Starting phenix.real_space_refine on Thu May 1 06:55:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ekc_48119/05_2025/9ekc_48119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ekc_48119/05_2025/9ekc_48119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ekc_48119/05_2025/9ekc_48119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ekc_48119/05_2025/9ekc_48119.map" model { file = "/net/cci-nas-00/data/ceres_data/9ekc_48119/05_2025/9ekc_48119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ekc_48119/05_2025/9ekc_48119.cif" } resolution = 3.8 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= 0.005 sd= 0.030 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 7242 2.51 5 N 1938 2.21 5 O 1479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10659 Number of models: 1 Model: "" Number of chains: 102 Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "z" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "0" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "1" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "D" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "2" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "E" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "3" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "F" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "4" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "G" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "5" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "H" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "6" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "I" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "7" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "J" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "8" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "K" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "9" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "L" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "AA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "M" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "BA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "N" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "CA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "O" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "DA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "P" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "EA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "Q" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "FA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "R" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "GA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "S" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "HA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "T" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "IA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "U" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "JA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "V" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "KA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "W" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "LA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "X" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "MA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "Y" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "NA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "Z" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "OA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "a" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "PA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "b" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "QA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "c" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "RA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "d" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "SA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "e" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "TA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "f" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "UA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "g" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "VA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "h" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "WA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "i" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "XA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "j" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "YA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "k" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "ZA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "l" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "aA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "m" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "bA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "n" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "cA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "o" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "dA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "p" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "eA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "q" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "fA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "r" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "gA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "s" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "hA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "t" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "iA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "u" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "jA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "v" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "kA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "w" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "lA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "x" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "mA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Chain: "y" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "nA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Time building chain proxies: 6.64, per 1000 atoms: 0.62 Number of scatterers: 10659 At special positions: 0 Unit cell: (89.64, 89.64, 139.32, 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 1479 8.00 N 1938 7.00 C 7242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.2 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2448 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 0 sheets defined 92.