Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 18 01:18:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl8_21817/08_2023/6wl8_21817.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl8_21817/08_2023/6wl8_21817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl8_21817/08_2023/6wl8_21817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl8_21817/08_2023/6wl8_21817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl8_21817/08_2023/6wl8_21817.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl8_21817/08_2023/6wl8_21817.pdb" } resolution = 4.1 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= 0.003 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 15370 2.51 5 N 3922 2.21 5 O 4558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 6": "OE1" <-> "OE2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "0 GLU 124": "OE1" <-> "OE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "2 GLU 124": "OE1" <-> "OE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "3 GLU 124": "OE1" <-> "OE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "4 GLU 124": "OE1" <-> "OE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "G GLU 6": "OE1" <-> "OE2" Residue "7 GLU 124": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "8 GLU 124": "OE1" <-> "OE2" Residue "I GLU 6": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "J GLU 6": "OE1" <-> "OE2" Residue "J GLU 10": "OE1" <-> "OE2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "AA GLU 124": "OE1" <-> "OE2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "K GLU 10": "OE1" <-> "OE2" Residue "BA GLU 124": "OE1" <-> "OE2" Residue "L GLU 6": "OE1" <-> "OE2" Residue "M GLU 6": "OE1" <-> "OE2" Residue "M GLU 10": "OE1" <-> "OE2" Residue "DA GLU 124": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 10": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O GLU 10": "OE1" <-> "OE2" Residue "P GLU 6": "OE1" <-> "OE2" Residue "P GLU 10": "OE1" <-> "OE2" Residue "GA GLU 124": "OE1" <-> "OE2" Residue "Q GLU 6": "OE1" <-> "OE2" Residue "Q GLU 10": "OE1" <-> "OE2" Residue "R GLU 6": "OE1" <-> "OE2" Residue "R GLU 10": "OE1" <-> "OE2" Residue "IA GLU 124": "OE1" <-> "OE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "T GLU 6": "OE1" <-> "OE2" Residue "T GLU 10": "OE1" <-> "OE2" Residue "KA GLU 124": "OE1" <-> "OE2" Residue "U GLU 6": "OE1" <-> "OE2" Residue "U GLU 10": "OE1" <-> "OE2" Residue "LA GLU 124": "OE1" <-> "OE2" Residue "V GLU 6": "OE1" <-> "OE2" Residue "V GLU 10": "OE1" <-> "OE2" Residue "MA GLU 124": "OE1" <-> "OE2" Residue "W GLU 6": "OE1" <-> "OE2" Residue "W GLU 10": "OE1" <-> "OE2" Residue "NA GLU 124": "OE1" <-> "OE2" Residue "X GLU 6": "OE1" <-> "OE2" Residue "X GLU 10": "OE1" <-> "OE2" Residue "Y GLU 6": "OE1" <-> "OE2" Residue "Y GLU 10": "OE1" <-> "OE2" Residue "Z GLU 6": "OE1" <-> "OE2" Residue "Z GLU 10": "OE1" <-> "OE2" Residue "QA GLU 124": "OE1" <-> "OE2" Residue "a GLU 6": "OE1" <-> "OE2" Residue "a GLU 10": "OE1" <-> "OE2" Residue "b GLU 6": "OE1" <-> "OE2" Residue "b GLU 10": "OE1" <-> "OE2" Residue "c GLU 6": "OE1" <-> "OE2" Residue "TA GLU 124": "OE1" <-> "OE2" Residue "d GLU 6": "OE1" <-> "OE2" Residue "d GLU 10": "OE1" <-> "OE2" Residue "UA GLU 124": "OE1" <-> "OE2" Residue "e GLU 6": "OE1" <-> "OE2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "VA GLU 124": "OE1" <-> "OE2" Residue "f GLU 6": "OE1" <-> "OE2" Residue "f GLU 10": "OE1" <-> "OE2" Residue "g GLU 6": "OE1" <-> "OE2" Residue "g GLU 10": "OE1" <-> "OE2" Residue "XA GLU 124": "OE1" <-> "OE2" Residue "h GLU 6": "OE1" <-> "OE2" Residue "h GLU 10": "OE1" <-> "OE2" Residue "YA GLU 124": "OE1" <-> "OE2" Residue "i GLU 6": "OE1" <-> "OE2" Residue "j GLU 6": "OE1" <-> "OE2" Residue "j GLU 10": "OE1" <-> "OE2" Residue "aA GLU 124": "OE1" <-> "OE2" Residue "k GLU 6": "OE1" <-> "OE2" Residue "k GLU 10": "OE1" <-> "OE2" Residue "bA GLU 124": "OE1" <-> "OE2" Residue "l GLU 6": "OE1" <-> "OE2" Residue "l GLU 10": "OE1" <-> "OE2" Residue "cA GLU 124": "OE1" <-> "OE2" Residue "m GLU 6": "OE1" <-> "OE2" Residue "m GLU 10": "OE1" <-> "OE2" Residue "dA GLU 124": "OE1" <-> "OE2" Residue "n GLU 6": "OE1" <-> "OE2" Residue "n GLU 10": "OE1" <-> "OE2" Residue "eA GLU 124": "OE1" <-> "OE2" Residue "o GLU 6": "OE1" <-> "OE2" Residue "o GLU 10": "OE1" <-> "OE2" Residue "fA GLU 124": "OE1" <-> "OE2" Residue "p GLU 6": "OE1" <-> "OE2" Residue "p GLU 10": "OE1" <-> "OE2" Residue "gA GLU 124": "OE1" <-> "OE2" Residue "q GLU 6": "OE1" <-> "OE2" Residue "r GLU 6": "OE1" <-> "OE2" Residue "r GLU 10": "OE1" <-> "OE2" Residue "iA GLU 124": "OE1" <-> "OE2" Residue "s GLU 6": "OE1" <-> "OE2" Residue "s GLU 10": "OE1" <-> "OE2" Residue "jA GLU 124": "OE1" <-> "OE2" Residue "t GLU 6": "OE1" <-> "OE2" Residue "t GLU 