Starting phenix.real_space_refine on Wed Sep 17 18:15:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ekc_48119/09_2025/9ekc_48119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ekc_48119/09_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_48119/09_2025/9ekc_48119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ekc_48119/09_2025/9ekc_48119.map" model { file = "/net/cci-nas-00/data/ceres_data/9ekc_48119/09_2025/9ekc_48119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ekc_48119/09_2025/9ekc_48119.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.76, per 1000 atoms: 0.26 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: 0.87 Conformation dependent library (CDL) restraints added in 341.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.36 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: 1.55 Time building geometry restraints manager: 1.16 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.050 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.001 ARG b 11 PHE 0.012 0.001 PHE q 6 Details of bonding type rmsd covalent geometry : bond 0.00431 (10761) covalent geometry : angle 0.86472 (14280) hydrogen bonds : bond 0.04670 ( 817) hydrogen bonds : angle 3.47269 ( 2451) *********************** 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 : 0.433 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: 0.1681 time to fit residues: 37.1638 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 : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3150 r_free = 0.3150 target = 0.046387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.042085 restraints weight = 43873.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.043393 restraints weight = 21606.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.044211 restraints weight = 12569.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044743 restraints weight = 8037.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.045122 restraints weight = 5496.046| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10761 Z= 0.127 Angle : 0.771 9.523 14280 Z= 0.319 Chirality : 0.027 0.103 1734 Planarity : 0.004 0.041 1683 Dihedral : 4.599 36.342 1479 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.31 % Allowed : 31.27 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.54 (0.23), residues: 1122 helix: 2.33 (0.14), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGOA 111 PHE 0.009 0.001 PHE i 6 Details of bonding type rmsd covalent geometry : bond 0.00327 (10761) covalent geometry : angle 0.77149 (14280) hydrogen bonds : bond 0.02163 ( 817) hydrogen bonds : angle 2.74886 ( 2451) *********************** 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 191 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.449 Fit side-chains REVERT: PA 113 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9177 (tp) outliers start: 44 outliers final: 15 residues processed: 179 average time/residue: 0.0819 time to fit residues: 23.0564 Evaluate side-chains 121 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 109 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 DA residue 109 LEU Chi-restraints excluded: chain DA residue 113 LEU Chi-restraints excluded: chain Q residue 9 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 71 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.044885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.040996 restraints weight = 46610.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.042221 restraints weight = 21756.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.042963 restraints weight = 12307.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043486 restraints weight = 7799.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.043832 restraints weight = 5191.633| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10761 Z= 0.114 Angle : 0.672 9.614 14280 Z= 0.272 Chirality : 0.027 0.104 1734 Planarity : 0.002 0.024 1683 Dihedral : 3.469 21.821 1479 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.96 % Allowed : 33.92 % Favored : 59.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.93 (0.23), residues: 1122 helix: 3.19 (0.14), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGUA 111 PHE 0.010 0.001 PHEQA 106 Details of bonding type rmsd covalent geometry : bond 0.00290 (10761) covalent geometry : angle 0.67221 (14280) hydrogen bonds : bond 0.02160 ( 817) hydrogen bonds : angle 2.75082 ( 2451) *********************** 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 194 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 123 time to evaluate : 0.464 Fit side-chains REVERT: H 9 LEU cc_start: 0.9468 (tp) cc_final: 0.9263 (tt) REVERT: a 9 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9013 (tt) REVERT: PA 113 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9202 (tp) REVERT: XA 106 PHE cc_start: 0.9470 (OUTLIER) cc_final: 0.8918 (m-10) outliers start: 71 outliers final: 26 residues processed: 175 average time/residue: 0.0780 time to fit residues: 21.8674 Evaluate side-chains 120 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 R residue 9 LEU Chi-restraints excluded: chain IA residue 109 LEU Chi-restraints excluded: chain U residue 2 LEU Chi-restraints excluded: chain V residue 9 LEU Chi-restraints excluded: chain KA residue 109 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain PA residue 113 LEU Chi-restraints excluded: chain d residue 2 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 67 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 47 optimal weight: 0.4980 chunk 59 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 14 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3119 r_free = 0.3119 target = 0.045928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.042248 restraints weight = 47544.