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'z' and resid 102 through 113 Processing helix chain 'B' and resid 2 through 13 Processing helix chain '0' and resid 102 through 113 Processing helix chain 'C' and resid 2 through 13 Processing helix chain '1' and resid 102 through 113 Processing helix chain 'D' and resid 2 through 13 Processing helix chain '2' and resid 102 through 113 Processing helix chain 'E' and resid 2 through 13 Processing helix chain '3' and resid 102 through 113 Processing helix chain 'F' and resid 2 through 13 Processing helix chain '4' and resid 102 through 113 Processing helix chain 'G' and resid 2 through 13 Processing helix chain '5' and resid 102 through 113 Processing helix chain 'H' and resid 2 through 13 Processing helix chain '6' and resid 102 through 113 Processing helix chain 'I' and resid 2 through 13 Processing helix chain '7' and resid 102 through 113 Processing helix chain 'J' and resid 2 through 13 Processing helix chain '8' and resid 102 through 113 Processing helix chain 'K' and resid 2 through 13 Processing helix chain '9' and resid 102 through 113 Processing helix chain 'L' and resid 2 through 13 Processing helix chain 'AA' and resid 102 through 113 Processing helix chain 'M' and resid 2 through 13 Processing helix chain 'BA' and resid 102 through 113 Processing helix chain 'N' and resid 2 through 13 Processing helix chain 'CA' and resid 102 through 113 Processing helix chain 'O' and resid 2 through 13 Processing helix chain 'DA' and resid 102 through 113 Processing helix chain 'P' and resid 2 through 13 Processing helix chain 'EA' and resid 102 through 113 Processing helix chain 'Q' and resid 2 through 13 Processing helix chain 'FA' and resid 102 through 113 Processing helix chain 'R' and resid 2 through 13 Processing helix chain 'GA' and resid 102 through 113 Processing helix chain 'S' and resid 2 through 13 Processing helix chain 'HA' and resid 102 through 113 Processing helix chain 'T' and resid 2 through 13 Processing helix chain 'IA' and resid 102 through 113 Processing helix chain 'U' and resid 2 through 13 Processing helix chain 'JA' and resid 102 through 113 Processing helix chain 'V' and resid 2 through 13 Processing helix chain 'KA' and resid 102 through 113 Processing helix chain 'W' and resid 2 through 13 Processing helix chain 'LA' and resid 102 through 113 Processing helix chain 'X' and resid 2 through 13 Processing helix chain 'MA' and resid 102 through 113 Processing helix chain 'Y' and resid 2 through 13 Processing helix chain 'NA' and resid 102 through 113 Processing helix chain 'Z' and resid 2 through 13 Processing helix chain 'OA' and resid 102 through 113 Processing helix chain 'a' and resid 2 through 13 Processing helix chain 'PA' and resid 102 through 113 Processing helix chain 'b' and resid 2 through 13 Processing helix chain 'QA' and resid 102 through 113 Processing helix chain 'c' and resid 2 through 13 Processing helix chain 'RA' and resid 102 through 113 Processing helix chain 'd' and resid 2 through 13 Processing helix chain 'SA' and resid 102 through 113 Processing helix chain 'e' and resid 2 through 13 Processing helix chain 'TA' and resid 102 through 113 Processing helix chain 'f' and resid 2 through 13 Processing helix chain 'UA' and resid 102 through 113 Processing helix chain 'g' and resid 2 through 13 Processing helix chain 'VA' and resid 102 through 113 Processing helix chain 'h' and resid 2 through 13 Processing helix chain 'WA' and resid 102 through 113 Processing helix chain 'i' and resid 2 through 13 Processing helix chain 'XA' and resid 102 through 113 Processing helix chain 'j' and resid 2 through 13 Processing helix chain 'YA' and resid 102 through 113 Processing helix chain 'k' and resid 2 through 13 Processing helix chain 'ZA' and resid 102 through 113 Processing helix chain 'l' and resid 2 through 13 Processing helix chain 'aA' and resid 102 through 113 Processing helix chain 'm' and resid 2 through 13 Processing helix chain 'bA' and resid 102 through 113 Processing helix chain 'n' and resid 2 through 13 Processing helix chain 'cA' and resid 102 through 113 Processing helix chain 'o' and resid 2 through 13 Processing helix chain 'dA' and resid 102 through 113 Processing helix chain 'p' and resid 2 through 13 Processing helix chain 'eA' and resid 102 through 113 Processing helix chain 'q' and resid 2 through 13 Processing helix chain 'fA' and resid 102 through 113 Processing helix chain 'r' and resid 2 through 13 Processing helix chain 'gA' and resid 102 through 113 Processing helix chain 's' and resid 2 through 13 Processing helix chain 'hA' and resid 102 through 113 Processing helix chain 't' and resid 2 through 13 Processing helix chain 'iA' and resid 102 through 113 Processing helix chain 'u' and resid 2 through 13 Processing helix chain 'jA' and resid 102 through 113 Processing helix chain 'v' and resid 2 through 13 Processing helix chain 'kA' and resid 102 through 113 Processing helix chain 'w' and resid 2 through 13 Processing helix chain 'lA' and resid 102 through 113 Processing helix chain 'x' and resid 2 through 13 Processing helix chain 'mA' and resid 102 through 113 Processing helix chain 'y' and resid 2 through 13 Processing helix chain 'nA' and resid 102 through 113 817 hydrogen bonds defined for protein. 2451 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: 2.67 Time building geometry restraints manager: 3.24 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: 1377 1.29 - 1.36: 1836 1.36 - 1.43: 1326 1.43 - 1.50: 1570 1.50 - 1.56: 4652 Bond restraints: 10761 Sorted by residual: bond pdb=" CB ARGNA 111 " pdb=" CG ARGNA 111 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.23e+00 bond pdb=" CB ARGeA 111 " pdb=" CG ARGeA 111 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" CB ARGMA 111 " pdb=" CG ARGMA 111 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CB ARG 6 111 " pdb=" CG ARG 6 111 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.49e+00 bond pdb=" CB ARG 1 111 " pdb=" CG ARG 1 111 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.45e+00 ... (remaining 10756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 13771 1.87 - 3.73: 309 3.73 - 5.60: 98 5.60 - 7.47: 87 7.47 - 9.33: 15 Bond angle restraints: 14280 Sorted by residual: angle pdb=" CA ARGNA 111 " pdb=" CB ARGNA 111 " pdb=" CG ARGNA 111 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 angle pdb=" CB ARGNA 111 " pdb=" CG ARGNA 111 " pdb=" CD ARGNA 111 " ideal model delta sigma weight residual 111.30 119.87 -8.57 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CG ARG b 11 " pdb=" CD ARG b 11 " pdb=" NE ARG b 11 " ideal model delta sigma weight residual 112.00 119.23 -7.23 2.20e+00 2.07e-01 1.08e+01 angle pdb=" CG ARG H 11 " pdb=" CD ARG H 11 " pdb=" NE