10": "OE1" <-> "OE2" Residue "kA GLU 124": "OE1" <-> "OE2" Residue "u GLU 6": "OE1" <-> "OE2" Residue "u GLU 10": "OE1" <-> "OE2" Residue "u GLU 24": "OE1" <-> "OE2" Residue "lA GLU 124": "OE1" <-> "OE2" Residue "v GLU 6": "OE1" <-> "OE2" Residue "v GLU 10": "OE1" <-> "OE2" Residue "mA GLU 124": "OE1" <-> "OE2" Residue "w GLU 6": "OE1" <-> "OE2" Residue "w GLU 10": "OE1" <-> "OE2" Residue "x GLU 6": "OE1" <-> "OE2" Residue "x GLU 10": "OE1" <-> "OE2" Residue "y GLU 6": "OE1" <-> "OE2" Residue "y GLU 10": "OE1" <-> "OE2" Residue "z GLU 6": "OE1" <-> "OE2" Residue "z GLU 10": "OE1" <-> "OE2" Residue "1 GLU 6": "OE1" <-> "OE2" Residue "1 GLU 10": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 23850 Number of models: 1 Model: "" Number of chains: 106 Chain: "A" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "0" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "2" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "3" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "D" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "4" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "5" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "F" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "6" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "G" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "7" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "H" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "8" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "9" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "AA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "K" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "BA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "L" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "CA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "M" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "DA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "N" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "EA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "O" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "FA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "P" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "GA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "Q" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "HA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "IA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "S" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "JA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "T" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "KA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "U" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "LA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "V" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "MA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "W" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "NA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "X" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "OA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "Y" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "PA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "Z" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "QA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "a" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "RA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "b" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "SA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "c" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "TA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "d" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "UA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "e" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "VA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "f" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "WA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "g" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "XA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "h" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "YA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "i" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "ZA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "j" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "aA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "k" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "bA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "l" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "cA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "m" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "dA