9068 (mm) REVERT: cA 212 LEU cc_start: 0.9187 (mm) cc_final: 0.8949 (mm) REVERT: eA 415 GLN cc_start: 0.9083 (mt0) cc_final: 0.8592 (mt0) REVERT: hA 315 GLN cc_start: 0.8777 (mt0) cc_final: 0.8449 (mt0) REVERT: T 3 GLU cc_start: 0.8712 (tp30) cc_final: 0.8391 (mm-30) REVERT: jA 112 LEU cc_start: 0.9245 (mm) cc_final: 0.9001 (mm) REVERT: lA 308 TYR cc_start: 0.9200 (t80) cc_final: 0.8928 (t80) REVERT: mA 408 TYR cc_start: 0.9252 (t80) cc_final: 0.8835 (t80) REVERT: nA 108 TYR cc_start: 0.9122 (t80) cc_final: 0.8882 (t80) REVERT: qA 408 TYR cc_start: 0.8993 (t80) cc_final: 0.8737 (t80) outliers start: 5 outliers final: 0 residues processed: 658 average time/residue: 0.1943 time to fit residues: 194.1338 Evaluate side-chains 568 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 567 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 415 GLN gA 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12915 Z= 0.201 Angle : 0.477 3.922 17325 Z= 0.249 Chirality : 0.042 0.138 1995 Planarity : 0.002 0.014 2310 Dihedral : 2.663 18.662 1890 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.17 % Allowed : 7.79 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.25), residues: 1365 helix: 1.82 (0.16), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.002 TYR 0 408 ARG 0.002 0.000 ARG o 410 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 631 time to evaluate : 1.661 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8663 (tp30) cc_final: 0.7381 (mm-30) REVERT: V 108 TYR cc_start: 0.9139 (t80) cc_final: 0.8839 (t80) REVERT: V 115 GLN cc_start: 0.8510 (tt0) cc_final: 0.8119 (tp-100) REVERT: W 203 GLU cc_start: 0.8749 (tp30) cc_final: 0.8485 (mm-30) REVERT: W 208 TYR cc_start: 0.9113 (t80) cc_final: 0.8899 (t80) REVERT: Y 408 TYR cc_start: 0.9174 (t80) cc_final: 0.8770 (t80) REVERT: Y 412 LEU cc_start: 0.9449 (mm) cc_final: 0.9240 (mm) REVERT: Y 415 GLN cc_start: 0.9034 (mt0) cc_final: 0.8499 (mt0) REVERT: B 12 LEU cc_start: 0.9433 (mm) cc_final: 0.9223 (mm) REVERT: b 315 GLN cc_start: 0.8806 (mt0) cc_final: 0.8422 (tt0) REVERT: C 8 TYR cc_start: 0.8908 (t80) cc_final: 0.8187 (t80) REVERT: d 108 TYR cc_start: 0.9214 (t80) cc_final: 0.8322 (t80) REVERT: d 112 LEU cc_start: 0.9493 (mm) cc_final: 0.9172 (mm) REVERT: e 208 TYR cc_start: 0.8806 (t80) cc_final: 0.8341 (t80) REVERT: e 215 GLN cc_start: 0.9069 (mt0) cc_final: 0.8833 (mt0) REVERT: f 308 TYR cc_start: 0.9104 (t80) cc_final: 0.8566 (t80) REVERT: g 408 TYR cc_start: 0.8890 (t80) cc_final: 0.8161 (t80) REVERT: h 115 GLN cc_start: 0.9015 (mt0) cc_final: 0.8692 (mt0) REVERT: i 208 TYR cc_start: 0.9122 (t80) cc_final: 0.8475 (t80) REVERT: j 308 TYR cc_start: 0.9139 (t80) cc_final: 0.8579 (t80) REVERT: j 312 LEU cc_start: 0.9458 (mm) cc_final: 0.9237 (mm) REVERT: k 408 TYR cc_start: 0.9229 (t80) cc_final: 0.8793 (t80) REVERT: l 115 GLN cc_start: 0.9001 (mt0) cc_final: 0.8585 (mt0) REVERT: m 211 ILE cc_start: 0.9405 (mt) cc_final: 0.8800 (mp) REVERT: m 212 LEU cc_start: 0.9319 (mm) cc_final: 0.8923 (mm) REVERT: m 215 GLN cc_start: 0.8884 (mt0) cc_final: 0.8501 (mt0) REVERT: t 108 TYR cc_start: 0.9155 (t80) cc_final: 0.8881 (t80) REVERT: t 112 LEU cc_start: 0.9486 (mm) cc_final: 0.9221 (mm) REVERT: u 208 TYR cc_start: 0.9187 (t80) cc_final: 0.8843 (t80) REVERT: u 212 LEU cc_start: 0.9391 (mm) cc_final: 0.9097 (mm) REVERT: v 315 GLN cc_start: 0.8969 (mt0) cc_final: 0.8477 (mt0) REVERT: H 3 GLU cc_start: 0.8593 (tp30) cc_final: 0.8382 (mm-30) REVERT: H 12 LEU cc_start: 0.9510 (mm) cc_final: 0.9273 (mm) REVERT: x 111 ILE cc_start: 0.9303 (mp) cc_final: 0.8999 (mt) REVERT: x 112 LEU cc_start: 0.9526 (mm) cc_final: 0.9007 (mm) REVERT: x 115 GLN cc_start: 0.8791 (mt0) cc_final: 0.8140 (mt0) REVERT: 0 415 GLN cc_start: 0.9102 (mt0) cc_final: 0.8798 (mt0) REVERT: I 8 TYR cc_start: 0.9306 (t80) cc_final: 0.8919 (t80) REVERT: I 11 ILE cc_start: 0.9339 (mt) cc_final: 0.9097 (mt) REVERT: 2 211 ILE cc_start: 0.9468 (mt) cc_final: 0.9257 (mt) REVERT: 3 303 GLU cc_start: 0.8623 (tp30) cc_final: 0.8276 (mm-30) REVERT: 4 412 LEU cc_start: 0.9410 (mp) cc_final: 0.9206 (mp) REVERT: 4 415 GLN cc_start: 0.9036 (mt0) cc_final: 0.8477 (mt0) REVERT: J 15 GLN cc_start: 0.9052 (mt0) cc_final: 0.8700 (mt0) REVERT: 5 115 GLN cc_start: 0.9011 (mt0) cc_final: 0.8762 (mt0) REVERT: 7 308 TYR cc_start: 0.8861 (t80) cc_final: 0.8616 (t80) REVERT: 8 408 TYR cc_start: 0.9034 (t80) cc_final: 0.8818 (t80) REVERT: K 8 TYR cc_start: 0.9228 (t80) cc_final: 0.8615 (t80) REVERT: 9 112 LEU cc_start: 0.9532 (mm) cc_final: 0.9262 (mm) REVERT: BA 315 GLN cc_start: 0.8964 (mt0) cc_final: 0.8669 (tt0) REVERT: CA 412 LEU cc_start: 0.9481 (mm) cc_final: 0.9251 (mm) REVERT: L 8 TYR cc_start: 0.9142 (t80) cc_final: 0.8589 (t80) REVERT: L 12 LEU cc_start: 0.9410 (mm) cc_final: 0.9177 (mm) REVERT: DA 108 TYR cc_start: 0.9104 (t80) cc_final: 0.8630 (t80) REVERT: DA 115 GLN cc_start: 0.9082 (mt0) cc_final: 0.8854 (tt0) REVERT: EA 208 TYR cc_start: 0.9236 (t80) cc_final: 0.8806 (t80) REVERT: EA 215 GLN cc_start: 0.8987 (mt0) cc_final: 0.8714 (tt0) REVERT: FA 308 TYR cc_start: 0.9141 (t80) cc_final: 0.8583 (t80) REVERT: GA 408 TYR cc_start: 0.9092 (t80) cc_final: 0.8510 (t80) REVERT: HA 115 GLN cc_start: 0.9002 (mt0) cc_final: 0.8763 (mt0) REVERT: KA 415 GLN cc_start: 0.8884 (mt0) cc_final: 0.8559 (mt0) REVERT: N 3 GLU cc_start: 0.8715 (tp30) cc_final: 0.8479 (tp30) REVERT: N 8 TYR cc_start: 0.9114 (t80) cc_final: 0.8906 (t80) REVERT: LA 115 GLN cc_start: 0.9074 (mt0) cc_final: 0.8804 (tt0) REVERT: MA 215 GLN cc_start: 0.9109 (mt0) cc_final: 0.8869 (tt0) REVERT: O 8 TYR cc_start: 0.9118 (t80) cc_final: 0.8754 (t80) REVERT: O 15 GLN cc_start: 0.8997 (mt0) cc_final: 0.8592 (tt0) REVERT: PA 115 GLN cc_start: 0.9027 (mt0) cc_final: 0.8811 (tt0) REVERT: QA 208 TYR cc_start: 0.9008 (t80) cc_final: 0.8802 (t80) REVERT: QA 215 GLN cc_start: 0.9163 (mt0) cc_final: 0.8883 (mt0) REVERT: RA 308 TYR cc_start: 0.9148 (t80) cc_final: 0.8764 (t80) REVERT: RA 315 GLN cc_start: 0.8965 (mt0) cc_final: 0.8657 (mt0) REVERT: SA 408 TYR cc_start: 0.9121 (t80) cc_final: 0.8786 (t80) REVERT: P 3 GLU cc_start: 0.8983 (tp30) cc_final: 0.8618 (tp30) REVERT: P 15 GLN cc_start: 0.8975 (mt0) cc_final: 0.8602 (mt0) REVERT: UA 212 LEU cc_start: 0.9462 (mm) cc_final: 0.9210 (mm) REVERT: Q 8 TYR cc_start: 0.9016 (t80) cc_final: 0.8264 (t80) REVERT: XA 108 TYR cc_start: 0.9122 (t80) cc_final: 0.8038 (t80) REVERT: XA 115 GLN cc_start: 0.8875 (mt0) cc_final: 0.8507 (mt0) REVERT: YA 208 TYR cc_start: 0.9106 (t80) cc_final: 0.8225 (t80) REVERT: YA 212 LEU cc_start: 0.9445 (mm) cc_final: 0.9171 (mm) REVERT: R 8 TYR cc_start: 0.9230 (t80) cc_final: 0.8620 (t80) REVERT: R 12 LEU cc_start: 0.9534 (mm) cc_final: 0.9185 (mm) REVERT: S 3 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8050 (mm-30) REVERT: gA 208 TYR cc_start: 0.9004 (t80) cc_final: 