ARG H 11 " ideal model delta sigma weight residual 112.00 118.99 -6.99 2.20e+00 2.07e-01 1.01e+01 angle pdb=" CG ARG J 11 " pdb=" CD ARG J 11 " pdb=" NE ARG J 11 " ideal model delta sigma weight residual 112.00 118.89 -6.89 2.20e+00 2.07e-01 9.81e+00 ... (remaining 14275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.96: 4841 10.96 - 21.92: 854 21.92 - 32.88: 429 32.88 - 43.84: 106 43.84 - 54.80: 43 Dihedral angle restraints: 6273 sinusoidal: 2601 harmonic: 3672 Sorted by residual: dihedral pdb=" CG ARG Z 11 " pdb=" CD ARG Z 11 " pdb=" NE ARG Z 11 " pdb=" CZ ARG Z 11 " ideal model delta sinusoidal sigma weight residual 90.00 37.38 52.62 2 1.50e+01 4.44e-03 1.35e+01 dihedral pdb=" CG ARG C 11 " pdb=" CD ARG C 11 " pdb=" NE ARG C 11 " pdb=" CZ ARG C 11 " ideal model delta sinusoidal sigma weight residual 90.00 40.45 49.55 2 1.50e+01 4.44e-03 1.24e+01 dihedral pdb=" CG ARG b 11 " pdb=" CD ARG b 11 " pdb=" NE ARG b 11 " pdb=" CZ ARG b 11 " ideal model delta sinusoidal sigma weight residual 90.00 40.60 49.40 2 1.50e+01 4.44e-03 1.23e+01 ... (remaining 6270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1191 0.024 - 0.048: 413 0.048 - 0.073: 55 0.073 - 0.097: 65 0.097 - 0.121: 10 Chirality restraints: 1734 Sorted by residual: chirality pdb=" CG LEUWA 112 " pdb=" CB LEUWA 112 " pdb=" CD1 LEUWA 112 " pdb=" CD2 LEUWA 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.71 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CG LEUYA 112 " pdb=" CB LEUYA 112 " pdb=" CD1 LEUYA 112 " pdb=" CD2 LEUYA 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.71 0.12 2.00e-01 2.50e+01 3.33e-01 chirality pdb=" CA PHETA 106 " pdb=" N PHETA 106 " pdb=" C PHETA 106 " pdb=" CB PHETA 106 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.88e-01 ... (remaining 1731 not shown) Planarity restraints: 1683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG y 7 " -0.183 9.50e-02 1.11e+02 8.25e-02 4.76e+00 pdb=" NE ARG y 7 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG y 7 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG y 7 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG y 7 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG b 11 " 0.145 9.50e-02 1.11e+02 6.55e-02 3.23e+00 pdb=" NE ARG b 11 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG b 11 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG b 11 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG b 11 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 11 " -0.132 9.50e-02 1.11e+02 5.93e-02 2.51e+00 pdb=" NE ARG J 11 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG J 11 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG J 11 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG J 11 " -0.001 2.00e-02 2.50e+03 ... (remaining 1680 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.08: 7644 3.08 - 3.53: 12889 3.53 - 3.99: 14301 3.99 - 4.44: 20776 4.44 - 4.90: 25292 Nonbonded interactions: 80902 Sorted by model distance: nonbonded pdb=" C SER g 10 " pdb=" OG SER g 10 " model vdw 2.625 2.616 nonbonded pdb=" C SER o 10 " pdb=" OG SER o 10 " model vdw 2.631 2.616 nonbonded pdb=" C SER d 10 " pdb=" OG SER d 10 " model vdw 2.632 2.616 nonbonded pdb=" C SER G 10 " pdb=" OG SER G 10 " model vdw 2.634 2.616 nonbonded pdb=" C SER y 10 " pdb=" OG SER y 10 " model vdw 2.635 2.616 ... (remaining 80897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and (resid 101 through 112 or (resid 113 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain '1' and (resid 101 through 112 or (resid 113 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain '2' and (resid 101 through 112 or (resid 113 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain '3' and (resid 101 through 112 or (resid 113 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain '4' and (resid 101 through 112 or (resid 113 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain '5' and (resid 101 through 112 or (resid 113 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain '6' and (resid 101 through 112 or (resid 113 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain '7' and (resid 101 through 112 or (resid 113 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain '8' and (resid 101 through 112 or (resid 113 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain '9' and (resid 101 through 112 or (resid 113 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'A' selection = (chain 'AA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'B' selection = (chain 'BA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'C' selection = (chain 'CA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'D' selection = (chain 'DA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'E' selection = (chain 'EA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'F' selection = (chain 'FA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'G' selection = (chain 'GA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'H' selection = (chain 'HA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'I' selection = (chain 'IA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'J' selection = (chain 'JA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'K' selection = (chain 'KA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'L' selection = (chain 'LA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'M' selection = (chain 'MA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'N' selection = (chain 'NA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'O' selection = (chain 'OA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'P' selection = (chain 'PA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'Q' selection = (chain 'QA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'R' selection = (chain 'RA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'S' selection = (chain 'SA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'T' selection = (chain 'TA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'U' selection = (chain 'UA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'V' selection = (chain 'VA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'W' selection = (chain 'WA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'X' selection = (chain 'XA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'Y' selection = (chain 'YA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'Z' selection = (chain 'ZA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'a' selection = (chain 'aA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'b' selection = (chain 'bA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'c' selection = (chain 'cA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'd' selection = (chain 'dA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'e' selection = (chain 