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "n" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "eA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "o" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "fA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "p" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "gA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "q" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "hA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "r" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "iA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "s" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "jA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "t" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "kA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "u" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "lA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "v" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "mA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "w" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "nA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "x" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "oA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "y" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "pA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "z" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "qA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "1" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "rA" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 225 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Time building chain proxies: 11.56, per 1000 atoms: 0.48 Number of scatterers: 23850 At special positions: 0 Unit cell: (118.8, 117.72, 137.16, 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 4558 8.00 N 3922 7.00 C 15370 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: 9.43 Conformation dependent library (CDL) restraints added in 3.3 seconds 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6148 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 0 sheets defined 96.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 1 through 29 removed outlier: 3.533A pdb=" N LEU A 5 " --> pdb=" O GLN A 1 " (cutoff:3.500A) Processing helix chain '0' and resid 102 through 129 Processing helix chain 'B' and resid 2 through 29 Processing helix chain '2' and resid 102 through 129 Processing helix chain 'C' and resid 2 through 29 Processing helix chain '3' and resid 102 through 129 Processing helix chain 'D' and resid 2 through 29 Processing helix chain '4' and resid 102 through 129 Processing helix chain 'E' and resid 2 through 29 Processing helix chain '5' and resid 102 through 129 Processing helix chain 'F' and resid 2 through 29 Processing helix chain '6' and resid 102 through 129 Processing helix chain 'G' and resid 2 through 29 Processing helix chain '7' and resid 102 through 129 Processing helix chain 'H' and resid 2 through 29 Processing helix chain '8' and resid 102 through 129 Processing helix chain 'I' and resid 2 through 29 Processing helix chain '9' and resid 102 through 129 Processing helix chain 'J' and resid 2 through 29 Processing helix chain 'AA' and resid 102 through 129 Processing helix chain 'K' and resid 2 through 29 Processing helix chain 'BA' and resid 102 through 129 Processing helix chain 'L' and resid 2 through 29 Processing helix chain 'CA' and resid 102 through 129 Processing helix chain 'M' and resid 2 through 29 Processing helix chain 'DA' and resid 102 through 129 Processing helix chain 'N' and resid 2 through 29 Processing helix chain 'EA' and resid 102 through 129 Processing helix chain 'O' and resid 2 through 29 Processing helix chain 'FA' and resid 102 through 129 Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'GA' and resid 102 through 129 Processing helix chain 'Q' and resid 2 through 29 Processing helix chain 'HA' and resid 102 through 129 Processing helix chain 'R' and resid 2 through 29 Processing helix chain 'IA' and resid 102 through 129 Processing helix chain 'S' and resid 2 through 29 Processing helix chain 'JA' and resid 102 through 129 Processing helix chain 'T' and resid 2 through 29 Processing helix chain 'KA' and resid 102 through 129 Processing helix chain 'U' and resid 2 through 29 Processing helix chain 'LA' and resid 102 through 129 Processing helix chain 'V' and resid 2 through 29 Processing helix chain 'MA' and resid 102 through 129 Processing helix chain 'W' and resid 2 through 29 Processing helix chain 'NA' and resid 102 through 129 Processing helix chain 'X' and resid 2 through 29 Processing helix chain 'OA' and resid 102 through 129 Processing helix