0.8798 (t80) REVERT: T 3 GLU cc_start: 0.8746 (tp30) cc_final: 0.8501 (tp30) REVERT: jA 112 LEU cc_start: 0.9440 (mm) cc_final: 0.9195 (mm) REVERT: lA 303 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8112 (mm-30) REVERT: lA 312 LEU cc_start: 0.9504 (mt) cc_final: 0.9301 (mt) REVERT: mA 408 TYR cc_start: 0.9154 (t80) cc_final: 0.8594 (t80) REVERT: qA 415 GLN cc_start: 0.8903 (mt0) cc_final: 0.8655 (tt0) outliers start: 2 outliers final: 0 residues processed: 632 average time/residue: 0.2063 time to fit residues: 196.6646 Evaluate side-chains 575 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 575 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 315 GLN ** 2 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN 9 115 GLN VA 315 GLN gA 215 GLN T 15 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12915 Z= 0.259 Angle : 0.483 5.953 17325 Z= 0.260 Chirality : 0.043 0.140 1995 Planarity : 0.002 0.016 2310 Dihedral : 3.027 19.367 1890 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer: Outliers : 0.09 % Allowed : 9.61 % Favored : 90.30 % 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: 2.95 (0.26), residues: 1365 helix: 1.97 (0.16), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.002 TYR r 308 ARG 0.002 0.000 ARG S 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 610 time to evaluate : 1.633 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 108 TYR cc_start: 0.9160 (t80) cc_final: 0.8877 (t80) REVERT: W 208 TYR cc_start: 0.8923 (t80) cc_final: 0.8536 (t80) REVERT: Y 408 TYR cc_start: 0.9150 (t80) cc_final: 0.8766 (t80) REVERT: Y 412 LEU cc_start: 0.9433 (mm) cc_final: 0.9188 (mm) REVERT: B 3 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8583 (tp30) REVERT: B 12 LEU cc_start: 0.9563 (mm) cc_final: 0.9214 (mm) REVERT: a 212 LEU cc_start: 0.9468 (mm) cc_final: 0.9224 (mm) REVERT: b 315 GLN cc_start: 0.8878 (mt0) cc_final: 0.8530 (tt0) REVERT: C 3 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8466 (mm-30) REVERT: C 8 TYR cc_start: 0.8885 (t80) cc_final: 0.8157 (t80) REVERT: d 108 TYR cc_start: 0.9243 (t80) cc_final: 0.8479 (t80) REVERT: d 112 LEU cc_start: 0.9502 (mm) cc_final: 0.9254 (mm) REVERT: e 208 TYR cc_start: 0.8760 (t80) cc_final: 0.8456 (t80) REVERT: e 215 GLN cc_start: 0.9051 (mt0) cc_final: 0.8751 (mt0) REVERT: f 308 TYR cc_start: 0.9136 (t80) cc_final: 0.8666 (t80) REVERT: g 403 GLU cc_start: 0.9148 (mp0) cc_final: 0.8873 (mp0) REVERT: g 408 TYR cc_start: 0.8781 (t80) cc_final: 0.8189 (t80) REVERT: h 115 GLN cc_start: 0.9051 (mt0) cc_final: 0.8736 (mt0) REVERT: i 208 TYR cc_start: 0.9090 (t80) cc_final: 0.8361 (t80) REVERT: j 308 TYR cc_start: 0.9135 (t80) cc_final: 0.8535 (t80) REVERT: j 312 LEU cc_start: 0.9568 (mm) cc_final: 0.9226 (mm) REVERT: k 408 TYR cc_start: 0.9234 (t80) cc_final: 0.8929 (t80) REVERT: E 8 TYR cc_start: 0.8884 (t80) cc_final: 0.8671 (t80) REVERT: l 115 GLN cc_start: 0.8994 (mt0) cc_final: 0.8597 (tt0) REVERT: m 211 ILE cc_start: 0.9417 (mt) cc_final: 0.8844 (mp) REVERT: m 212 LEU cc_start: 0.9343 (mm) cc_final: 0.8960 (mm) REVERT: m 215 GLN cc_start: 0.8928 (mt0) cc_final: 0.8561 (mt0) REVERT: n 308 TYR cc_start: 0.8991 (t80) cc_final: 0.8748 (t80) REVERT: o 403 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8521 (mm-30) REVERT: F 12 LEU cc_start: 0.9610 (mm) cc_final: 0.9408 (mm) REVERT: q 208 TYR cc_start: 0.8921 (t80) cc_final: 0.8654 (t80) REVERT: t 108 TYR cc_start: 0.9192 (t80) cc_final: 0.8972 (t80) REVERT: t 112 LEU cc_start: 0.9602 (mm) cc_final: 0.9319 (mm) REVERT: u 208 TYR cc_start: 0.9235 (t80) cc_final: 0.8902 (t80) REVERT: v 303 GLU cc_start: 0.8858 (mm-30) cc_final: 0.7764 (mm-30) REVERT: v 315 GLN cc_start: 0.8993 (mt0) cc_final: 0.8506 (mt0) REVERT: H 3 GLU cc_start: 0.8612 (tp30) cc_final: 0.8337 (mm-30) REVERT: H 12 LEU cc_start: 0.9590 (mm) cc_final: 0.9322 (mm) REVERT: y 212 LEU cc_start: 0.9506 (mm) cc_final: 0.9217 (mm) REVERT: z 303 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8421 (mm-30) REVERT: z 308 TYR cc_start: 0.8688 (t80) cc_final: 0.8400 (t80) REVERT: 0 415 GLN cc_start: 0.9127 (mt0) cc_final: 0.8744 (mt0) REVERT: I 8 TYR cc_start: 0.9303 (t80) cc_final: 0.8817 (t80) REVERT: I 12 LEU cc_start: 0.9613 (mm) cc_final: 0.9318 (mm) REVERT: 4 415 GLN cc_start: 0.9097 (mt0) cc_final: 0.8639 (mt0) REVERT: 5 115 GLN cc_start: 0.9043 (mt0) cc_final: 0.8795 (mt0) REVERT: 7 308 TYR cc_start: 0.8786 (t80) cc_final: 0.7884 (t80) REVERT: 8 408 TYR cc_start: 0.9000 (t80) cc_final: 0.8740 (t80) REVERT: 8 415 GLN cc_start: 0.9179 (mt0) cc_final: 0.8786 (mt0) REVERT: K 3 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8206 (mm-30) REVERT: K 8 TYR cc_start: 0.9252 (t80) cc_final: 0.8736 (t80) REVERT: K 12 LEU cc_start: 0.9560 (mm) cc_final: 0.9230 (mm) REVERT: 9 112 LEU cc_start: 0.9591 (mm) cc_final: 0.9329 (mm) REVERT: AA 203 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8562 (mm-30) REVERT: AA 208 TYR cc_start: 0.8871 (t80) cc_final: 0.8575 (t80) REVERT: BA 315 GLN cc_start: 0.8966 (mt0) cc_final: 0.8744 (tt0) REVERT: CA 412 LEU cc_start: 0.9538 (mm) cc_final: 0.9226 (mm) REVERT: CA 415 GLN cc_start: 0.9071 (mt0) cc_final: 0.8798 (mt0) REVERT: L 8 TYR cc_start: 0.9188 (t80) cc_final: 0.8552 (t80) REVERT: DA 108 TYR cc_start: 0.9107 (t80) cc_final: 0.8671 (t80) REVERT: DA 115 GLN cc_start: 0.9116 (mt0) cc_final: 0.8881 (tt0) REVERT: EA 208 TYR cc_start: 0.9205 (t80) cc_final: 0.8747 (t80) REVERT: EA 215 GLN cc_start: 0.9013 (mt0) cc_final: 0.8717 (mt0) REVERT: FA 308 TYR cc_start: 0.9166 (t80) cc_final: 0.8597 (t80) REVERT: FA 312 LEU cc_start: 0.9505 (mm) cc_final: 0.9236 (mm) REVERT: GA 408 TYR cc_start: 0.9117 (t80) cc_final: 0.8567 (t80) REVERT: M 12 LEU cc_start: 0.9449 (mm) cc_final: 0.9247 (mm) REVERT: HA 112 LEU cc_start: 0.9517 (mm) cc_final: 0.9267 (mm) REVERT: IA 215 GLN cc_start: 0.9067 (mt0) cc_final: 0.8727 (tt0) REVERT: JA 312 LEU cc_start: 0.9555 (mm) cc_final: 0.9286 (mm) REVERT: KA 415 GLN cc_start: 0.8990 (mt0) cc_final: 0.8671 (mt0) REVERT: N 3 GLU cc_start: 0.8670 (tp30) cc_final: 0.8447 (tp30) REVERT: N 8 TYR cc_start: 0.9088 (t80) cc_final: 0.8857 (t80) REVERT: N 15 GLN cc_start: 0.9086 (mt0) cc_final: 0.8856 (mt0) REVERT: LA 115 GLN cc_start: 0.9107 (mt0) cc_final: 0.8768 (tt0) REVERT: MA 212 LEU cc_start: 0.9488 (mm) cc_final: 0.9256 (mm) REVERT: MA 215 GLN cc_start: 0.9100 (mt0) cc_final: 0.8804 (tt0) REVERT: OA 412 LEU cc_start: 0.9459 (mm) cc_final: 0.9240 (mm) REVERT: O 3 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8437 (tp30) REVERT: O 8 TYR cc_start: 0.9155 (t80) cc_final: 0.8814 (t80) REVERT: O 15 GLN cc_start: 0.9105 (mt0) cc_final: 0.8888 (mt0) REVERT: PA 115 GLN cc_start: 0.9075 (mt0) cc_final: 0.8719 (tt0) REVERT: QA 208 TYR cc_start: 0.9097 (t80) cc_final: 0.8762 (t80) REVERT: RA 308 TYR cc_start: 0.9153 (t80) cc_final: 