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.043426 restraints weight = 22637.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.044119 restraints weight = 12968.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.044588 restraints weight = 8238.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.044925 restraints weight = 5536.074| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2702 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= 0.101 Angle : 0.633 8.316 14280 Z= 0.249 Chirality : 0.027 0.103 1734 Planarity : 0.002 0.018 1683 Dihedral : 3.120 15.750 1479 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.59 % Allowed : 37.06 % Favored : 57.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.68 (0.23), residues: 1122 helix: 3.65 (0.14), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGUA 111 PHE 0.007 0.000 PHE 5 106 Details of bonding type rmsd covalent geometry : bond 0.00258 (10761) covalent geometry : angle 0.63278 (14280) hydrogen bonds : bond 0.02073 ( 817) hydrogen bonds : angle 2.71788 ( 2451) *********************** 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 166 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 109 time to evaluate : 0.459 Fit side-chains REVERT: a 9 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9060 (tt) REVERT: XA 111 ARG cc_start: 0.8815 (tmm-80) cc_final: 0.8585 (tmm-80) REVERT: n 2 LEU cc_start: 0.9464 (tp) cc_final: 0.9252 (tp) outliers start: 57 outliers final: 33 residues processed: 149 average time/residue: 0.0729 time to fit residues: 17.7943 Evaluate side-chains 127 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 4 residue 109 LEU Chi-restraints excluded: chain J residue 2 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 9 LEU Chi-restraints excluded: chain DA residue 109 LEU Chi-restraints excluded: chain DA residue 113 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 NA residue 112 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain RA residue 112 LEU Chi-restraints excluded: chain d residue 2 LEU Chi-restraints excluded: chain WA residue 112 LEU Chi-restraints excluded: chain i residue 9 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 eA residue 109 LEU Chi-restraints excluded: chain iA residue 112 LEU Chi-restraints excluded: chain jA residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3182 r_free = 0.3182 target = 0.046935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.042429 restraints weight = 43649.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.043818 restraints weight = 21432.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.044708 restraints weight = 12395.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.045270 restraints weight = 7919.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.045644 restraints weight = 5398.175| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10761 Z= 0.098 Angle : 0.596 8.686 14280 Z= 0.232 Chirality : 0.025 0.097 1734 Planarity : 0.002 0.021 1683 Dihedral : 3.225 31.915 1479 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer: Outliers : 5.10 % Allowed : 38.24 % Favored : 56.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.28 (0.21), residues: 1122 helix: 4.03 (0.13), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGTA 111 PHE 0.007 0.000 PHEQA 106 Details of bonding type rmsd covalent geometry : bond 0.00246 (10761) covalent geometry : angle 0.59649 (14280) hydrogen bonds : bond 0.02012 ( 817) hydrogen bonds : angle 2.69012 ( 2451) *********************** 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 173 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 121 time to evaluate : 0.443 Fit side-chains REVERT: 1 113 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8848 (tt) REVERT: 9 113 LEU cc_start: 0.9466 (tp) cc_final: 0.9250 (tp) REVERT: a 9 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9110 (tt) REVERT: n 2 LEU cc_start: 0.9481 (tp) cc_final: 0.9212 (tp) REVERT: s 2 LEU cc_start: 0.8830 (tt) cc_final: 0.8612 (tt) REVERT: mA 109 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9166 (tp) outliers start: 52 outliers final: 32 residues processed: 158 average time/residue: 0.0766 time to fit residues: 19.3693 Evaluate side-chains 134 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 1 residue 113 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 4 residue 109 LEU Chi-restraints excluded: chain K residue 2 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 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 JA residue 112 LEU Chi-restraints excluded: chain MA 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 YA residue 109 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 eA residue 109 LEU Chi-restraints excluded: chain q residue 2 LEU Chi-restraints excluded: chain iA 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 95 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.047250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.042721 restraints weight = 43810.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.044132 restraints weight = 21456.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.044987 restraints weight = 12486.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.045592 restraints weight = 8030.