chain 'Y' and resid 2 through 29 Processing helix chain 'PA' and resid 102 through 129 Processing helix chain 'Z' and resid 2 through 29 Processing helix chain 'QA' and resid 102 through 129 Processing helix chain 'a' and resid 2 through 29 Processing helix chain 'RA' and resid 102 through 129 removed outlier: 3.520A pdb=" N GLNRA 129 " --> pdb=" O ILERA 125 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 29 Processing helix chain 'SA' and resid 102 through 129 Processing helix chain 'c' and resid 2 through 29 Processing helix chain 'TA' and resid 102 through 129 Processing helix chain 'd' and resid 2 through 29 Processing helix chain 'UA' and resid 102 through 129 Processing helix chain 'e' and resid 2 through 29 Processing helix chain 'VA' and resid 102 through 129 Processing helix chain 'f' and resid 2 through 29 Processing helix chain 'WA' and resid 102 through 129 Processing helix chain 'g' and resid 2 through 29 Processing helix chain 'XA' and resid 102 through 129 Processing helix chain 'h' and resid 2 through 29 Processing helix chain 'YA' and resid 102 through 129 Processing helix chain 'i' and resid 2 through 29 Processing helix chain 'ZA' and resid 102 through 129 Processing helix chain 'j' and resid 2 through 29 Processing helix chain 'aA' and resid 102 through 129 Processing helix chain 'k' and resid 2 through 29 Processing helix chain 'bA' and resid 102 through 129 Processing helix chain 'l' and resid 2 through 29 Processing helix chain 'cA' and resid 102 through 129 Processing helix chain 'm' and resid 2 through 29 Processing helix chain 'dA' and resid 102 through 129 Processing helix chain 'n' and resid 2 through 29 removed outlier: 3.641A pdb=" N GLN n 29 " --> pdb=" O ILE n 25 " (cutoff:3.500A) Processing helix chain 'eA' and resid 102 through 129 Processing helix chain 'o' and resid 2 through 29 Processing helix chain 'fA' and resid 102 through 129 Processing helix chain 'p' and resid 2 through 29 Processing helix chain 'gA' and resid 102 through 129 Processing helix chain 'q' and resid 2 through 29 Processing helix chain 'hA' and resid 102 through 129 Processing helix chain 'r' and resid 2 through 29 Processing helix chain 'iA' and resid 102 through 129 Processing helix chain 's' and resid 2 through 29 Processing helix chain 'jA' and resid 102 through 129 Processing helix chain 't' and resid 2 through 28 Processing helix chain 'kA' and resid 102 through 129 Processing helix chain 'u' and resid 2 through 29 Processing helix chain 'lA' and resid 102 through 129 Processing helix chain 'v' and resid 2 through 29 removed outlier: 3.613A pdb=" N GLN v 29 " --> pdb=" O ILE v 25 " (cutoff:3.500A) Processing helix chain 'mA' and resid 102 through 129 Processing helix chain 'w' and resid 2 through 29 Processing helix chain 'nA' and resid 102 through 129 Processing helix chain 'x' and resid 2 through 29 Processing helix chain 'oA' and resid 102 through 129 Processing helix chain 'y' and resid 2 through 29 Processing helix chain 'pA' and resid 102 through 129 Processing helix chain 'z' and resid 2 through 29 Processing helix chain 'qA' and resid 102 through 129 Processing helix chain '1' and resid 2 through 29 Processing helix chain 'rA' and resid 102 through 129 2540 hydrogen bonds defined for protein. 7620 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: 8.23 Time building geometry restraints manager: 10.09 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: 4452 1.29 - 1.35: 3419 1.35 - 1.42: 1033 1.42 - 1.48: 3145 1.48 - 1.54: 11907 Bond restraints: 23956 Sorted by residual: bond pdb=" CG1 ILE h 25 " pdb=" CD1 ILE h 25 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.69e+00 bond pdb=" CG1 ILE A 25 " pdb=" CD1 ILE A 25 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" CG1 ILE E 25 " pdb=" CD1 ILE E 25 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.62e+00 bond pdb=" CG1 ILE O 25 " pdb=" CD1 ILE O 25 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.57e+00 bond pdb=" CG1 ILE G 25 " pdb=" CD1 ILE G 25 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.48e+00 ... (remaining 23951 not shown) Histogram of bond angle deviations from ideal: 106.08 - 111.15: 9960 111.15 - 116.22: 6346 116.22 - 121.29: 11369 121.29 - 126.36: 4337 126.36 - 131.43: 106 Bond angle restraints: 32118 Sorted by residual: angle pdb=" C ILE X 25 " pdb=" CA ILE X 25 " pdb=" CB ILE X 25 " ideal model delta sigma weight residual 111.97 108.70 3.27 1.28e+00 6.10e-01 6.54e+00 angle pdb=" C ILE F 25 " pdb=" CA ILE F 25 " pdb=" CB ILE F 25 " ideal model delta sigma weight residual 111.97 108.79 3.18 1.28e+00 6.10e-01 6.17e+00 angle pdb=" C ILE W 25 " pdb=" CA ILE W 25 " pdb=" CB ILE W 25 " ideal model delta sigma weight residual 111.97 108.83 3.14 