0.8808 (t80) REVERT: SA 408 TYR cc_start: 0.9097 (t80) cc_final: 0.8794 (t80) REVERT: P 3 GLU cc_start: 0.8949 (tp30) cc_final: 0.8146 (mm-30) REVERT: P 15 GLN cc_start: 0.9068 (mt0) cc_final: 0.8731 (mt0) REVERT: UA 212 LEU cc_start: 0.9514 (mm) cc_final: 0.9304 (mm) REVERT: VA 312 LEU cc_start: 0.9570 (mm) cc_final: 0.9300 (mm) REVERT: WA 415 GLN cc_start: 0.8972 (mt0) cc_final: 0.8675 (mm-40) REVERT: Q 3 GLU cc_start: 0.8833 (tp30) cc_final: 0.7510 (tp30) REVERT: Q 8 TYR cc_start: 0.8873 (t80) cc_final: 0.8296 (t80) REVERT: XA 108 TYR cc_start: 0.9063 (t80) cc_final: 0.8518 (t80) REVERT: YA 208 TYR cc_start: 0.9143 (t80) cc_final: 0.8193 (t80) REVERT: YA 212 LEU cc_start: 0.9459 (mm) cc_final: 0.9201 (mm) REVERT: ZA 308 TYR cc_start: 0.8972 (t80) cc_final: 0.8234 (t80) REVERT: R 3 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8468 (tp30) REVERT: R 8 TYR cc_start: 0.9220 (t80) cc_final: 0.8543 (t80) REVERT: R 12 LEU cc_start: 0.9644 (mm) cc_final: 0.9171 (mm) REVERT: cA 212 LEU cc_start: 0.9554 (mm) cc_final: 0.9302 (mm) REVERT: dA 315 GLN cc_start: 0.9108 (mt0) cc_final: 0.8829 (mt0) REVERT: gA 208 TYR cc_start: 0.8912 (t80) cc_final: 0.8617 (t80) REVERT: T 3 GLU cc_start: 0.8691 (tp30) cc_final: 0.8416 (tp30) REVERT: jA 112 LEU cc_start: 0.9279 (mm) cc_final: 0.9076 (mm) REVERT: lA 303 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8832 (mp0) REVERT: U 8 TYR cc_start: 0.8847 (t80) cc_final: 0.8646 (t80) outliers start: 1 outliers final: 0 residues processed: 611 average time/residue: 0.2235 time to fit residues: 207.8636 Evaluate side-chains 572 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 572 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 115 GLN E 15 GLN z 315 GLN 2 215 GLN NA 315 GLN fA 115 GLN gA 215 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12915 Z= 0.195 Angle : 0.495 5.063 17325 Z= 0.249 Chirality : 0.041 0.143 1995 Planarity : 0.002 0.013 2310 Dihedral : 3.110 18.602 1890 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer: Outliers : 0.26 % Allowed : 5.97 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.25), residues: 1365 helix: 2.25 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.002 TYR 3 308 ARG 0.002 0.000 ARG n 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 622 time to evaluate : 1.328 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8398 (mm-30) REVERT: A 12 LEU cc_start: 0.9517 (mm) cc_final: 0.9274 (mm) REVERT: W 203 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8778 (mm-30) REVERT: W 208 TYR cc_start: 0.8571 (t80) cc_final: 0.8270 (t80) REVERT: Y 408 TYR cc_start: 0.9117 (t80) cc_final: 0.8882 (t80) REVERT: B 3 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8553 (tp30) REVERT: B 12 LEU cc_start: 0.9588 (mm) cc_final: 0.9241 (mm) REVERT: a 212 LEU cc_start: 0.9553 (mm) cc_final: 0.9217 (mm) REVERT: b 315 GLN cc_start: 0.8900 (mt0) cc_final: 0.8627 (tt0) REVERT: C 3 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8477 (mm-30) REVERT: C 8 TYR cc_start: 0.8795 (t80) cc_final: 0.8137 (t80) REVERT: d 108 TYR cc_start: 0.9173 (t80) cc_final: 0.8456 (t80) REVERT: d 112 LEU cc_start: 0.9570 (mm) cc_final: 0.9225 (mm) REVERT: e 212 LEU cc_start: 0.9392 (mm) cc_final: 0.9187 (mm) REVERT: f 308 TYR cc_start: 0.9065 (t80) cc_final: 0.8584 (t80) REVERT: g 403 GLU cc_start: 0.9151 (mp0) cc_final: 0.8900 (mp0) REVERT: g 412 LEU cc_start: 0.9359 (mp) cc_final: 0.9141 (mp) REVERT: g 415 GLN cc_start: 0.8757 (tt0) cc_final: 0.8539 (tt0) REVERT: i 208 TYR cc_start: 0.9059 (t80) cc_final: 0.8506 (t80) REVERT: j 308 TYR cc_start: 0.9047 (t80) cc_final: 0.8411 (t80) REVERT: j 312 LEU cc_start: 0.9563 (mm) cc_final: 0.9249 (mm) REVERT: k 408 TYR cc_start: 0.9178 (t80) cc_final: 0.8900 (t80) REVERT: E 8 TYR cc_start: 0.8823 (t80) cc_final: 0.8568 (t80) REVERT: m 212 LEU cc_start: 0.9400 (mm) cc_final: 0.8891 (mm) REVERT: m 215 GLN cc_start: 0.8852 (mt0) cc_final: 0.8477 (mt0) REVERT: o 403 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8547 (mm-30) REVERT: q 208 TYR cc_start: 0.8812 (t80) cc_final: 0.8490 (t80) REVERT: t 112 LEU cc_start: 0.9617 (mm) cc_final: 0.9303 (mm) REVERT: u 208 TYR cc_start: 0.9173 (t80) cc_final: 0.8751 (t80) REVERT: v 315 GLN cc_start: 0.8983 (mt0) cc_final: 0.8607 (mt0) REVERT: H 3 GLU cc_start: 0.8590 (tp30) cc_final: 0.7847 (mm-30) REVERT: H 12 LEU cc_start: 0.9581 (mm) cc_final: 0.9310 (mm) REVERT: x 111 ILE cc_start: 0.9464 (mt) cc_final: 0.8936 (mp) REVERT: x 112 LEU cc_start: 0.9372 (mm) cc_final: 0.8821 (mm) REVERT: x 115 GLN cc_start: 0.8892 (mt0) cc_final: 0.8167 (mt0) REVERT: y 212 LEU cc_start: 0.9461 (mm) cc_final: 0.9209 (mm) REVERT: 0 415 GLN cc_start: 0.8965 (mt0) cc_final: 0.8654 (mt0) REVERT: I 8 TYR cc_start: 0.9265 (t80) cc_final: 0.8723 (t80) REVERT: 1 108 TYR cc_start: 0.8811 (t80) cc_final: 0.8591 (t80) REVERT: 2 208 TYR cc_start: 0.8830 (t80) cc_final: 0.8545 (t80) REVERT: 3 312 LEU cc_start: 0.9552 (mp) cc_final: 0.9342 (mp) REVERT: 4 415 GLN cc_start: 0.9056 (mt0) cc_final: 0.8674 (mt0) REVERT: 5 115 GLN cc_start: 0.9001 (mt0) cc_final: 0.8724 (mt0) REVERT: 6 208 TYR cc_start: 0.8928 (t80) cc_final: 0.8216 (t80) REVERT: 7 308 TYR cc_start: 0.8788 (t80) cc_final: 0.7715 (t80) REVERT: 8 408 TYR cc_start: 0.8958 (t80) cc_final: 0.7870 (t80) REVERT: 8 411 ILE cc_start: 0.9472 (mt) cc_final: 0.8942 (mt) REVERT: 8 412 LEU cc_start: 0.9305 (mm) cc_final: 0.9039 (mm) REVERT: 8 415 GLN cc_start: 0.8905 (mt0) cc_final: 0.8550 (mt0) REVERT: K 3 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8148 (mm-30) REVERT: K 8 TYR cc_start: 0.9154 (t80) cc_final: 0.8684 (t80) REVERT: K 12 LEU cc_start: 0.9587 (mm) cc_final: 0.9280 (mm) REVERT: BA 312 LEU cc_start: 0.9407 (mm) cc_final: 0.9199 (mm) REVERT: BA 315 GLN cc_start: 0.9016 (mt0) cc_final: 0.8783 (tt0) REVERT: CA 412 LEU cc_start: 0.9510 (mm) cc_final: 0.9200 (mm) REVERT: CA 415 GLN cc_start: 0.8980 (mt0) cc_final: 0.8701 (mt0) REVERT: L 3 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8517 (mm-30) REVERT: L 8 TYR cc_start: 0.9155 (t80) cc_final: 0.8650 (t80) REVERT: L 12 LEU cc_start: 0.9582 (mm) cc_final: 0.9345 (mm) REVERT: DA 108 TYR cc_start: 0.9038 (t80) cc_final: 0.8607 (t80) REVERT: EA 208 TYR cc_start: 0.9122 (t80) cc_final: 0.8734 (t80) REVERT: FA 308 TYR cc_start: 0.9121 (t80) cc_final: 0.8509 (t80) REVERT: FA 312 LEU cc_start: 0.9488 (mm) cc_final: 0.9210 (mm) REVERT: GA 408 TYR cc_start: 0.9022 (t80) cc_final: 0.8555 (t80) REVERT: HA 115 GLN cc_start: 0.9328 (mt0) cc_final: 0.9058 (tt0) REVERT: JA 312 LEU cc_start: 0.9553 (mm) cc_final: 0.9296 (mm) REVERT: LA 115 GLN cc_start: 0.9061 (mt0) cc_final: 0.8715 (tt0) REVERT: MA 212 LEU cc_start: 0.9482 (mm) cc_final: 0.9232 (mm) REVERT: OA 403 GLU cc_start: 0.9058 (mp0) cc_final: 0.8816 (mp0) REVERT: OA 412 LEU cc_start: 0.9444 (mm) cc_final: 0.9212 (mm) REVERT: O 3 GLU cc_start: 0.8802 (mm-30) cc_final: 0.7771 (tp30) REVERT: O 8 TYR cc_start: 0.9094 (t80) cc_final: 0.8756 (t80) REVERT: O 15 GLN cc_start: 0.9073 (mt0) cc_final: 0.8869 (mt0) REVERT: PA 115 GLN cc_start: 0.9086 (mt0) cc_final: 0.8781 (tt0) REVERT: QA 208 TYR cc_start: 0.9075 (t80) cc_final: 0.8814 (t80) REVERT: QA 215 GLN cc_start: 0.9146 (mt0) cc_final: 0.8873 (mt0) REVERT: RA 308 TYR cc_start: 0.9143 (t80) cc_final: 0.8919 (t80) REVERT: SA 408 TYR cc_start: 0.9080 (t80) cc_final: 0.8797 (t80) REVERT: P 15 GLN cc_start: 0.9063 (mt0) cc_final: 0.8820 (mt0) REVERT: VA 312 LEU cc_start: 0.9597 (mm) cc_final: 0.9335 (mm) REVERT: Q 3 GLU cc_start: 0.8672 (tp30) cc_final: 0.7697 (mm-30) REVERT: Q 8 TYR cc_start: 0.8651 (t80) cc_final: 0.8009 (t80) REVERT: YA 208 TYR cc_start: 0.9123 (t80) cc_final: 0.8371 (t80) REVERT: YA 212 LEU cc_start: 0.9358 (mm) cc_final: 0.9115 (mm) REVERT: ZA 308 TYR cc_start: 0.8877 (t80) cc_final: 0.8209 (t80) REVERT: R 8 TYR cc_start: 0.9178 (t80) cc_final: 0.8778 (t80) REVERT: R 12 LEU cc_start: 0.9636 (mm) cc_final: 0.9208 (mm) REVERT: S 3 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8465 (mm-30) REVERT: gA 208 TYR cc_start: 0.8852 (t80) cc_final: 0.8454 (t80) REVERT: iA 403 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8750 (mp0) REVERT: T 3 GLU cc_start: 0.8681 (tp30) cc_final: 0.8478 (tp30) REVERT: jA 112 LEU cc_start: 0.9296 (mm) cc_final: 0.9030 (mm) REVERT: lA 308 TYR cc_start: 0.8856 (t80) cc_final: 0.8629 (t80) REVERT: mA 408 TYR cc_start: 0.9071 (t80) cc_final: 0.8819 (t80) REVERT: nA 112 LEU cc_start: 0.9584 (mm) cc_final: 0.9353 (mm) REVERT: oA 215 GLN cc_start: 0.8888 (tt0) cc_final: 0.8469 (tt0) outliers start: 3 outliers final: 0 residues processed: 625 average time/residue: 0.1968 time to fit residues: 185.3404 Evaluate side-chains 579 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 579 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 59 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 53 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN o 415 GLN 9 115 GLN Q 15 GLN fA 115 GLN hA 315 GLN qA 415 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12915 Z= 0.177 Angle : 0.498 4.873 17325 Z= 0.244 Chirality : 0.040 0.157 1995 Planarity : 0.002 0.010 2310 Dihedral : 3.119 20.002 1890 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.26 % Allowed : 3.98 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.24), residues: 1365 helix: 2.49 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.002 TYR 3 308 ARG 0.003 0.000 ARGqA 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 628 time to evaluate : 1.511 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8457 (mm-30) REVERT: A 12 LEU cc_start: 0.9545 (mm) cc_final: 0.9328 (mm) REVERT: W 208 TYR cc_start: 0.8497 (t80) cc_final: 0.8172 (t80) REVERT: B 3 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8573 (tp30) REVERT: B 12 LEU cc_start: 0.9599 (mm) cc_final: 0.9241 (mm) REVERT: a 212 LEU cc_start: 0.9569 (mm) cc_final: 0.9304 (mm) REVERT: C 3 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8326 (mm-30) REVERT: C 8 TYR cc_start: 0.8802 (t80) cc_final: 0.8223 (t80) REVERT: d 108 TYR cc_start: 0.9147 (t80) cc_final: 0.8431 (t80) REVERT: d 112 LEU cc_start: 0.9596 (mm) cc_final: 0.9247 (mm) REVERT: e 212 LEU cc_start: 0.9416 (mm) cc_final: 0.9197 (mm) REVERT: f 308 TYR cc_start: 0.9001 (t80) cc_final: 0.8612 (t80) REVERT: g 403 GLU cc_start: 0.9171 (mp0) cc_final: 0.8869 (mp0) REVERT: g 412 LEU cc_start: 0.9482 (mp) cc_final: 0.9221 (mp) REVERT: i 203 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8637 (mm-30) REVERT: i 208 TYR cc_start: 0.9038 (t80) cc_final: 0.8480 (t80) REVERT: j 308 TYR cc_start: 0.9037 (t80) cc_final: 0.8613 (t80) REVERT: j 312 LEU cc_start: 0.9552 (mm) cc_final: 0.9287 (mm) REVERT: E 8 TYR cc_start: 0.8759 (t80) cc_final: 0.8493 (t80) REVERT: m 212 LEU cc_start: 0.9342 (mm) cc_final: 0.8873 (mm) REVERT: m 215 GLN cc_start: 0.8875 (mt0) cc_final: 0.8471 (mt0) REVERT: n 308 TYR cc_start: 0.8863 (t80) cc_final: 0.8653 (t80) REVERT: q 208 TYR cc_start: 0.8814 (t80) cc_final: 0.8423 (t80) REVERT: t 112 LEU cc_start: 0.9665 (mm) cc_final: 0.9281 (mm) REVERT: u 208 TYR cc_start: 0.9136 (t80) cc_final: 0.8732 (t80) REVERT: v 311 ILE cc_start: 0.9317 (mt) cc_final: 0.9116 (mt) REVERT: v 315 GLN cc_start: 0.8882 (mt0) cc_final: 0.8665 (mt0) REVERT: H 12 LEU cc_start: 0.9591 (mm) cc_final: 0.9376 (mm) REVERT: y 212 LEU cc_start: 0.9463 (mm) cc_final: 0.9215 (mm) REVERT: 0 415 GLN cc_start: 0.9037 (mt0) cc_final: 0.8702 (mt0) REVERT: I 8 TYR cc_start: 0.9219 (t80) cc_final: 0.8731 (t80) REVERT: 2 208 TYR cc_start: 0.8750 (t80) cc_final: 0.8445 (t80) REVERT: 3 311 ILE cc_start: 0.9438 (mt) cc_final: 0.9187 (mt) REVERT: J 15 GLN cc_start: 0.8976 (mt0) cc_final: 0.8761 (mt0) REVERT: 6 208 TYR cc_start: 0.8819 (t80) cc_final: 0.8097 (t80) REVERT: 8 408 TYR cc_start: 0.8938 (t80) cc_final: 0.7817 (t80) REVERT: 8 415 GLN cc_start: 0.9169 (mt0) cc_final: 0.8705 (mt0) REVERT: K 3 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8021 (mm-30) REVERT: K 8 TYR cc_start: 0.9036 (t80) cc_final: 0.8663 (t80) REVERT: K 12 LEU cc_start: 0.9589 (mm) cc_final: 0.9341 (mm) REVERT: BA 312 LEU cc_start: 0.9423 (mm) cc_final: 0.9184 (mm) REVERT: CA 412 LEU cc_start: 0.9496 (mm) cc_final: 0.9285 (mm) REVERT: CA 415 GLN cc_start: 0.8857 (mt0) cc_final: 0.8568 (mt0) REVERT: L 3 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8562 (mm-30) REVERT: L 8 TYR cc_start: 0.9099 (t80) cc_final: 0.8589 (t80) REVERT: L 12 LEU cc_start: 0.9594 (mm) cc_final: 0.9317 (mm) REVERT: DA 108 TYR cc_start: 0.8987 (t80) cc_final: 0.8617 (t80) REVERT: EA 208 TYR cc_start: 0.9081 (t80) cc_final: 0.8741 (t80) REVERT: FA 308 TYR cc_start: 0.9117 (t80) cc_final: 0.8566 (t80) REVERT: FA 312 LEU cc_start: 0.9479 (mm) cc_final: 0.9202 (mm) REVERT: GA 408 TYR cc_start: 0.9002 (t80) cc_final: 0.8568 (t80) REVERT: M 12 LEU cc_start: 0.9622 (mm) cc_final: 0.9367 (mm) REVERT: HA 115 GLN cc_start: 0.9238 (mt0) cc_final: 0.8896 (tt0) REVERT: N 3 GLU cc_start: 0.8789 (mm-30) cc_final: 0.7411 (mm-30) REVERT: LA 115 GLN cc_start: 0.9011 (mt0) cc_final: 0.8676 (tt0) REVERT: MA 212 LEU cc_start: 0.9511 (mm) cc_final: 0.9261 (mm) REVERT: OA 412 LEU cc_start: 0.9464 (mm) cc_final: 0.9251 (mm) REVERT: O 3 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8587 (mm-30) REVERT: O 8 TYR cc_start: 0.9024 (t80) cc_final: 0.8696 (t80) REVERT: PA 115 GLN cc_start: 0.9061 (mt0) cc_final: 0.8790 (tt0) REVERT: QA 208 TYR cc_start: 0.9001 (t80) cc_final: 0.8711 (t80) REVERT: QA 215 GLN cc_start: 0.9139 (mt0) cc_final: 0.8858 (mt0) REVERT: RA 308 TYR cc_start: 0.9113 (t80) cc_final: 0.8911 (t80) REVERT: SA 408 TYR cc_start: 0.9042 (t80) cc_final: 0.8790 (t80) REVERT: P 3 GLU cc_start: 0.8883 (mm-30) cc_final: 