'eA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'f' selection = (chain 'fA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'g' selection = (chain 'gA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'h' selection = (chain 'hA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'i' selection = (chain 'iA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'j' selection = (chain 'jA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'k' selection = (chain 'kA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'l' selection = (chain 'lA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'm' selection = (chain 'mA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'n' selection = (chain 'nA' and (resid 101 through 112 or (resid 113 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2)))) selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = (chain 'z' and (resid 101 through 112 or (resid 113 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) } 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.040 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.040 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 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 : 0.004 0.045 10761 Z= 0.180 Angle : 0.865 9.331 14280 Z= 0.394 Chirality : 0.029 0.121 1734 Planarity : 0.008 0.082 1683 Dihedral : 15.016 54.797 3825 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.10 % Allowed : 31.08 % Favored : 68.82 % 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: 1.16 (0.23), residues: 1122 helix: 0.86 (0.14), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE q 6 ARG 0.014 0.001 ARG b 11 Details of bonding type rmsd hydrogen bonds : bond 0.04670 ( 817) hydrogen bonds : angle 3.47269 ( 2451) covalent geometry : bond 0.00431 (10761) covalent geometry : angle 0.86472 (14280) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 1.326 Fit side-chains REVERT: T 12 LEU cc_start: 0.9506 (tp) cc_final: 0.9288 (tt) REVERT: l 11 ARG cc_start: 0.8231 (ttp80) cc_final: 0.8008 (ttp80) REVERT: n 11 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7808 (ttp80) REVERT: dA 112 LEU cc_start: 0.9535 (tp) cc_final: 0.9212 (tt) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.3298 time to fit residues: 73.1644 Evaluate side-chains 91 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.042265 restraints weight = 43100.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.043584 restraints weight = 21265.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.044386 restraints weight = 12360.312| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10761 Z= 0.132 Angle : 0.774 9.654 14280 Z= 0.320 Chirality : 0.027 0.103 1734 Planarity : 0.004 0.043 1683 Dihedral : 4.501 35.468 1479 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.22 % Allowed : 31.47 % Favored : 64.31 % 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: 3.60 (0.23), residues: 1122 helix: 2.37 (0.14), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE i 6 ARG 0.007 0.001 ARGOA 111 Details of bonding type rmsd hydrogen bonds : bond 0.02129 ( 817) hydrogen bonds : angle 2.72741 ( 2451) covalent geometry : bond 0.00333 (10761) covalent geometry : angle 0.77414 (14280) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 1.188 Fit side-chains REVERT: PA 113 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9171 (tp) REVERT: e 9 LEU cc_start: 0.9533 (tp) cc_final: 0.9277 (tp) outliers start: 43 outliers final: 13 residues processed: 181 average time/residue: 0.1631 time to fit residues: 45.9167 Evaluate side-chains 122 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 113 LEU Chi-restraints excluded: chain BA residue 109 LEU Chi-restraints excluded: chain BA residue 113 LEU Chi-restraints excluded: chain DA residue 109 LEU Chi-restraints excluded: chain DA residue 113 LEU Chi-restraints excluded: chain GA residue 109 LEU Chi-restraints excluded: chain KA residue 109 LEU Chi-restraints excluded: chain PA residue 113 LEU Chi-restraints excluded: chain aA residue 109 LEU Chi-restraints excluded: chain cA residue 109 LEU Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain eA residue 109 LEU Chi-restraints excluded: chain iA residue 112 LEU Chi-restraints excluded: chain kA residue 113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 22 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.044696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.040783 restraints weight = 46902.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.042011 restraints weight = 21970.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.042779 restraints weight = 12506.984| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10761 Z= 0.116 Angle : 0.670 9.427 14280 Z= 0.272 Chirality : 0.027 0.099 1734 Planarity : 0.002 0.023 1683 Dihedral : 3.492 22.606 1479 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.96 % Allowed : 33.82 % Favored : 59.22 % 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: 4.89 (0.23), residues: 1122 helix: 3.17 (0.14), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.000 PHEQA 106 ARG 0.006 0.001 ARG n 11 Details of bonding type rmsd hydrogen bonds : bond 0.02186 ( 817) hydrogen bonds : angle 2.75024 ( 2451) covalent geometry : bond 0.00297 (10761) covalent geometry : angle 0.67033 (14280) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 116 time to evaluate : 1.205 Fit side-chains REVERT: H 9 LEU cc_start: 0.9461 (tp) cc_final: 0.9259 (tt) REVERT: a 9 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.8983 (tt) REVERT: PA 113 LEU cc_start: 0.9458 (tp) cc_final: 0.9208 (tp) REVERT: XA 106 PHE cc_start: 0.9471 (OUTLIER) cc_final: 0.8918 (m-10) outliers start: 71 outliers final: 28 residues processed: 169 average time/residue: 0.1643 time to fit residues: 44.1331 Evaluate side-chains 115 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 112 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain 4 residue 109 LEU Chi-restraints excluded: chain 5 residue 113 LEU Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain BA residue 109 LEU Chi-restraints excluded: chain BA residue 113 LEU Chi-restraints excluded: chain DA residue 113 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain IA residue 109 LEU Chi-restraints excluded: chain U residue 2 LEU Chi-restraints excluded: chain JA residue 112 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain WA residue 112 LEU Chi-restraints excluded: chain XA residue 106 PHE Chi-restraints excluded: chain YA residue 109 LEU Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain cA residue 109 LEU Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain eA residue 109 LEU Chi-restraints excluded: chain q residue 2 LEU Chi-restraints excluded: chain iA residue 112 LEU Chi-restraints excluded: chain kA residue 113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.045260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041271 restraints weight = 46691.