1.28e+00 6.10e-01 6.03e+00 angle pdb=" C ILE p 25 " pdb=" CA ILE p 25 " pdb=" CB ILE p 25 " ideal model delta sigma weight residual 111.97 109.13 2.84 1.28e+00 6.10e-01 4.93e+00 angle pdb=" C ILE H 25 " pdb=" CA ILE H 25 " pdb=" CB ILE H 25 " ideal model delta sigma weight residual 111.97 109.21 2.76 1.28e+00 6.10e-01 4.64e+00 ... (remaining 32113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 13110 15.62 - 31.24: 1605 31.24 - 46.86: 445 46.86 - 62.48: 36 62.48 - 78.10: 68 Dihedral angle restraints: 15264 sinusoidal: 6042 harmonic: 9222 Sorted by residual: dihedral pdb=" CB GLU k 6 " pdb=" CG GLU k 6 " pdb=" CD GLU k 6 " pdb=" OE1 GLU k 6 " ideal model delta sinusoidal sigma weight residual 0.00 78.10 -78.10 1 3.00e+01 1.11e-03 8.47e+00 dihedral pdb=" CB GLU D 6 " pdb=" CG GLU D 6 " pdb=" CD GLU D 6 " pdb=" OE1 GLU D 6 " ideal model delta sinusoidal sigma weight residual 0.00 77.97 -77.97 1 3.00e+01 1.11e-03 8.44e+00 dihedral pdb=" CB GLU Y 6 " pdb=" CG GLU Y 6 " pdb=" CD GLU Y 6 " pdb=" OE1 GLU Y 6 " ideal model delta sinusoidal sigma weight residual 0.00 77.74 -77.74 1 3.00e+01 1.11e-03 8.40e+00 ... (remaining 15261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2938 0.042 - 0.085: 641 0.085 - 0.127: 237 0.127 - 0.170: 55 0.170 - 0.212: 51 Chirality restraints: 3922 Sorted by residual: chirality pdb=" CG LEU B 12 " pdb=" CB LEU B 12 " pdb=" CD1 LEU B 12 " pdb=" CD2 LEU B 12 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU B 19 " pdb=" CB LEU B 19 " pdb=" CD1 LEU B 19 " pdb=" CD2 LEU B 19 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CG LEU n 12 " pdb=" CB LEU n 12 " pdb=" CD1 LEU n 12 " pdb=" CD2 LEU n 12 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 3919 not shown) Planarity restraints: 4028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILEAA 125 " 0.007 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C ILEAA 125 " -0.022 2.00e-02 2.50e+03 pdb=" O ILEAA 125 " 0.008 2.00e-02 2.50e+03 pdb=" N LEUAA 126 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILEXA 125 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" C ILEXA 125 " -0.021 2.00e-02 2.50e+03 pdb=" O ILEXA 125 " 0.008 2.00e-02 2.50e+03 pdb=" N LEUXA 126 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILESA 125 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.48e+00 pdb=" C ILESA 125 " -0.021 2.00e-02 2.50e+03 pdb=" O ILESA 125 " 0.008 2.00e-02 2.50e+03 pdb=" N LEUSA 126 " 0.007 2.00e-02 2.50e+03 ... (remaining 4025 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 7580 2.90 - 3.40: 25771 3.40 - 3.90: 38370 3.90 - 4.40: 43504 4.40 - 4.90: 66795 Nonbonded interactions: 182020 Sorted by model distance: nonbonded pdb=" O GLN B 29 " pdb=" N GLN X 1 " model vdw 2.395 2.520 nonbonded pdb=" O GLN R 29 " pdb=" N GLN n 1 " model vdw 2.404 2.520 nonbonded pdb=" N GLN Y 1 " pdb=" O GLN u 29 " model vdw 2.404 2.520 nonbonded pdb=" N GLN a 1 " pdb=" O GLN w 29 " model vdw 2.407 2.520 nonbonded pdb=" O GLN A 29 " pdb=" N GLN V 1 " model vdw 2.409 2.520 ... (remaining 182015 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 'rA' 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.860 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 58.080 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.650 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 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 : 0.005 0.051 23956 Z= 0.324 Angle : 0.653 5.180 32118 Z= 0.368 Chirality : 0.047 0.212 3922 Planarity : 0.004 0.013 4028 Dihedral : 15.478 78.099 9116 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.78 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: -1.08 (0.11), residues: 2862 helix: -0.52 (0.07), residues: 2862 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1721 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1721 time to evaluate : 2.762 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 1721 average time/residue: 0.3995 time to fit residues: 1006.6529 Evaluate side-chains 997 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 997 time to evaluate : 2.786 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 101 GLN D 1 GLN 7 101 GLN 8 101 GLN 9 101 GLN AA 101 GLN CA 101 GLN DA 101 GLN GA 101 GLN ** IA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 101 GLN ** MA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PA 101 GLN RA 101 GLN SA 101 GLN g 1 GLN XA 101 GLN ** fA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** hA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 1 GLN t 1 GLN pA 101 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 23956 Z= 0.264 Angle : 0.518 5.464 32118 Z= 0.301 Chirality : 0.039 0.140 3922 Planarity : 0.003 0.012 4028 Dihedral : 5.989 58.650 3180 