0.7585 (mm-30) REVERT: VA 303 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8415 (tp30) REVERT: WA 415 GLN cc_start: 0.8864 (mt0) cc_final: 0.8099 (mt0) REVERT: Q 12 LEU cc_start: 0.9465 (mp) cc_final: 0.9098 (mp) REVERT: YA 208 TYR cc_start: 0.9101 (t80) cc_final: 0.8463 (t80) REVERT: ZA 308 TYR cc_start: 0.8831 (t80) cc_final: 0.8207 (t80) REVERT: R 8 TYR cc_start: 0.9158 (t80) cc_final: 0.8890 (t80) REVERT: R 12 LEU cc_start: 0.9616 (mm) cc_final: 0.9258 (mm) REVERT: S 3 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8541 (mm-30) REVERT: fA 108 TYR cc_start: 0.8846 (t80) cc_final: 0.8003 (t80) REVERT: gA 208 TYR cc_start: 0.8716 (t80) cc_final: 0.8222 (t80) REVERT: iA 403 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8709 (mm-30) REVERT: T 3 GLU cc_start: 0.8660 (tp30) cc_final: 0.8429 (mm-30) REVERT: jA 108 TYR cc_start: 0.8900 (t80) cc_final: 0.8653 (t80) REVERT: jA 112 LEU cc_start: 0.9321 (mm) cc_final: 0.9088 (mm) REVERT: kA 212 LEU cc_start: 0.9405 (mm) cc_final: 0.9181 (mm) REVERT: mA 408 TYR cc_start: 0.9057 (t80) cc_final: 0.8810 (t80) REVERT: oA 208 TYR cc_start: 0.8853 (t80) cc_final: 0.8279 (t80) outliers start: 3 outliers final: 0 residues processed: 631 average time/residue: 0.1984 time to fit residues: 189.6239 Evaluate side-chains 587 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 587 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 57 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 415 GLN ** kA 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 15 GLN nA 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12915 Z= 0.205 Angle : 0.501 6.785 17325 Z= 0.251 Chirality : 0.041 0.133 1995 Planarity : 0.002 0.012 2310 Dihedral : 2.962 18.714 1890 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.09 % Allowed : 5.11 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.05 (0.24), residues: 1365 helix: 2.65 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.002 TYRaA 408 ARG 0.002 0.000 ARG o 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 615 time to evaluate : 1.538 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8466 (mm-30) REVERT: A 12 LEU cc_start: 0.9568 (mm) cc_final: 0.9361 (mm) REVERT: W 208 TYR cc_start: 0.9028 (t80) cc_final: 0.8774 (t80) REVERT: B 12 LEU cc_start: 0.9620 (mm) cc_final: 0.9256 (mm) REVERT: a 212 LEU cc_start: 0.9579 (mm) cc_final: 0.9290 (mm) REVERT: C 3 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8101 (mm-30) REVERT: C 12 LEU cc_start: 0.9517 (mm) cc_final: 0.9230 (mm) REVERT: d 108 TYR cc_start: 0.9149 (t80) cc_final: 0.8388 (t80) REVERT: d 112 LEU cc_start: 0.9595 (mm) cc_final: 0.9277 (mm) REVERT: e 212 LEU cc_start: 0.9460 (mm) cc_final: 0.9099 (mm) REVERT: f 308 TYR cc_start: 0.8978 (t80) cc_final: 0.8531 (t80) REVERT: g 403 GLU cc_start: 0.9166 (mp0) cc_final: 0.8841 (mp0) REVERT: g 408 TYR cc_start: 0.8991 (t80) cc_final: 0.8507 (t80) REVERT: g 412 LEU cc_start: 0.9477 (mp) cc_final: 0.9102 (mp) REVERT: i 203 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8585 (mm-30) REVERT: i 208 TYR cc_start: 0.9049 (t80) cc_final: 0.8488 (t80) REVERT: j 308 TYR cc_start: 0.9056 (t80) cc_final: 0.8545 (t80) REVERT: j 312 LEU cc_start: 0.9612 (mm) cc_final: 0.9319 (mm) REVERT: k 412 LEU cc_start: 0.9524 (mm) cc_final: 0.9298 (mm) REVERT: E 8 TYR cc_start: 0.8808 (t80) cc_final: 0.8508 (t80) REVERT: m 211 ILE cc_start: 0.9352 (mt) cc_final: 0.8866 (mp) REVERT: m 212 LEU cc_start: 0.9219 (mm) cc_final: 0.8873 (mm) REVERT: m 215 GLN cc_start: 0.8934 (mt0) cc_final: 0.8472 (mt0) REVERT: q 208 TYR cc_start: 0.8798 (t80) cc_final: 0.8399 (t80) REVERT: t 112 LEU cc_start: 0.9645 (mm) cc_final: 0.9284 (mm) REVERT: u 208 TYR cc_start: 0.9231 (t80) cc_final: 0.9010 (t80) REVERT: v 303 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8861 (mm-30) REVERT: v 315 GLN cc_start: 0.8957 (mt0) cc_final: 0.8580 (mt0) REVERT: H 12 LEU cc_start: 0.9631 (mm) cc_final: 0.9417 (mm) REVERT: y 212 LEU cc_start: 0.9479 (mm) cc_final: 0.9218 (mm) REVERT: 0 408 TYR cc_start: 0.8645 (t80) cc_final: 0.8352 (t80) REVERT: I 3 GLU cc_start: 0.8716 (mm-30) cc_final: 0.7398 (mm-30) REVERT: I 8 TYR cc_start: 0.9230 (t80) cc_final: 0.8709 (t80) REVERT: 3 311 ILE cc_start: 0.9456 (mt) cc_final: 0.9209 (mt) REVERT: 4 415 GLN cc_start: 0.8812 (mt0) cc_final: 0.8116 (mt0) REVERT: 6 208 TYR cc_start: 0.8809 (t80) cc_final: 0.8024 (t80) REVERT: 8 408 TYR cc_start: 0.8936 (t80) cc_final: 0.7873 (t80) REVERT: K 8 TYR cc_start: 0.9069 (t80) cc_final: 0.8682 (t80) REVERT: K 12 LEU cc_start: 0.9597 (mm) cc_final: 0.9384 (mm) REVERT: AA 203 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8504 (mm-30) REVERT: BA 312 LEU cc_start: 0.9430 (mm) cc_final: 0.9205 (mm) REVERT: CA 415 GLN cc_start: 0.8990 (mt0) cc_final: 0.8751 (mt0) REVERT: L 3 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8514 (mm-30) REVERT: L 8 TYR cc_start: 0.9110 (t80) cc_final: 0.8602 (t80) REVERT: L 12 LEU cc_start: 0.9579 (mm) cc_final: 0.9315 (mm) REVERT: DA 108 TYR cc_start: 0.9031 (t80) cc_final: 0.8574 (t80) REVERT: EA 208 TYR cc_start: 0.9094 (t80) cc_final: 0.8731 (t80) REVERT: FA 308 TYR cc_start: 0.9123 (t80) cc_final: 0.8526 (t80) REVERT: FA 312 LEU cc_start: 0.9487 (mm) cc_final: 0.9200 (mm) REVERT: GA 408 TYR cc_start: 0.9018 (t80) cc_final: 0.8538 (t80) REVERT: M 12 LEU cc_start: 0.9645 (mm) cc_final: 0.9368 (mm) REVERT: HA 115 GLN cc_start: 0.9240 (mt0) cc_final: 0.8862 (mt0) REVERT: N 12 LEU cc_start: 0.9612 (mm) cc_final: 0.9364 (mm) REVERT: LA 115 GLN cc_start: 0.9057 (mt0) cc_final: 0.8728 (tt0) REVERT: MA 212 LEU cc_start: 0.9532 (mm) cc_final: 0.9259 (mm) REVERT: NA 303 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8117 (mm-30) REVERT: OA 403 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8708 (mm-30) REVERT: OA 412 LEU cc_start: 0.9507 (mm) cc_final: 0.9255 (mm) REVERT: O 3 GLU cc_start: 0.8828 (mm-30) cc_final: 0.7863 (mm-30) REVERT: O 8 TYR cc_start: 0.9040 (t80) cc_final: 0.8740 (t80) REVERT: PA 115 GLN cc_start: 0.9090 (mt0) cc_final: 0.8803 (tt0) REVERT: QA 208 TYR cc_start: 0.9038 (t80) cc_final: 0.8712 (t80) REVERT: RA 308 TYR cc_start: 0.9123 (t80) cc_final: 0.8909 (t80) REVERT: SA 403 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8492 (mm-30) REVERT: SA 408 TYR cc_start: 0.9014 (t80) cc_final: 0.8415 (t80) REVERT: SA 415 GLN cc_start: 0.8830 (mt0) cc_final: 0.7956 (mt0) REVERT: P 3 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8609 (mm-30) REVERT: VA 303 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8597 (tp30) REVERT: Q 8 TYR cc_start: 0.8810 (t80) cc_final: 0.8489 (t80) REVERT: Q 12 LEU cc_start: 0.9440 (mp) cc_final: 0.9070 (mp) REVERT: XA 103 GLU cc_start: 0.8972 (mp0) cc_final: 0.8764 (mp0) REVERT: YA 208 TYR cc_start: 0.9077 (t80) cc_final: 0.8492 (t80) REVERT: YA 212 LEU cc_start: 