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.042504 restraints weight = 22113.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.043261 restraints weight = 12733.333| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10761 Z= 0.102 Angle : 0.623 8.345 14280 Z= 0.245 Chirality : 0.027 0.101 1734 Planarity : 0.002 0.029 1683 Dihedral : 3.111 19.370 1479 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.29 % Allowed : 37.55 % Favored : 57.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.86 (0.22), residues: 1122 helix: 3.76 (0.14), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.000 PHEQA 106 ARG 0.005 0.000 ARGQA 111 Details of bonding type rmsd hydrogen bonds : bond 0.02001 ( 817) hydrogen bonds : angle 2.75127 ( 2451) covalent geometry : bond 0.00260 (10761) covalent geometry : angle 0.62292 (14280) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 116 time to evaluate : 1.181 Fit side-chains REVERT: 3 113 LEU cc_start: 0.9255 (tp) cc_final: 0.8842 (tt) REVERT: 9 113 LEU cc_start: 0.9395 (tp) cc_final: 0.9156 (tp) REVERT: a 9 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9042 (tt) REVERT: XA 111 ARG cc_start: 0.8871 (tmm-80) cc_final: 0.8665 (tmm-80) REVERT: n 2 LEU cc_start: 0.9428 (tp) cc_final: 0.9201 (tp) REVERT: s 2 LEU cc_start: 0.8856 (tt) cc_final: 0.8539 (tt) outliers start: 54 outliers final: 25 residues processed: 156 average time/residue: 0.1803 time to fit residues: 43.1204 Evaluate side-chains 131 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 112 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain BA residue 109 LEU Chi-restraints excluded: chain BA residue 113 LEU Chi-restraints excluded: chain DA residue 113 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain GA residue 109 LEU Chi-restraints excluded: chain IA residue 109 LEU Chi-restraints excluded: chain JA residue 112 LEU Chi-restraints excluded: chain KA residue 109 LEU Chi-restraints excluded: chain NA residue 112 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain RA residue 112 LEU Chi-restraints excluded: chain TA residue 113 LEU Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain WA residue 112 LEU Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain YA residue 112 LEU Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain aA residue 109 LEU Chi-restraints excluded: chain cA residue 109 LEU Chi-restraints excluded: chain iA residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.042587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.038523 restraints weight = 46385.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.039759 restraints weight = 22990.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.040525 restraints weight = 13471.482| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 10761 Z= 0.202 Angle : 0.638 7.804 14280 Z= 0.267 Chirality : 0.029 0.105 1734 Planarity : 0.002 0.026 1683 Dihedral : 4.068 28.042 1479 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 8.04 % Allowed : 36.47 % Favored : 55.49 % 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: 4.75 (0.22), residues: 1122 helix: 3.08 (0.13), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHEjA 106 ARG 0.008 0.000 ARG 9 111 Details of bonding type rmsd hydrogen bonds : bond 0.02570 ( 817) hydrogen bonds : angle 3.04999 ( 2451) covalent geometry : bond 0.00476 (10761) covalent geometry : angle 0.63803 (14280) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 67 time to evaluate : 1.517 Fit side-chains REVERT: G 9 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9213 (tt) REVERT: a 9 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9172 (tt) REVERT: s 2 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8936 (tt) REVERT: jA 113 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9139 (tt) REVERT: mA 109 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9119 (tt) outliers start: 82 outliers final: 51 residues processed: 139 average time/residue: 0.1730 time to fit residues: 39.6594 Evaluate side-chains 116 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 60 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 112 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain 5 residue 113 LEU Chi-restraints excluded: chain 8 residue 113 LEU Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain BA residue 109 LEU Chi-restraints excluded: chain BA residue 113 LEU Chi-restraints excluded: chain DA residue 109 LEU Chi-restraints excluded: chain DA residue 113 LEU Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain GA residue 109 LEU Chi-restraints excluded: chain GA residue 112 LEU Chi-restraints excluded: chain IA residue 109 LEU Chi-restraints excluded: chain U residue 2 LEU Chi-restraints excluded: chain JA residue 112 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain KA residue 109 LEU Chi-restraints excluded: chain KA residue 113 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain d residue 2 LEU Chi-restraints excluded: chain TA residue 113 LEU Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain WA residue 112 LEU Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain XA residue 112 LEU Chi-restraints excluded: chain YA residue 109 LEU Chi-restraints excluded: chain YA residue 112 LEU Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain aA residue 109 LEU Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain cA residue 109 LEU Chi-restraints excluded: chain dA residue 112 LEU Chi-restraints excluded: chain eA residue 113 LEU Chi-restraints excluded: chain q residue 2 LEU Chi-restraints excluded: chain r residue 2 LEU Chi-restraints excluded: chain gA residue 112 LEU Chi-restraints excluded: chain s residue 2 LEU Chi-restraints excluded: chain iA residue 112 LEU Chi-restraints excluded: chain jA residue 112 LEU Chi-restraints excluded: chain jA residue 113 LEU Chi-restraints excluded: chain lA residue 112 LEU Chi-restraints excluded: chain mA residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.045466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.041091 restraints weight = 45172.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.042394 restraints weight = 22585.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043227 restraints weight = 13254.314| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10761 Z= 0.100 Angle : 0.591 8.606 14280 Z= 0.229 Chirality : 0.026 0.100 1734 Planarity : 0.002 0.030 1683 Dihedral : 3.421 21.397 1479 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.10 % Allowed : 39.51 % Favored : 55.