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.045987 restraints weight = 5402.336| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10761 Z= 0.095 Angle : 0.603 8.791 14280 Z= 0.230 Chirality : 0.026 0.093 1734 Planarity : 0.002 0.037 1683 Dihedral : 3.198 22.521 1479 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.08 % Allowed : 38.33 % Favored : 55.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.84 (0.21), residues: 1122 helix: 4.37 (0.13), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 9 111 PHE 0.006 0.000 PHE 5 106 Details of bonding type rmsd covalent geometry : bond 0.00241 (10761) covalent geometry : angle 0.60293 (14280) hydrogen bonds : bond 0.01997 ( 817) hydrogen bonds : angle 2.66342 ( 2451) *********************** 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 174 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 112 time to evaluate : 0.463 Fit side-chains REVERT: G 9 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9192 (tt) REVERT: 9 113 LEU cc_start: 0.9504 (tp) cc_final: 0.9260 (tp) REVERT: a 9 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9083 (tt) REVERT: n 2 LEU cc_start: 0.9442 (tp) cc_final: 0.9191 (tp) REVERT: s 2 LEU cc_start: 0.8823 (tt) cc_final: 0.8517 (tt) REVERT: mA 109 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9180 (tp) outliers start: 62 outliers final: 44 residues processed: 157 average time/residue: 0.0728 time to fit residues: 18.6377 Evaluate side-chains 134 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 87 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 112 LEU Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain D residue 2 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 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 CA residue 112 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 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 KA residue 113 LEU Chi-restraints excluded: chain MA residue 109 LEU Chi-restraints excluded: chain Y residue 2 LEU Chi-restraints excluded: chain NA residue 112 LEU Chi-restraints excluded: chain Z residue 12 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 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 aA residue 112 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain cA residue 109 LEU Chi-restraints excluded: chain eA residue 109 LEU Chi-restraints excluded: chain q residue 2 LEU Chi-restraints excluded: chain q residue 9 LEU Chi-restraints excluded: chain iA residue 112 LEU Chi-restraints excluded: chain kA residue 113 LEU Chi-restraints excluded: chain mA residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3176 r_free = 0.3176 target = 0.046649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.042330 restraints weight = 43907.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.043679 restraints weight = 21504.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.044519 restraints weight = 12522.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.045083 restraints weight = 7975.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.045463 restraints weight = 5403.247| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10761 Z= 0.102 Angle : 0.600 8.196 14280 Z= 0.231 Chirality : 0.026 0.096 1734 Planarity : 0.002 0.033 1683 Dihedral : 3.321 20.603 1479 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.86 % Allowed : 38.04 % Favored : 55.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 7.08 (0.20), residues: 1122 helix: 4.52 (0.12), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 9 111 PHE 0.007 0.000 PHE u 6 Details of bonding type rmsd covalent geometry : bond 0.00257 (10761) covalent geometry : angle 0.60035 (14280) hydrogen bonds : bond 0.02019 ( 817) hydrogen bonds : angle 2.62808 ( 2451) *********************** 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 162 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 92 time to evaluate : 0.448 Fit side-chains REVERT: G 9 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9199 (tt) REVERT: 9 113 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9234 (tp) REVERT: R 2 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9114 (tt) REVERT: a 9 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9094 (tt) REVERT: n 2 LEU cc_start: 0.9436 (tp) cc_final: 0.9185 (tp) REVERT: s 2 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8590 (tt) REVERT: mA 109 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9189 (tp) outliers start: 70 outliers final: 54 residues processed: 138 average time/residue: 0.0629 time to fit residues: 15.0168 Evaluate side-chains 144 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 84 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 112 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain D residue 2 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 7 residue 112 LEU Chi-restraints excluded: chain 8 residue 113 LEU Chi-restraints excluded: chain 9 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 109 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 2 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 KA residue 113 LEU Chi-restraints excluded: chain MA residue 109 LEU Chi-restraints excluded: chain Y residue 2 LEU Chi-restraints excluded: chain NA residue 112 LEU Chi-restraints excluded: chain Z residue 12 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain c residue 2 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 VA residue 112 LEU Chi-restraints excluded: chain WA residue 112 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 aA residue 112 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 109 LEU Chi-restraints excluded: chain q residue 2 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 mA residue 102 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 18 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3097 r_free = 0.3097 target = 0.045128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.041640 restraints weight = 48359.