0.9520 (mm) cc_final: 0.9298 (mm) REVERT: ZA 312 LEU cc_start: 0.9549 (mm) cc_final: 0.9253 (mm) REVERT: R 12 LEU cc_start: 0.9632 (mm) cc_final: 0.9286 (mm) REVERT: S 3 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8511 (mm-30) REVERT: gA 212 LEU cc_start: 0.9619 (mm) cc_final: 0.9314 (mm) REVERT: iA 403 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8410 (mm-30) REVERT: jA 108 TYR cc_start: 0.8865 (t80) cc_final: 0.8655 (t80) REVERT: kA 212 LEU cc_start: 0.9504 (mm) cc_final: 0.9222 (mm) REVERT: mA 408 TYR cc_start: 0.9081 (t80) cc_final: 0.8822 (t80) REVERT: nA 112 LEU cc_start: 0.9591 (mm) cc_final: 0.9389 (mm) REVERT: qA 415 GLN cc_start: 0.8990 (mt0) cc_final: 0.8450 (mt0) outliers start: 1 outliers final: 0 residues processed: 616 average time/residue: 0.1997 time to fit residues: 186.1395 Evaluate side-chains 580 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 580 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 415 GLN ** x 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** kA 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12915 Z= 0.218 Angle : 0.514 4.767 17325 Z= 0.258 Chirality : 0.042 0.145 1995 Planarity : 0.002 0.011 2310 Dihedral : 2.973 18.900 1890 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: 4.22 (0.23), residues: 1365 helix: 2.75 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.002 TYR o 408 ARG 0.002 0.000 ARGqA 406 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 602 time to evaluate : 1.205 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 208 TYR cc_start: 0.8922 (t80) cc_final: 0.8656 (t80) REVERT: B 3 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8551 (tp30) REVERT: B 12 LEU cc_start: 0.9629 (mm) cc_final: 0.9284 (mm) REVERT: a 212 LEU cc_start: 0.9600 (mm) cc_final: 0.9282 (mm) REVERT: C 3 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8532 (mm-30) REVERT: C 12 LEU cc_start: 0.9574 (mm) cc_final: 0.9229 (mm) REVERT: d 108 TYR cc_start: 0.9150 (t80) cc_final: 0.8411 (t80) REVERT: d 112 LEU cc_start: 0.9592 (mm) cc_final: 0.9299 (mm) REVERT: e 212 LEU cc_start: 0.9520 (mm) cc_final: 0.9065 (mm) REVERT: f 308 TYR cc_start: 0.8999 (t80) cc_final: 0.8612 (t80) REVERT: g 403 GLU cc_start: 0.9185 (mp0) cc_final: 0.8878 (mp0) REVERT: g 408 TYR cc_start: 0.9071 (t80) cc_final: 0.8455 (t80) REVERT: g 412 LEU cc_start: 0.9494 (mp) cc_final: 0.9110 (mp) REVERT: i 203 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8471 (mm-30) REVERT: i 208 TYR cc_start: 0.9017 (t80) cc_final: 0.8509 (t80) REVERT: j 308 TYR cc_start: 0.9045 (t80) cc_final: 0.8536 (t80) REVERT: j 312 LEU cc_start: 0.9587 (mm) cc_final: 0.9302 (mm) REVERT: E 8 TYR cc_start: 0.8806 (t80) cc_final: 0.8493 (t80) REVERT: m 211 ILE cc_start: 0.9396 (mt) cc_final: 0.8838 (mp) REVERT: m 212 LEU cc_start: 0.9505 (mm) cc_final: 0.8955 (mm) REVERT: m 215 GLN cc_start: 0.8948 (mt0) cc_final: 0.8514 (mt0) REVERT: o 408 TYR cc_start: 0.8817 (t80) cc_final: 0.8165 (t80) REVERT: t 112 LEU cc_start: 0.9644 (mm) cc_final: 0.9254 (mm) REVERT: u 208 TYR cc_start: 0.9200 (t80) cc_final: 0.8968 (t80) REVERT: v 315 GLN cc_start: 0.8873 (mt0) cc_final: 0.8552 (mt0) REVERT: H 3 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8553 (mm-30) REVERT: y 212 LEU cc_start: 0.9494 (mm) cc_final: 0.9203 (mm) REVERT: I 3 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8503 (mm-30) REVERT: I 8 TYR cc_start: 0.9199 (t80) cc_final: 0.8724 (t80) REVERT: 6 208 TYR cc_start: 0.8755 (t80) cc_final: 0.7926 (t80) REVERT: 8 408 TYR cc_start: 0.8973 (t80) cc_final: 0.7984 (t80) REVERT: K 3 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8272 (mm-30) REVERT: K 8 TYR cc_start: 0.9089 (t80) cc_final: 0.8691 (t80) REVERT: 9 115 GLN cc_start: 0.8827 (mt0) cc_final: 0.8528 (mt0) REVERT: BA 312 LEU cc_start: 0.9520 (mm) cc_final: 0.9223 (mm) REVERT: CA 411 ILE cc_start: 0.9349 (mt) cc_final: 0.9132 (mt) REVERT: CA 415 GLN cc_start: 0.9025 (mt0) cc_final: 0.8467 (mt0) REVERT: L 3 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8538 (mm-30) REVERT: L 8 TYR cc_start: 0.9156 (t80) cc_final: 0.8626 (t80) REVERT: L 12 LEU cc_start: 0.9566 (mm) cc_final: 0.9327 (mm) REVERT: DA 108 TYR cc_start: 0.9005 (t80) cc_final: 0.8552 (t80) REVERT: EA 208 TYR cc_start: 0.9119 (t80) cc_final: 0.8716 (t80) REVERT: FA 308 TYR cc_start: 0.9136 (t80) cc_final: 0.8563 (t80) REVERT: FA 312 LEU cc_start: 0.9491 (mm) cc_final: 0.9188 (mm) REVERT: GA 408 TYR cc_start: 0.9006 (t80) cc_final: 0.8494 (t80) REVERT: M 12 LEU cc_start: 0.9660 (mm) cc_final: 0.9348 (mm) REVERT: HA 115 GLN cc_start: 0.9214 (mt0) cc_final: 0.8897 (mt0) REVERT: KA 412 LEU cc_start: 0.9588 (mm) cc_final: 0.9247 (mm) REVERT: N 12 LEU cc_start: 0.9639 (mm) cc_final: 0.9400 (mm) REVERT: LA 115 GLN cc_start: 0.9042 (mt0) cc_final: 0.8713 (tt0) REVERT: MA 212 LEU cc_start: 0.9552 (mm) cc_final: 0.9244 (mm) REVERT: NA 303 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8190 (mm-30) REVERT: OA 403 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8897 (mm-30) REVERT: OA 412 LEU cc_start: 0.9642 (mm) cc_final: 0.9283 (mm) REVERT: O 3 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8092 (mm-30) REVERT: O 8 TYR cc_start: 0.9064 (t80) cc_final: 0.8790 (t80) REVERT: PA 115 GLN cc_start: 0.9006 (mt0) cc_final: 0.8659 (tt0) REVERT: QA 208 TYR cc_start: 0.9003 (t80) cc_final: 0.8667 (t80) REVERT: QA 215 GLN cc_start: 0.8884 (mt0) cc_final: 0.8674 (tt0) REVERT: RA 303 GLU cc_start: 0.8776 (mm-30) cc_final: 0.7693 (mm-30) REVERT: SA 403 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8516 (mm-30) REVERT: SA 408 TYR cc_start: 0.8872 (t80) cc_final: 0.8469 (t80) REVERT: SA 415 GLN cc_start: 0.8825 (mt0) cc_final: 0.8115 (mt0) REVERT: VA 303 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8408 (tp30) REVERT: Q 3 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8175 (mm-30) REVERT: XA 103 GLU cc_start: 0.8986 (mp0) cc_final: 0.8776 (mp0) REVERT: XA 108 TYR cc_start: 0.8943 (t80) cc_final: 0.8715 (t80) REVERT: YA 208 TYR cc_start: 0.9061 (t80) cc_final: 0.8445 (t80) REVERT: YA 212 LEU cc_start: 0.9521 (mm) cc_final: 0.9299 (mm) REVERT: aA 408 TYR cc_start: 0.8932 (t80) cc_final: 0.8309 (t80) REVERT: R 12 LEU cc_start: 0.9686 (mm) cc_final: 0.9315 (mm) REVERT: bA 112 LEU cc_start: 0.9623 (mm) cc_final: 0.9414 (mm) REVERT: S 3 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8518 (mm-30) REVERT: fA 108 TYR cc_start: 0.8751 (t80) cc_final: 0.8142 (t80) REVERT: gA 212 LEU cc_start: 0.9597 (mm) cc_final: 0.9322 (mm) REVERT: iA 403 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8902 (mm-30) REVERT: kA 212 LEU cc_start: 0.9516 (mm) cc_final: 0.9241 (mm) REVERT: mA 408 TYR cc_start: 0.9124 (t80) cc_final: 0.8870 (t80) outliers start: 0 outliers final: 0 residues processed: 602 average time/residue: 0.2106 time to fit residues: 