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.89 (0.22), residues: 1122 helix: 3.78 (0.13), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.000 PHEQA 106 ARG 0.008 0.000 ARG 9 111 Details of bonding type rmsd hydrogen bonds : bond 0.02040 ( 817) hydrogen bonds : angle 2.78024 ( 2451) covalent geometry : bond 0.00254 (10761) covalent geometry : angle 0.59062 (14280) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 99 time to evaluate : 1.218 Fit side-chains REVERT: 3 113 LEU cc_start: 0.9221 (tp) cc_final: 0.8936 (tt) REVERT: a 9 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9109 (tt) REVERT: s 2 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8690 (tt) outliers start: 52 outliers final: 38 residues processed: 141 average time/residue: 0.1620 time to fit residues: 37.6405 Evaluate side-chains 119 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 79 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 112 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain 2 residue 112 LEU Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain BA residue 109 LEU Chi-restraints excluded: chain BA residue 113 LEU Chi-restraints excluded: chain DA residue 113 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain GA residue 109 LEU Chi-restraints excluded: chain GA residue 112 LEU Chi-restraints excluded: chain HA residue 112 LEU Chi-restraints excluded: chain IA residue 109 LEU Chi-restraints excluded: chain JA residue 112 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain KA residue 109 LEU Chi-restraints excluded: chain MA residue 109 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain QA residue 110 SER Chi-restraints excluded: chain TA residue 113 LEU Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain WA residue 112 LEU Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain XA residue 109 LEU Chi-restraints excluded: chain YA residue 109 LEU Chi-restraints excluded: chain YA residue 112 LEU Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain aA residue 109 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain cA residue 109 LEU Chi-restraints excluded: chain p residue 2 LEU Chi-restraints excluded: chain eA residue 113 LEU Chi-restraints excluded: chain q residue 2 LEU Chi-restraints excluded: chain fA residue 112 LEU Chi-restraints excluded: chain s residue 2 LEU Chi-restraints excluded: chain iA residue 112 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.0570 chunk 24 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.045514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.041170 restraints weight = 44750.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.042525 restraints weight = 21602.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.043352 restraints weight = 12474.201| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10761 Z= 0.104 Angle : 0.609 9.401 14280 Z= 0.234 Chirality : 0.026 0.098 1734 Planarity : 0.002 0.028 1683 Dihedral : 3.441 21.182 1479 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.88 % Allowed : 39.41 % Favored : 54.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.41 (0.21), residues: 1122 helix: 4.10 (0.13), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.000 PHE 5 106 ARG 0.006 0.000 ARGPA 111 Details of bonding type rmsd hydrogen bonds : bond 0.02067 ( 817) hydrogen bonds : angle 2.73965 ( 2451) covalent geometry : bond 0.00263 (10761) covalent geometry : angle 0.60870 (14280) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 81 time to evaluate : 1.746 Fit side-chains REVERT: 3 113 LEU cc_start: 0.9211 (tp) cc_final: 0.8926 (tt) REVERT: G 9 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9196 (tt) REVERT: a 9 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9060 (tt) REVERT: n 2 LEU cc_start: 0.9425 (tp) cc_final: 0.9191 (tp) REVERT: s 2 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8741 (tt) REVERT: mA 109 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9212 (tp) outliers start: 60 outliers final: 48 residues processed: 125 average time/residue: 0.1807 time to fit residues: 38.3587 Evaluate side-chains 125 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 73 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 112 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 2 residue 112 LEU Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 4 residue 109 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain 8 residue 113 LEU Chi-restraints excluded: chain BA residue 109 LEU Chi-restraints excluded: chain BA residue 113 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain DA residue 113 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain GA residue 109 LEU Chi-restraints excluded: chain GA residue 112 LEU Chi-restraints excluded: chain HA residue 112 LEU Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain IA residue 109 LEU Chi-restraints excluded: chain JA residue 112 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain KA residue 109 LEU Chi-restraints excluded: chain MA residue 109 LEU Chi-restraints excluded: chain MA residue 112 LEU Chi-restraints excluded: chain NA residue 112 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain QA residue 110 SER Chi-restraints excluded: chain RA residue 112 LEU Chi-restraints excluded: chain TA residue 113 LEU Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain WA residue 112 LEU Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain XA residue 109 LEU Chi-restraints excluded: chain XA residue 112 LEU Chi-restraints excluded: chain YA residue 109 LEU Chi-restraints excluded: chain YA residue 112 LEU Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain aA residue 109 LEU Chi-restraints excluded: chain cA residue 109 LEU Chi-restraints excluded: chain p residue 2 LEU Chi-restraints excluded: chain eA residue 113 LEU Chi-restraints excluded: chain q residue 2 LEU Chi-restraints excluded: chain fA residue 112 LEU Chi-restraints excluded: chain s residue 2 LEU Chi-restraints excluded: chain iA residue 112 LEU Chi-restraints excluded: chain jA residue 105 LEU Chi-restraints excluded: chain jA residue 112 LEU Chi-restraints excluded: chain lA residue 112 LEU Chi-restraints excluded: chain mA residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.044179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.039993 restraints weight = 45822.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.041275 restraints weight = 22547.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.042089 restraints weight = 13168.817| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10761 Z= 0.143 Angle : 0.621 9.083 14280 Z= 0.244 Chirality : 0.028 0.099 1734 Planarity : 0.002 0.025 1683 Dihedral : 3.797 23.306 1479 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 7.25 % Allowed : 38.14 % Favored : 54.