Starting phenix.real_space_refine on Sat Mar 7 11:01:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q5q_13844/03_2026/7q5q_13844.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q5q_13844/03_2026/7q5q_13844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q5q_13844/03_2026/7q5q_13844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q5q_13844/03_2026/7q5q_13844.map" model { file = "/net/cci-nas-00/data/ceres_data/7q5q_13844/03_2026/7q5q_13844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q5q_13844/03_2026/7q5q_13844.cif" } resolution = 4.38 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.001 sd= 0.147 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: 4 Type Number sf(0) Gaussians S 240 5.16 5 C 26856 2.51 5 N 7392 2.21 5 O 7848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 528 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42336 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "C" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "D" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "E" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "F" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "G" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "H" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "I" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "J" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "K" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "L" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "M" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "N" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "O" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "P" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "Q" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "R" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "S" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "T" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "V" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "W" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "X" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Chain: "Y" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1764 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 219} Time building chain proxies: 8.45, per 1000 atoms: 0.20 Number of scatterers: 42336 At special positions: 0 Unit cell: (155.212, 155.212, 155.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 240 16.00 O 7848 8.00 N 7392 7.00 C 26856 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: 3.67 Conformation dependent library (CDL) restraints added in 1.9 seconds 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10128 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 96 sheets defined 50.4% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'B' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 116 through 133 Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 205 through 222 Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'A' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 133 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 205 through 222 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP C 43 " --> pdb=" O ASN C 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 70 Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 116 through 133 Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'C' and resid 205 through 222 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'D' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 70 Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 111 through 115 Processing helix chain 'D' and resid 116 through 133 Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 205 through 222 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'E' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP E 43 " --> pdb=" O ASN E 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 70 Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 111 through 115 Processing helix chain 'E' and resid 116 through 133 Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 205 through 222 Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'F' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS F 14 " --> pdb=" O ALA F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP F 43 " --> pdb=" O ASN F 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 70 Processing helix chain 'F' and resid 71 through 74 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 116 through 133 Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'F' and resid 205 through 222 Processing helix chain 'F' and resid 223 through 228 Processing helix chain 'G' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP G 43 " --> pdb=" O ASN G 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU G 44 " --> pdb=" O LYS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 70 Processing helix chain 'G' and resid 71 through 74 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'G' and resid 116 through 133 Processing helix chain 'G' and resid 137 through 141 Processing helix chain 'G' and resid 205 through 222 Processing helix chain 'G' and resid 223 through 228 Processing helix chain 'H' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP H 43 " --> pdb=" O ASN H 39 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLU H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 70 Processing helix chain 'H' and resid 71 through 74 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 116 through 133 Processing helix chain 'H' and resid 137 through 141 Processing helix chain 'H' and resid 205 through 222 Processing helix chain 'H' and resid 223 through 228 Processing helix chain 'I' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS I 14 " --> pdb=" O ALA I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP I 43 " --> pdb=" O ASN I 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU I 44 " --> pdb=" O LYS I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 70 Processing helix chain 'I' and resid 71 through 74 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'I' and resid 111 through 115 Processing helix chain 'I' and resid 116 through 133 Processing helix chain 'I' and resid 137 through 141 Processing helix chain 'I' and resid 205 through 222 Processing helix chain 'I' and resid 223 through 228 Processing helix chain 'J' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS J 14 " --> pdb=" O ALA J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLU J 44 " --> pdb=" O LYS J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 70 Processing helix chain 'J' and resid 71 through 74 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'J' and resid 111 through 115 Processing helix chain 'J' and resid 116 through 133 Processing helix chain 'J' and resid 137 through 141 Processing helix chain 'J' and resid 205 through 222 Processing helix chain 'J' and resid 223 through 228 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.748A pdb=" N LYS K 14 " --> pdb=" O ALA K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU K 44 " --> pdb=" O LYS K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 70 Processing helix chain 'K' and resid 71 through 74 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'K' and resid 111 through 115 Processing helix chain 'K' and resid 116 through 133 Processing helix chain 'K' and resid 137 through 141 Processing helix chain 'K' and resid 205 through 222 Processing helix chain 'K' and resid 223 through 228 Processing helix chain 'L' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS L 14 " --> pdb=" O ALA L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 50 removed outlier: 5.543A pdb=" N ASP L 43 " --> pdb=" O ASN L 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU L 44 " --> pdb=" O LYS L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 70 Processing helix chain 'L' and resid 71 through 74 