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.042771 restraints weight = 22955.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.043434 restraints weight = 13130.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.043886 restraints weight = 8307.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.044209 restraints weight = 5572.979| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10761 Z= 0.121 Angle : 0.611 9.139 14280 Z= 0.238 Chirality : 0.027 0.100 1734 Planarity : 0.002 0.030 1683 Dihedral : 3.660 20.532 1479 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.04 % Allowed : 37.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.83 (0.20), residues: 1122 helix: 4.36 (0.12), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 9 111 PHE 0.012 0.000 PHEmA 106 Details of bonding type rmsd covalent geometry : bond 0.00299 (10761) covalent geometry : angle 0.61107 (14280) hydrogen bonds : bond 0.02173 ( 817) hydrogen bonds : angle 2.69901 ( 2451) *********************** 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 160 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 78 time to evaluate : 0.431 Fit side-chains REVERT: G 9 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9161 (tt) REVERT: 9 113 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9258 (tp) REVERT: R 2 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9109 (tt) REVERT: a 9 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9039 (tt) REVERT: n 2 LEU cc_start: 0.9420 (tp) cc_final: 0.9189 (tp) REVERT: gA 113 LEU cc_start: 0.9505 (tp) cc_final: 0.9289 (tp) REVERT: s 2 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8758 (tt) REVERT: v 2 LEU cc_start: 0.9163 (tt) cc_final: 0.8791 (tt) REVERT: mA 109 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9123 (tt) outliers start: 82 outliers final: 62 residues processed: 139 average time/residue: 0.0623 time to fit residues: 14.9128 Evaluate side-chains 137 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 69 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 C residue 2 LEU Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain D residue 2 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 K residue 2 LEU Chi-restraints excluded: chain 9 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 DA residue 109 LEU Chi-restraints excluded: chain DA residue 113 LEU Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain R residue 2 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 Y residue 2 LEU Chi-restraints excluded: chain NA residue 112 LEU Chi-restraints excluded: chain Z residue 12 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 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 l residue 9 LEU Chi-restraints excluded: chain aA residue 109 LEU Chi-restraints excluded: chain aA residue 112 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain cA residue 109 LEU Chi-restraints excluded: chain o residue 2 LEU Chi-restraints excluded: chain dA residue 112 LEU Chi-restraints excluded: chain eA residue 109 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 hA residue 112 LEU Chi-restraints excluded: chain iA residue 112 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 38 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 = 0.3074 r_free = 0.3074 target = 0.043359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039226 restraints weight = 46412.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.040483 restraints weight = 22838.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.041287 restraints weight = 13362.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.041826 restraints weight = 8570.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.042202 restraints weight = 5814.525| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10761 Z= 0.180 Angle : 0.653 8.172 14280 Z= 0.261 Chirality : 0.029 0.107 1734 Planarity : 0.002 0.028 1683 Dihedral : 4.221 28.299 1479 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 7.06 % Allowed : 38.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.78 (0.20), residues: 1122 helix: 3.71 (0.12), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGPA 111 PHE 0.007 0.001 PHE u 6 Details of bonding type rmsd covalent geometry : bond 0.00431 (10761) covalent geometry : angle 0.65307 (14280) hydrogen bonds : bond 0.02431 ( 817) hydrogen bonds : angle 2.97794 ( 2451) *********************** 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 137 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 65 time to evaluate : 0.448 Fit side-chains REVERT: G 9 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9234 (tt) REVERT: 9 113 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9183 (tp) REVERT: a 9 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9133 (tt) REVERT: gA 113 LEU cc_start: 0.9560 (tp) cc_final: 0.9247 (tp) REVERT: s 2 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.9012 (tt) REVERT: mA 109 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9177 (tt) outliers start: 72 outliers final: 56 residues processed: 126 average time/residue: 0.0609 time to fit