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.02 (0.20), residues: 1122 helix: 3.86 (0.13), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.000 PHE u 6 ARG 0.006 0.000 ARGPA 111 Details of bonding type rmsd hydrogen bonds : bond 0.02257 ( 817) hydrogen bonds : angle 2.83045 ( 2451) covalent geometry : bond 0.00347 (10761) covalent geometry : angle 0.62066 (14280) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 70 time to evaluate : 1.340 Fit side-chains REVERT: G 9 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9240 (tt) REVERT: a 9 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9094 (tt) REVERT: s 2 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8884 (tt) REVERT: mA 109 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9237 (tp) outliers start: 74 outliers final: 59 residues processed: 131 average time/residue: 0.1487 time to fit residues: 33.3108 Evaluate side-chains 126 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 63 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 112 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain 0 residue 112 LEU Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 2 residue 112 LEU Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 4 residue 109 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain 5 residue 113 LEU Chi-restraints excluded: chain 8 residue 113 LEU Chi-restraints excluded: chain BA residue 109 LEU Chi-restraints excluded: chain BA residue 113 LEU Chi-restraints excluded: chain CA residue 112 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain DA residue 113 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain EA residue 113 LEU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain FA residue 109 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain GA residue 109 LEU Chi-restraints excluded: chain GA residue 112 LEU Chi-restraints excluded: chain HA residue 112 LEU Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain IA residue 109 LEU Chi-restraints excluded: chain JA residue 112 LEU Chi-restraints excluded: chain KA residue 109 LEU Chi-restraints excluded: chain KA residue 113 LEU Chi-restraints excluded: chain MA residue 109 LEU Chi-restraints excluded: chain MA residue 112 LEU Chi-restraints excluded: chain NA residue 112 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain QA residue 110 SER Chi-restraints excluded: chain RA residue 112 LEU Chi-restraints excluded: chain TA residue 113 LEU Chi-restraints excluded: chain f residue 2 LEU Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain UA residue 110 SER Chi-restraints excluded: chain VA residue 112 LEU Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain WA residue 112 LEU Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain XA residue 109 LEU Chi-restraints excluded: chain XA residue 112 LEU Chi-restraints excluded: chain YA residue 109 LEU Chi-restraints excluded: chain YA residue 112 LEU Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain aA residue 109 LEU Chi-restraints excluded: chain cA residue 109 LEU Chi-restraints excluded: chain dA residue 112 LEU Chi-restraints excluded: chain p residue 2 LEU Chi-restraints excluded: chain eA residue 113 LEU Chi-restraints excluded: chain q residue 2 LEU Chi-restraints excluded: chain fA residue 112 LEU Chi-restraints excluded: chain gA residue 112 LEU Chi-restraints excluded: chain s residue 2 LEU Chi-restraints excluded: chain iA residue 112 LEU Chi-restraints excluded: chain jA residue 105 LEU Chi-restraints excluded: chain jA residue 112 LEU Chi-restraints excluded: chain lA residue 112 LEU Chi-restraints excluded: chain mA residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.044748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.041169 restraints weight = 49411.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.042300 restraints weight = 23849.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.042992 restraints weight = 13798.486| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10761 Z= 0.119 Angle : 0.618 9.123 14280 Z= 0.237 Chirality : 0.027 0.096 1734 Planarity : 0.002 0.024 1683 Dihedral : 3.603 21.541 1479 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.57 % Allowed : 38.82 % Favored : 54.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.37 (0.20), residues: 1122 helix: 4.08 (0.13), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.000 PHE 5 106 ARG 0.006 0.000 ARGPA 111 Details of bonding type rmsd hydrogen bonds : bond 0.02124 ( 817) hydrogen bonds : angle 2.77922 ( 2451) covalent geometry : bond 0.00296 (10761) covalent geometry : angle 0.61785 (14280) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 71 time to evaluate : 1.260 Fit side-chains REVERT: G 9 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9173 (tt) REVERT: a 9 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9020 (tt) REVERT: s 2 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8779 (tt) REVERT: mA 109 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9188 (tp) outliers start: 67 outliers final: 60 residues processed: 122 average time/residue: 0.1755 time to fit residues: 35.2176 Evaluate side-chains 130 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 66 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 112 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain 0 residue 112 LEU Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 2 residue 112 LEU Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 4 residue 109 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain 5 residue 113 LEU Chi-restraints excluded: chain 7 residue 112 LEU Chi-restraints excluded: chain 8 residue 113 LEU Chi-restraints excluded: chain BA residue 109 LEU Chi-restraints excluded: chain BA residue 113 LEU Chi-restraints excluded: chain CA residue 112 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain DA residue 113 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain FA residue 109 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain GA residue 109 LEU Chi-restraints excluded: chain GA residue 112 LEU Chi-restraints excluded: chain HA residue 112 LEU Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain IA residue 109 LEU Chi-restraints excluded: chain U residue 2 LEU Chi-restraints excluded: chain JA residue 112 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain KA residue 109 LEU Chi-restraints excluded: chain KA residue 113 LEU Chi-restraints excluded: chain MA residue 109 LEU Chi-restraints excluded: chain MA residue 112 LEU Chi-restraints excluded: chain NA residue 112 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain QA residue 110 SER Chi-restraints excluded: chain RA residue 112 LEU Chi-restraints excluded: chain TA residue 113 LEU Chi-restraints excluded: chain f residue 2 LEU Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain UA residue 110 SER Chi-restraints excluded: chain VA residue 112 LEU Chi-restraints excluded: chain WA residue 