Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 00:20:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/08_2023/6wkx_21812.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/08_2023/6wkx_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_21812/08_2023/6wkx_21812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/08_2023/6wkx_21812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/08_2023/6wkx_21812.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkx_21812/08_2023/6wkx_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 6.71, per 1000 atoms: 0.52 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: 5.56 Conformation dependent library (CDL) restraints added in 1.6 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: 1.08 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: 3.81 Time building geometry restraints manager: 5.96 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: 2.530 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: 0.000 Extract box with map and model: 7.990 Check model and map are aligned: 0.210 Set scattering table: 0.110 Process input model: 34.170 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.490 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.603 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 outliers start: 0 outliers final: 0 residues processed: 650 average time/residue: 0.2093 time to fit residues: 208.3114 Evaluate side-chains 582 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 582 time to evaluate : 1.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0048 ------------------------------------------------------------------------------- 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: 2.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 53 optimal weight: 0.0060 chunk 42 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- 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: 0.8821 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 12915 Z= 0.222 Angle : 0.526 4.134 17325 Z= 0.293 Chirality : 0.038 0.125 1995 Planarity : 0.004 0.026 2310 Dihedral : 3.268 10.924 1890 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer Outliers : 0.26 % 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: 0.76 (0.23), residues: 1365 helix: 0.62 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 675 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 672 time to evaluate : 1.534 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 outliers start: 3 outliers final: 0 residues processed: 672 average time/residue: 0.2043 time to fit residues: 207.4771 Evaluate side-chains 570 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 570 time to evaluate : 1.453 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8354 ------------------------------------------------------------------------------- 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: 7.9990 chunk 29 optimal weight: 0.0370 chunk 79 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: aA 415 GLN oA 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 12915 Z= 0.168 Angle : 0.533 4.516 17325 Z= 0.271 Chirality : 0.040 0.130 1995 Planarity : 0.002 0.016 2310 Dihedral : 3.114 19.874 1890 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer Outliers : 0.09 % 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: 2.82 (0.25), residues: 1365 helix: 1.89 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 652 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 651 time to evaluate : 1.905 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 outliers start: 1 outliers final: 0 residues processed: 652 average time/residue: 0.2086 time to fit residues: 204.6837 Evaluate side-chains 540 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 540 time to evaluate : 1.584 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0075 ------------------------------------------------------------------------------- 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: 0.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 415 GLN E 15 GLN m 215 GLN F 15 GLN s 415 GLN u 215 GLN H 15 GLN y 215 GLN K 15 GLN HA 115 GLN QA 215 GLN ** eA 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** gA 215 GLN ** mA 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** oA 215 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 12915 Z= 0.271 Angle : 0.554 5.487 17325 Z= 0.300 Chirality : 0.045 0.150 1995 Planarity : 0.002 0.016 2310 Dihedral : 3.117 16.765 1890 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.35 % 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: 3.02 (0.25), residues: 1365 helix: 2.01 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 597 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 593 time to evaluate : 1.550 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 outliers start: 4 outliers final: 0 residues processed: 597 average time/residue: 0.2083 time to fit residues: 187.3712 Evaluate side-chains 548 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9154 ------------------------------------------------------------------------------- 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: 0.0770 chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 415 GLN o 415 GLN H 15 GLN 0 415 GLN JA 315 GLN fA 115 GLN ** mA 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 12915 Z= 0.250 Angle : 0.548 5.465 17325 Z= 0.289 Chirality : 0.044 0.160 1995 Planarity : 0.002 0.012 2310 Dihedral : 3.257 20.806 1890 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.25), residues: 1365 helix: 2.24 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 581 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 579 time to evaluate : 1.423 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 outliers start: 2 outliers final: 0 residues processed: 581 average time/residue: 0.2025 time to fit residues: 177.9370 Evaluate side-chains 537 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 537 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9780 ------------------------------------------------------------------------------- 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: 9.9990 chunk 91 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 315 GLN l 115 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN fA 115 GLN ** kA 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** mA 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 12915 Z= 0.338 Angle : 0.594 4.927 17325 Z= 0.322 Chirality : 0.047 0.156 1995 Planarity : 0.003 0.016 2310 Dihedral : 3.173 20.238 1890 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer Outliers : 0.26 % 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: 3.28 (0.24), residues: 1365 helix: 2.17 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 570 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 567 time to evaluate : 1.708 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 outliers start: 3 outliers final: 0 residues processed: 570 average time/residue: 0.2040 time to fit residues: 176.1771 Evaluate side-chains 523 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 523 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8150 ------------------------------------------------------------------------------- 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: 4.9990 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN E 15 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN ** z 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 GLN DA 115 GLN aA 415 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 12915 Z= 0.211 Angle : 0.576 7.061 17325 Z= 0.291 Chirality : 0.043 0.135 1995 Planarity : 0.002 0.013 2310 Dihedral : 3.435 19.387 1890 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.24), residues: 1365 helix: 2.54 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 570 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 568 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 570 average time/residue: 0.2010 time to fit residues: 173.5789 Evaluate side-chains 530 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 1.627 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0901 ------------------------------------------------------------------------------- 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: 0.9990 chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN M 15 GLN O 15 GLN oA 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 12915 Z= 0.207 Angle : 0.607 6.091 17325 Z= 0.304 Chirality : 0.044 0.152 1995 Planarity : 0.002 0.013 2310 Dihedral : 3.501 19.844 1890 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.09 % 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: 4.09 (0.24), residues: 1365 helix: 2.67 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 577 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 576 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 577 average time/residue: 0.2021 time to fit residues: 177.2104 Evaluate side-chains 523 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 523 time to evaluate : 1.570 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0021 ------------------------------------------------------------------------------- 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: 6.9990 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 315 GLN r 315 GLN ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN M 15 GLN ** mA 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 12915 Z= 0.296 Angle : 0.639 7.907 17325 Z= 0.337 Chirality : 0.048 0.168 1995 Planarity : 0.002 0.015 2310 Dihedral : 3.147 21.351 1890 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer Outliers : 0.09 % 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: 4.17 (0.24), residues: 1365 helix: 2.72 (0.15), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** 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 562 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 561 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 562 average time/residue: 0.2096 time to fit residues: 179.4509 Evaluate side-chains 521 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 521 time to evaluate : 1.531 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8369 ------------------------------------------------------------------------------- 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: 5.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.6418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 12915 Z= 0.285 Angle : 0.637 7.215 17325 Z= 0.332 Chirality : 0.047 0.146 1995 Planarity : 0.002 0.017 2310 Dihedral : 3.208 20.796 1890 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer Outliers : 0.09 % 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: 4.28 (0.23), residues: 1365 helix: 2.79 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 ********************** 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 554 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 553 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 554 average time/residue: 0.2066 time to fit residues: 174.2342 Evaluate side-chains 514 residues out of total 1155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 514 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9784 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.055799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.047106 restraints weight = 46003.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.049119 restraints weight = 29019.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.050502 restraints weight = 19843.097| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.6732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 12915 Z= 0.215 Angle : 0.621 5.808 17325 Z= 0.313 Chirality : 0.044 0.163 1995 Planarity : 0.002 0.010 2310 Dihedral : 3.555 21.606 1890 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.37 (0.23), residues: 1365 helix: 2.84 (0.14), residues: 1365 sheet: None (None), residues: 0 loop : None (None), residues: 0 =============================================================================== Job complete usr+sys time: 3246.36 seconds wall clock time: 58 minutes 38.58 seconds (3518.58 seconds total)