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Rotamer Outliers : 0.58 % 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 (0.12), residues: 2862 helix: 2.24 (0.08), residues: 2862 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1380 time to evaluate : 2.966 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 outliers start: 13 outliers final: 2 residues processed: 1384 average time/residue: 0.3446 time to fit residues: 731.4763 Evaluate side-chains 1015 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1013 time to evaluate : 2.747 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2475 time to fit residues: 4.3903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 101 GLN 8 101 GLN 9 101 GLN CA 101 GLN IA 101 GLN MA 101 GLN PA 101 GLN RA 101 GLN SA 101 GLN ** TA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 101 GLN cA 101 GLN ** fA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** gA 101 GLN hA 101 GLN ** mA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** oA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 23956 Z= 0.321 Angle : 0.580 6.252 32118 Z= 0.338 Chirality : 0.041 0.143 3922 Planarity : 0.002 0.010 4028 Dihedral : 6.045 62.920 3180 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer Outliers : 0.04 % 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 (0.13), residues: 2862 helix: 2.68 (0.08), residues: 2862 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1297 time to evaluate : 2.921 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 outliers start: 1 outliers final: 0 residues processed: 1297 average time/residue: 0.3487 time to fit residues: 703.9829 Evaluate side-chains 964 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 964 time to evaluate : 2.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 204 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 101 GLN fA 101 GLN hA 101 GLN iA 101 GLN mA 101 GLN oA 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 23956 Z= 0.253 Angle : 0.540 4.869 32118 Z= 0.315 Chirality : 0.038 0.138 3922 Planarity : 0.002 0.009 4028 Dihedral : 5.857 61.162 3180 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 4.42 (0.13), residues: 2862 helix: 2.88 (0.08), residues: 2862 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1307 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1307 time to evaluate : 2.927 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1307 average time/residue: 0.3367 time to fit residues: 685.6090 Evaluate side-chains 1001 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1001 time to evaluate : 2.743 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 122 HIS DA 101 GLN ** JA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MA 122 HIS ** OA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** kA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** mA 101 GLN oA 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 23956 Z= 0.263 Angle : 0.563 5.064 32118 Z= 0.327 Chirality : 0.038 0.140 3922 Planarity : 0.002 0.010 4028 Dihedral : 5.840 58.870 3180 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.25 (0.13), residues: 2862 helix: 2.77 (0.08), residues: 2862 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1299 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1291 time to evaluate : 2.878 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 1291 average time/residue: 0.3501 time to fit residues: 711.3831 Evaluate side-chains 999 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 996 time to evaluate : 2.847 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2598 time to fit residues: 5.0684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 205 optimal weight: 0.9980 chunk 170 optimal weight: 0.0770 chunk 94 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 overall best weight: 2.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 122 HIS ** JA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KA 101 GLN ** OA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** kA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 23956 Z= 0.208 Angle : 0.568 7.030 32118 Z= 0.323 Chirality : 0.037 0.154 3922 Planarity : 0.002 0.013 4028 Dihedral : 5.654 56.474 3180 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer Outliers : 0.13 % 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: 4.55 (0.13), residues: 2862 helix: 2.95 (0.08), residues: 2862 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1301 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1298 time to evaluate : 2.926 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 outliers start: 3 outliers final: 0 residues processed: 1298 average time/residue: 0.3336 time to fit residues: 677.6779 Evaluate side-chains 1027 