residues: 13.0044 Evaluate side-chains 124 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 63 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 2 LEU Chi-restraints excluded: chain 2 residue 112 LEU Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain F residue 2 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 K residue 2 LEU Chi-restraints excluded: chain 9 residue 113 LEU Chi-restraints excluded: chain BA residue 109 LEU Chi-restraints excluded: chain BA residue 113 LEU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain CA residue 112 LEU Chi-restraints excluded: chain DA residue 109 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 U residue 2 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 Y residue 2 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 TA residue 113 LEU Chi-restraints excluded: chain f residue 2 LEU Chi-restraints excluded: chain f residue 12 LEU 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 l 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 dA residue 112 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 hA residue 112 LEU Chi-restraints excluded: chain iA residue 112 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 97 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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 = 0.3115 r_free = 0.3115 target = 0.045022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.040917 restraints weight = 47400.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.042171 restraints weight = 22877.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.042942 restraints weight = 13307.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.043475 restraints weight = 8641.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.043836 restraints weight = 5904.524| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10761 Z= 0.099 Angle : 0.635 8.981 14280 Z= 0.236 Chirality : 0.026 0.094 1734 Planarity : 0.002 0.029 1683 Dihedral : 3.462 20.861 1479 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.49 % Allowed : 39.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.79 (0.20), residues: 1122 helix: 4.34 (0.13), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 9 111 PHE 0.006 0.001 PHE u 6 Details of bonding type rmsd covalent geometry : bond 0.00254 (10761) covalent geometry : angle 0.63532 (14280) hydrogen bonds : bond 0.01986 ( 817) hydrogen bonds : angle 2.75267 ( 2451) ********************** 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 137 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 81 time to evaluate : 0.471 Fit side-chains REVERT: 1 113 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8954 (tt) REVERT: 9 113 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9250 (tp) REVERT: BA 109 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9046 (tt) REVERT: a 9 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.8994 (tt) REVERT: gA 113 LEU cc_start: 0.9487 (tp) cc_final: 0.9277 (tp) REVERT: s 2 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8674 (tt) outliers start: 56 outliers final: 45 residues processed: 121 average time/residue: 0.0624 time to fit residues: 13.1302 Evaluate side-chains 125 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 75 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 1 residue 113 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain 2 residue 112 LEU Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 4 residue 109 LEU Chi-restraints excluded: chain 7 residue 112 LEU Chi-restraints excluded: chain 8 residue 113 LEU Chi-restraints excluded: chain 9 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 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 KA residue 109 LEU Chi-restraints excluded: chain KA residue 113 LEU Chi-restraints excluded: chain MA residue 109 LEU Chi-restraints excluded: chain Y residue 2 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 TA residue 113 LEU Chi-restraints excluded: chain f residue 12 LEU 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 cA residue 109 LEU Chi-restraints excluded: chain dA residue 112 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 mA residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3167 r_free = 0.3167 target = 0.046700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.042420 restraints weight = 47034.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.043728 restraints weight = 22649.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.044543 restraints weight = 13130.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.045085 restraints weight = 8565.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.045461 restraints weight = 5861.011| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10761 Z= 0.087 Angle : 0.627 9.048 14280 Z= 0.231 Chirality : 0.025 0.091 1734 Planarity : 0.002 0.029 1683 Dihedral : 3.199 19.544 1479 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.51 % Allowed : 40.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 7.64 (0.19), residues: 1122 helix: 4.86 (0.12), residues: 1122 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGPA 111 PHE 0.006 0.000 PHEQA 106 Details of bonding type rmsd covalent geometry : bond 0.00224 (10761) covalent geometry : angle 0.62670 (14280) hydrogen bonds : bond 0.01843 ( 817) hydrogen bonds : angle 2.60214 ( 2451) =============================================================================== Job complete usr+sys time: 1270.87 seconds wall clock time: 22 minutes 50.33 seconds (1370.33 seconds total)