193.7359 Evaluate side-chains 571 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 571 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 415 GLN n 315 GLN ** x 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 GLN ** 8 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** kA 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12915 Z= 0.272 Angle : 0.545 5.843 17325 Z= 0.285 Chirality : 0.044 0.144 1995 Planarity : 0.002 0.012 2310 Dihedral : 2.920 18.074 1890 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 0.09 % Allowed : 1.21 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.23), residues: 1365 helix: 2.68 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.002 TYR o 408 ARG 0.002 0.000 ARGqA 406 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 587 time to evaluate : 1.615 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.9569 (mm) cc_final: 0.9324 (mm) REVERT: W 203 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8485 (mm-30) REVERT: W 208 TYR cc_start: 0.8932 (t80) cc_final: 0.8659 (t80) REVERT: Y 412 LEU cc_start: 0.9432 (mm) cc_final: 0.9212 (mm) REVERT: B 3 GLU cc_start: 0.8757 (mm-30) cc_final: 0.7466 (tp30) REVERT: B 12 LEU cc_start: 0.9648 (mm) cc_final: 0.9270 (mm) REVERT: a 212 LEU cc_start: 0.9581 (mm) cc_final: 0.9253 (mm) REVERT: C 3 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8536 (mm-30) REVERT: d 108 TYR cc_start: 0.9163 (t80) cc_final: 0.8356 (t80) REVERT: d 112 LEU cc_start: 0.9583 (mm) cc_final: 0.9309 (mm) REVERT: e 208 TYR cc_start: 0.9010 (t80) cc_final: 0.8654 (t80) REVERT: e 212 LEU cc_start: 0.9563 (mm) cc_final: 0.9040 (mm) REVERT: f 308 TYR cc_start: 0.9056 (t80) cc_final: 0.8688 (t80) REVERT: g 403 GLU cc_start: 0.9166 (mp0) cc_final: 0.8886 (mp0) REVERT: g 408 TYR cc_start: 0.9185 (t80) cc_final: 0.8332 (t80) REVERT: g 412 LEU cc_start: 0.9490 (mp) cc_final: 0.8957 (mp) REVERT: i 208 TYR cc_start: 0.9041 (t80) cc_final: 0.8630 (t80) REVERT: j 308 TYR cc_start: 0.9078 (t80) cc_final: 0.8433 (t80) REVERT: j 312 LEU cc_start: 0.9611 (mm) cc_final: 0.9348 (mm) REVERT: E 8 TYR cc_start: 0.8806 (t80) cc_final: 0.8490 (t80) REVERT: m 211 ILE cc_start: 0.9453 (mt) cc_final: 0.8904 (mp) REVERT: m 212 LEU cc_start: 0.9305 (mm) cc_final: 0.8926 (mm) REVERT: m 215 GLN cc_start: 0.8969 (mt0) cc_final: 0.8498 (mt0) REVERT: p 112 LEU cc_start: 0.9600 (mm) cc_final: 0.9272 (mm) REVERT: t 112 LEU cc_start: 0.9661 (mm) cc_final: 0.9270 (mm) REVERT: u 208 TYR cc_start: 0.9228 (t80) cc_final: 0.9021 (t80) REVERT: v 303 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8721 (mm-30) REVERT: v 315 GLN cc_start: 0.8979 (mt0) cc_final: 0.8585 (mt0) REVERT: H 3 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8572 (mm-30) REVERT: y 212 LEU cc_start: 0.9515 (mm) cc_final: 0.9155 (mm) REVERT: I 8 TYR cc_start: 0.9227 (t80) cc_final: 0.8756 (t80) REVERT: 3 303 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8869 (mm-30) REVERT: 6 203 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8074 (mm-30) REVERT: 8 408 TYR cc_start: 0.8946 (t80) cc_final: 0.8625 (t80) REVERT: K 3 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8200 (mm-30) REVERT: K 8 TYR cc_start: 0.9142 (t80) cc_final: 0.8649 (t80) REVERT: K 12 LEU cc_start: 0.9588 (mm) cc_final: 0.9372 (mm) REVERT: 9 115 GLN cc_start: 0.8828 (mt0) cc_final: 0.8550 (mt0) REVERT: BA 312 LEU cc_start: 0.9500 (mm) cc_final: 0.9228 (mm) REVERT: CA 408 TYR cc_start: 0.9074 (t80) cc_final: 0.8748 (t80) REVERT: CA 412 LEU cc_start: 0.9547 (mm) cc_final: 0.9266 (mm) REVERT: CA 415 GLN cc_start: 0.8964 (mt0) cc_final: 0.8591 (mt0) REVERT: L 3 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8516 (mm-30) REVERT: L 8 TYR cc_start: 0.9159 (t80) cc_final: 0.8599 (t80) REVERT: L 12 LEU cc_start: 0.9578 (mm) cc_final: 0.9317 (mm) REVERT: DA 108 TYR cc_start: 0.9072 (t80) cc_final: 0.8621 (t80) REVERT: EA 208 TYR cc_start: 0.9123 (t80) cc_final: 0.8726 (t80) REVERT: FA 308 TYR cc_start: 0.9189 (t80) cc_final: 0.8541 (t80) REVERT: FA 312 LEU cc_start: 0.9508 (mm) cc_final: 0.9173 (mm) REVERT: GA 408 TYR cc_start: 0.9000 (t80) cc_final: 0.8504 (t80) REVERT: M 12 LEU cc_start: 0.9676 (mm) cc_final: 0.9354 (mm) REVERT: HA 115 GLN cc_start: 0.9198 (mt0) cc_final: 0.8634 (mt0) REVERT: N 12 LEU cc_start: 0.9639 (mm) cc_final: 0.9372 (mm) REVERT: LA 115 GLN cc_start: 0.9078 (mt0) cc_final: 0.8827 (tt0) REVERT: MA 212 LEU cc_start: 0.9546 (mm) cc_final: 0.9331 (mm) REVERT: OA 403 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8941 (mm-30) REVERT: OA 412 LEU cc_start: 0.9642 (mm) cc_final: 0.9258 (mm) REVERT: O 3 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8105 (mm-30) REVERT: O 8 TYR cc_start: 0.9116 (t80) cc_final: 0.8782 (t80) REVERT: PA 115 GLN cc_start: 0.9058 (mt0) cc_final: 0.8702 (tt0) REVERT: QA 208 TYR cc_start: 0.9021 (t80) cc_final: 0.8704 (t80) REVERT: QA 215 GLN cc_start: 0.8915 (mt0) cc_final: 0.8537 (tt0) REVERT: RA 303 GLU cc_start: 0.8784 (mm-30) cc_final: 0.7789 (mm-30) REVERT: RA 312 LEU cc_start: 0.9588 (mm) cc_final: 0.9375 (mm) REVERT: SA 403 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8755 (mm-30) REVERT: SA 408 TYR cc_start: 0.8936 (t80) cc_final: 0.8442 (t80) REVERT: SA 415 GLN cc_start: 0.8868 (mt0) cc_final: 0.8135 (mt0) REVERT: TA 112 LEU cc_start: 0.9605 (mm) cc_final: 0.9403 (mm) REVERT: VA 303 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8424 (tp30) REVERT: Q 3 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8442 (mm-30) REVERT: Q 8 TYR cc_start: 0.8885 (t80) cc_final: 0.8112 (t80) REVERT: XA 103 GLU cc_start: 0.8966 (mp0) cc_final: 0.8746 (mp0) REVERT: XA 108 TYR cc_start: 0.8979 (t80) cc_final: 0.8714 (t80) REVERT: YA 208 TYR cc_start: 0.9079 (t80) cc_final: 0.8391 (t80) REVERT: YA 212 LEU cc_start: 0.9528 (mm) cc_final: 0.9281 (mm) REVERT: aA 408 TYR cc_start: 0.8958 (t80) cc_final: 0.8337 (t80) REVERT: R 12 LEU cc_start: 0.9691 (mm) cc_final: 0.9287 (mm) REVERT: bA 112 LEU cc_start: 0.9632 (mm) cc_final: 0.9427 (mm) REVERT: S 3 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8430 (mm-30) REVERT: gA 212 LEU cc_start: 0.9622 (mm) cc_final: 0.9346 (mm) REVERT: kA 208 TYR cc_start: 0.9104 (t80) cc_final: 0.8886 (t80) REVERT: kA 212 LEU cc_start: 0.9512 (mm) cc_final: 0.9203 (mm) REVERT: mA 408 TYR cc_start: 0.9134 (t80) cc_final: 0.8838 (t80) REVERT: U 3 GLU cc_start: 0.9322 (mm-30) cc_final: 0.9108 (mm-30) REVERT: nA 103 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8967 (mm-30) outliers start: 1 outliers final: 0 residues processed: 588 average time/residue: 0.1978 time to fit residues: 177.2682 Evaluate side-chains 564 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 564 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.0670 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 115 GLN ** 8 