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1027 time to evaluate : 2.868 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DA 101 GLN JA 101 GLN OA 101 GLN ** TA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** eA 101 GLN ** kA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 23956 Z= 0.267 Angle : 0.627 6.378 32118 Z= 0.364 Chirality : 0.038 0.153 3922 Planarity : 0.002 0.017 4028 Dihedral : 5.888 59.444 3180 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 4.06 (0.13), residues: 2862 helix: 2.65 (0.08), residues: 2862 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1272 time to evaluate : 2.895 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: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1272 average time/residue: 0.3303 time to fit residues: 659.7485 Evaluate side-chains 998 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 998 time to evaluate : 2.835 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** kA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 23956 Z= 0.286 Angle : 0.669 6.260 32118 Z= 0.390 Chirality : 0.039 0.155 3922 Planarity : 0.003 0.015 4028 Dihedral : 5.895 59.824 3180 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 3.59 (0.14), residues: 2862 helix: 2.36 (0.08), residues: 2862 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1241 time to evaluate : 2.950 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 outliers start: 0 outliers final: 0 residues processed: 1241 average time/residue: 0.3359 time to fit residues: 655.4220 Evaluate side-chains 995 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 995 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 122 HIS ** BA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** aA 101 GLN ** kA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 23956 Z= 0.248 Angle : 0.684 7.288 32118 Z= 0.393 Chirality : 0.038 0.156 3922 Planarity : 0.003 0.016 4028 Dihedral : 5.737 56.280 3180 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 3.71 (0.14), residues: 2862 helix: 2.44 (0.08), residues: 2862 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1258 time to evaluate : 2.810 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 outliers start: 0 outliers final: 0 residues processed: 1258 average time/residue: 0.3428 time to fit residues: 676.4465 Evaluate side-chains 1028 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1028 time to evaluate : 2.751 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 6.9990 chunk 122 optimal weight: 0.0970 chunk 95 optimal weight: 0.0670 chunk 139 optimal weight: 10.0000 chunk 211 optimal weight: 0.2980 chunk 194 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 101 GLN ** BA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 101 GLN JA 122 HIS PA 101 GLN ** QA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 101 GLN cA 101 GLN eA 101 GLN gA 101 GLN kA 101 GLN kA 122 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 23956 Z= 0.221 Angle : 0.699 7.823 32118 Z= 0.391 Chirality : 0.037 0.159 3922 Planarity : 0.003 0.018 4028 Dihedral : 5.549 53.091 3180 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 3.93 (0.14), residues: 2862 helix: 2.58 (0.08), residues: 2862 sheet: None (None), residues: 0 loop : None (None), residues: 0 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1280 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1280 time to evaluate : 3.168 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 outliers start: 0 outliers final: 0 residues processed: 1280 average time/residue: 0.3434 time to fit residues: 689.5363 Evaluate side-chains 1039 residues out of total 2226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1039 time to evaluate : 2.775 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 101 GLN ** BA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** kA 122 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.050439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.035682 restraints weight = 98414.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.037524 restraints weight = 53222.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.038767 restraints weight = 35184.720| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 23956 Z= 0.270 Angle : 0.751 8.969 32118 Z= 0.429 Chirality : 0.040 0.200 3922 Planarity : 0.003 0.019 4028 Dihedral : 5.621 54.253 3180 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 3.52 (0.14), residues: 2862 helix: 2.32 (0.09), residues: 2862 sheet: None (None), residues: 0 loop : None (None), residues: 0 =============================================================================== Job complete usr+sys time: 9215.30 seconds wall clock time: 164 minutes 30.80 seconds (9870.80 seconds total)