112 LEU Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain XA residue 109 LEU Chi-restraints excluded: chain YA residue 109 LEU Chi-restraints excluded: chain YA residue 112 LEU Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain aA residue 109 LEU Chi-restraints excluded: chain bA residue 112 LEU Chi-restraints excluded: chain cA residue 109 LEU Chi-restraints excluded: chain dA residue 112 LEU Chi-restraints excluded: chain p residue 2 LEU Chi-restraints excluded: chain eA residue 113 LEU Chi-restraints excluded: chain q residue 2 LEU Chi-restraints excluded: chain fA residue 112 LEU Chi-restraints excluded: chain gA residue 109 LEU Chi-restraints excluded: chain s residue 2 LEU Chi-restraints excluded: chain iA residue 112 LEU Chi-restraints excluded: chain jA residue 105 LEU Chi-restraints excluded: chain jA residue 112 LEU Chi-restraints excluded: chain lA residue 112 LEU Chi-restraints excluded: chain mA residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 49 optimal weight: 0.0170 chunk 46 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.044418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.040876 restraints weight = 49171.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.041990 restraints weight = 23769.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.042661 restraints weight = 13754.082| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10761 Z= 0.130 Angle : 0.635 8.924 14280 Z= 0.244 Chirality : 0.027 0.099 1734 Planarity : 0.002 0.024 1683 Dihedral : 3.730 21.953 1479 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer: Outliers : 6.57 % Allowed : 39.02 % Favored : 54.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.26 (0.20), residues: 1122 helix: 4.01 (0.12), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.000 PHEjA 106 ARG 0.006 0.000 ARGPA 111 Details of bonding type rmsd hydrogen bonds : bond 0.02189 ( 817) hydrogen bonds : angle 2.80015 ( 2451) covalent geometry : bond 0.00320 (10761) covalent geometry : angle 0.63457 (14280) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 61 time to evaluate : 1.291 Fit side-chains REVERT: 3 113 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8960 (tt) REVERT: G 9 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9203 (tt) REVERT: a 9 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9038 (tt) REVERT: s 2 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8844 (tt) REVERT: mA 109 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9211 (tp) outliers start: 67 outliers final: 61 residues processed: 114 average time/residue: 0.1779 time to fit residues: 34.3947 Evaluate side-chains 127 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 61 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 112 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain 0 residue 112 LEU Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 2 residue 112 LEU Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 3 residue 113 LEU Chi-restraints excluded: chain 4 residue 109 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain 5 residue 113 LEU Chi-restraints excluded: chain 7 residue 112 LEU Chi-restraints excluded: chain 8 residue 113 LEU Chi-restraints excluded: chain BA residue 109 LEU Chi-restraints excluded: chain BA residue 113 LEU Chi-restraints excluded: chain CA residue 112 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain DA residue 113 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain FA residue 109 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain GA residue 109 LEU Chi-restraints excluded: chain GA residue 112 LEU Chi-restraints excluded: chain HA residue 112 LEU Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain IA residue 109 LEU Chi-restraints excluded: chain U residue 2 LEU Chi-restraints excluded: chain JA residue 112 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain KA residue 109 LEU Chi-restraints excluded: chain KA residue 113 LEU Chi-restraints excluded: chain MA residue 109 LEU Chi-restraints excluded: chain MA residue 112 LEU Chi-restraints excluded: chain NA residue 112 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain QA residue 110 SER Chi-restraints excluded: chain RA residue 112 LEU Chi-restraints excluded: chain TA residue 113 LEU Chi-restraints excluded: chain f residue 2 LEU Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain UA residue 110 SER Chi-restraints excluded: chain VA residue 112 LEU Chi-restraints excluded: chain h residue 9 LEU Chi-restraints excluded: chain WA residue 112 LEU Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain XA residue 109 LEU Chi-restraints excluded: chain YA residue 109 LEU Chi-restraints excluded: chain YA residue 112 LEU Chi-restraints excluded: chain k residue 9 LEU Chi-restraints excluded: chain ZA residue 112 LEU Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain aA residue 109 LEU Chi-restraints excluded: chain cA residue 109 LEU Chi-restraints excluded: chain dA residue 112 LEU Chi-restraints excluded: chain p residue 2 LEU Chi-restraints excluded: chain eA residue 113 LEU Chi-restraints excluded: chain q residue 2 LEU Chi-restraints excluded: chain fA residue 112 LEU Chi-restraints excluded: chain gA residue 112 LEU Chi-restraints excluded: chain s residue 2 LEU Chi-restraints excluded: chain iA residue 112 LEU Chi-restraints excluded: chain jA residue 105 LEU Chi-restraints excluded: chain jA residue 112 LEU Chi-restraints excluded: chain lA residue 112 LEU Chi-restraints excluded: chain mA residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 85 optimal weight: 0.0370 chunk 53 optimal weight: 0.1980 chunk 22 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.046955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.042641 restraints weight = 46781.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.043939 restraints weight = 22629.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.044741 restraints weight = 13272.773| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10761 Z= 0.081 Angle : 0.624 9.458 14280 Z= 0.229 Chirality : 0.025 0.093 1734 Planarity : 0.002 0.023 1683 Dihedral : 3.125 18.027 1479 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.61 % Allowed : 40.88 % Favored : 54.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 7.43 (0.20), residues: 1122 helix: 4.73 (0.12), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE i 6 ARG 0.006 0.000 ARGPA 111 Details of bonding type rmsd hydrogen bonds : bond 0.01792 ( 817) hydrogen bonds : angle 2.66625 ( 2451) covalent geometry : bond 0.00212 (10761) covalent geometry : angle 0.62426 (14280) =============================================================================== Job complete usr+sys time: 2617.56 seconds wall clock time: 48 minutes 0.53 seconds (2880.53 seconds total)