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN ** kA 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.6590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12915 Z= 0.195 Angle : 0.557 4.087 17325 Z= 0.274 Chirality : 0.041 0.170 1995 Planarity : 0.002 0.009 2310 Dihedral : 3.201 19.526 1890 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.42 (0.22), residues: 1365 helix: 2.88 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.002 TYR w 408 ARG 0.003 0.000 ARGCA 406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 605 time to evaluate : 1.570 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.9553 (mm) cc_final: 0.9269 (mm) REVERT: W 203 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8581 (mm-30) REVERT: B 3 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8453 (tp30) REVERT: B 12 LEU cc_start: 0.9641 (mm) cc_final: 0.9259 (mm) REVERT: a 212 LEU cc_start: 0.9569 (mm) cc_final: 0.9267 (mm) REVERT: C 3 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8368 (mm-30) REVERT: d 108 TYR cc_start: 0.9131 (t80) cc_final: 0.8382 (t80) REVERT: d 112 LEU cc_start: 0.9552 (mm) cc_final: 0.9239 (mm) REVERT: e 208 TYR cc_start: 0.8929 (t80) cc_final: 0.8696 (t80) REVERT: e 212 LEU cc_start: 0.9561 (mm) cc_final: 0.9050 (mm) REVERT: f 308 TYR cc_start: 0.8984 (t80) cc_final: 0.8583 (t80) REVERT: g 403 GLU cc_start: 0.9161 (mp0) cc_final: 0.8870 (mp0) REVERT: i 208 TYR cc_start: 0.9003 (t80) cc_final: 0.8637 (t80) REVERT: j 308 TYR cc_start: 0.8976 (t80) cc_final: 0.8540 (t80) REVERT: E 8 TYR cc_start: 0.8740 (t80) cc_final: 0.8449 (t80) REVERT: m 211 ILE cc_start: 0.9409 (mt) cc_final: 0.8861 (mp) REVERT: m 212 LEU cc_start: 0.9286 (mm) cc_final: 0.8891 (mm) REVERT: m 215 GLN cc_start: 0.8889 (mt0) cc_final: 0.8367 (mt0) REVERT: p 112 LEU cc_start: 0.9594 (mm) cc_final: 0.9302 (mm) REVERT: s 412 LEU cc_start: 0.9194 (mm) cc_final: 0.8977 (mm) REVERT: s 415 GLN cc_start: 0.8859 (mt0) cc_final: 0.8605 (mt0) REVERT: G 12 LEU cc_start: 0.9668 (mm) cc_final: 0.9457 (mm) REVERT: t 112 LEU cc_start: 0.9657 (mm) cc_final: 0.9240 (mm) REVERT: u 208 TYR cc_start: 0.9172 (t80) cc_final: 0.8889 (t80) REVERT: x 115 GLN cc_start: 0.8915 (mt0) cc_final: 0.8701 (mt0) REVERT: y 212 LEU cc_start: 0.9479 (mm) cc_final: 0.9122 (mm) REVERT: 0 411 ILE cc_start: 0.9417 (mt) cc_final: 0.8949 (mt) REVERT: 0 412 LEU cc_start: 0.9327 (mm) cc_final: 0.8786 (mm) REVERT: 0 415 GLN cc_start: 0.8816 (mt0) cc_final: 0.8264 (mt0) REVERT: I 8 TYR cc_start: 0.9162 (t80) cc_final: 0.8648 (t80) REVERT: 8 408 TYR cc_start: 0.8892 (t80) cc_final: 0.7867 (t80) REVERT: 8 411 ILE cc_start: 0.9360 (mt) cc_final: 0.9127 (mt) REVERT: 8 412 LEU cc_start: 0.9294 (mm) cc_final: 0.8925 (mm) REVERT: 8 415 GLN cc_start: 0.8891 (mt0) cc_final: 0.8373 (mt0) REVERT: K 8 TYR cc_start: 0.9074 (t80) cc_final: 0.8740 (t80) REVERT: BA 312 LEU cc_start: 0.9414 (mm) cc_final: 0.9161 (mm) REVERT: CA 408 TYR cc_start: 0.8839 (t80) cc_final: 0.8595 (t80) REVERT: CA 412 LEU cc_start: 0.9476 (mm) cc_final: 0.9229 (mm) REVERT: L 3 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8528 (mm-30) REVERT: L 8 TYR cc_start: 0.9137 (t80) cc_final: 0.8621 (t80) REVERT: DA 108 TYR cc_start: 0.8992 (t80) cc_final: 0.8565 (t80) REVERT: EA 208 TYR cc_start: 0.9091 (t80) cc_final: 0.8733 (t80) REVERT: FA 308 TYR cc_start: 0.9134 (t80) cc_final: 0.8423 (t80) REVERT: FA 312 LEU cc_start: 0.9477 (mm) cc_final: 0.9109 (mm) REVERT: GA 408 TYR cc_start: 0.8993 (t80) cc_final: 0.8530 (t80) REVERT: M 12 LEU cc_start: 0.9676 (mm) cc_final: 0.9352 (mm) REVERT: LA 115 GLN cc_start: 0.9033 (mt0) cc_final: 0.8759 (tt0) REVERT: MA 212 LEU cc_start: 0.9649 (mm) cc_final: 0.9348 (mm) REVERT: OA 403 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8718 (mm-30) REVERT: OA 412 LEU cc_start: 0.9636 (mm) cc_final: 0.9281 (mm) REVERT: O 3 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8022 (mm-30) REVERT: O 8 TYR cc_start: 0.9060 (t80) cc_final: 0.8777 (t80) REVERT: QA 208 TYR cc_start: 0.8937 (t80) cc_final: 0.8615 (t80) REVERT: QA 215 GLN cc_start: 0.8896 (mt0) cc_final: 0.8635 (mt0) REVERT: RA 303 GLU cc_start: 0.8807 (mm-30) cc_final: 0.7844 (mm-30) REVERT: SA 403 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8749 (mm-30) REVERT: SA 408 TYR cc_start: 0.8794 (t80) cc_final: 0.8401 (t80) REVERT: SA 415 GLN cc_start: 0.8820 (mt0) cc_final: 0.8087 (mt0) REVERT: VA 303 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8685 (tp30) REVERT: Q 3 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8340 (mm-30) REVERT: Q 8 TYR cc_start: 0.8876 (t80) cc_final: 0.8086 (t80) REVERT: XA 103 GLU cc_start: 0.8984 (mp0) cc_final: 0.8767 (mp0) REVERT: YA 208 TYR cc_start: 0.9023 (t80) cc_final: 0.8421 (t80) REVERT: YA 212 LEU cc_start: 0.9509 (mm) cc_final: 0.9299 (mm) REVERT: ZA 308 TYR cc_start: 0.8861 (t80) cc_final: 0.8201 (t80) REVERT: aA 408 TYR cc_start: 0.8914 (t80) cc_final: 0.8453 (t80) REVERT: aA 415 GLN cc_start: 0.8508 (tp-100) cc_final: 0.8128 (tp-100) REVERT: R 12 LEU cc_start: 0.9679 (mm) cc_final: 0.9295 (mm) REVERT: S 3 GLU cc_start: 0.9071 (mm-30) cc_final: 0.7722 (mm-30) REVERT: gA 212 LEU cc_start: 0.9608 (mm) cc_final: 0.9324 (mm) REVERT: iA 415 GLN cc_start: 0.9014 (mm110) cc_final: 0.8236 (mm-40) REVERT: kA 212 LEU cc_start: 0.9504 (mm) cc_final: 0.9232 (mm) REVERT: nA 103 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8936 (mm-30) outliers start: 0 outliers final: 0 residues processed: 605 average time/residue: 0.2024 time to fit residues: 185.8067 Evaluate side-chains 575 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 575 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 0.0570 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 0.4980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 115 GLN ** 8 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JA 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** hA 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.055232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.046620 restraints weight = 46088.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.048626 restraints weight = 28558.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.050099 restraints weight = 19388.441| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.6819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12915 Z= 0.187 Angle : 0.562 6.307 17325 Z= 0.272 Chirality : 0.041 0.138 1995 Planarity : 0.002 0.010 2310 Dihedral : 3.319 19.893 1890 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.60 (0.22), residues: 1365 helix: 2.98 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.002 TYR g 408 ARG 0.002 0.000 ARGXA 110 =============================================================================== Job complete usr+sys time: 3363.65 seconds wall clock time: 60 minutes 20.18 seconds (3620.18 seconds total)