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 111 through 115 Processing helix chain 'L' and resid 116 through 133 Processing helix chain 'L' and resid 137 through 141 Processing helix chain 'L' and resid 205 through 222 Processing helix chain 'L' and resid 223 through 228 Processing helix chain 'M' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP M 43 " --> pdb=" O ASN M 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU M 44 " --> pdb=" O LYS M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 70 Processing helix chain 'M' and resid 71 through 74 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'M' and resid 111 through 115 Processing helix chain 'M' and resid 116 through 133 Processing helix chain 'M' and resid 137 through 141 Processing helix chain 'M' and resid 205 through 222 Processing helix chain 'M' and resid 223 through 228 Processing helix chain 'N' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS N 14 " --> pdb=" O ALA N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP N 43 " --> pdb=" O ASN N 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 70 Processing helix chain 'N' and resid 71 through 74 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'N' and resid 111 through 115 Processing helix chain 'N' and resid 116 through 133 Processing helix chain 'N' and resid 137 through 141 Processing helix chain 'N' and resid 205 through 222 Processing helix chain 'N' and resid 223 through 228 Processing helix chain 'O' and resid 3 through 20 removed outlier: 3.746A pdb=" N LYS O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP O 43 " --> pdb=" O ASN O 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU O 44 " --> pdb=" O LYS O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 70 Processing helix chain 'O' and resid 71 through 74 Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'O' and resid 116 through 133 Processing helix chain 'O' and resid 137 through 141 Processing helix chain 'O' and resid 205 through 222 Processing helix chain 'O' and resid 223 through 228 Processing helix chain 'P' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS P 14 " --> pdb=" O ALA P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 50 removed outlier: 5.545A pdb=" N ASP P 43 " --> pdb=" O ASN P 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU P 44 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 70 Processing helix chain 'P' and resid 71 through 74 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'P' and resid 111 through 115 Processing helix chain 'P' and resid 116 through 133 Processing helix chain 'P' and resid 137 through 141 Processing helix chain 'P' and resid 205 through 222 Processing helix chain 'P' and resid 223 through 228 Processing helix chain 'Q' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS Q 14 " --> pdb=" O ALA Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP Q 43 " --> pdb=" O ASN Q 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU Q 44 " --> pdb=" O LYS Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 70 Processing helix chain 'Q' and resid 71 through 74 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'Q' and resid 111 through 115 Processing helix chain 'Q' and resid 116 through 133 Processing helix chain 'Q' and resid 137 through 141 Processing helix chain 'Q' and resid 205 through 222 Processing helix chain 'Q' and resid 223 through 228 Processing helix chain 'R' and resid 3 through 20 removed outlier: 3.748A pdb=" N LYS R 14 " --> pdb=" O ALA R 10 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP R 43 " --> pdb=" O ASN R 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU R 44 " --> pdb=" O LYS R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 70 Processing helix chain 'R' and resid 71 through 74 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'R' and resid 111 through 115 Processing helix chain 'R' and resid 116 through 133 Processing helix chain 'R' and resid 137 through 141 Processing helix chain 'R' and resid 205 through 222 Processing helix chain 'R' and resid 223 through 228 Processing helix chain 'S' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS S 14 " --> pdb=" O ALA S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP S 43 " --> pdb=" O ASN S 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU S 44 " --> pdb=" O LYS S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 70 Processing helix chain 'S' and resid 71 through 74 Processing helix chain 'S' and resid 79 through 83 Processing helix chain 'S' and resid 111 through 115 Processing helix chain 'S' and resid 116 through 133 Processing helix chain 'S' and resid 137 through 141 Processing helix chain 'S' and resid 205 through 222 Processing helix chain 'S' and resid 223 through 228 Processing helix chain 'T' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS T 14 " --> pdb=" O ALA T 10 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP T 43 " --> pdb=" O ASN T 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 70 Processing helix chain 'T' and resid 71 through 74 Processing helix chain 'T' and resid 79 through 83 Processing helix chain 'T' and resid 111 through 115 Processing helix chain 'T' and resid 116 through 133 Processing helix chain 'T' and resid 137 through 141 Processing helix chain 'T' and resid 205 through 222 Processing helix chain 'T' and resid 223 through 228 Processing helix chain 'V' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS V 14 " --> pdb=" O ALA V 10 " (cutoff:3.500A) Processing helix chain 'V' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP V 43 " --> pdb=" O ASN V 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU V 44 " --> pdb=" O LYS V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 70 Processing helix chain 'V' and resid 71 through 74 Processing helix chain 'V' and resid 79 through 83 Processing helix chain 'V' and resid 111 through 115 Processing helix chain 'V' and resid 116 through 133 Processing helix chain 'V' and resid 137 through 141 Processing helix chain 'V' and resid 205 through 222 Processing helix chain 'V' and resid 223 through 228 Processing helix chain 'W' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS W 14 " --> pdb=" O ALA W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP W 43 " --> pdb=" O ASN W 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU W 44 " --> pdb=" O LYS W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 55 through 70 Processing helix chain 'W' and resid 71 through 74 Processing helix chain 'W' and resid 79 through 83 Processing helix chain 'W' and resid 111 through 115 Processing helix chain 'W' and resid 116 through 133 Processing helix chain 'W' and resid 137 through 141 Processing helix chain 'W' and resid 205 through 222 Processing helix chain 'W' and resid 223 through 228 Processing helix chain 'X' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS X 14 " --> pdb=" O ALA X 10 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP X 43 " --> pdb=" O ASN X 39 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLU X 44 " --> pdb=" O LYS X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 55 through 70 Processing helix chain 'X' and resid 71 through 74 Processing helix chain 'X' and resid 79 through 83 Processing helix chain 'X' and resid 111 through 115 Processing helix chain 'X' and resid 116 through 133 Processing helix chain 'X' and resid 137 through 141 Processing helix chain 'X' and resid 205 through 222 Processing helix chain 'X' and resid 223 through 228 Processing helix chain 'Y' and resid 3 through 20 removed outlier: 3.747A pdb=" N LYS Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 50 removed outlier: 5.544A pdb=" N ASP Y 43 " --> pdb=" O ASN Y 39 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU Y 44 " --> pdb=" O LYS Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 55 through 70 Processing helix chain 'Y' and resid 71 through 74 Processing helix chain 'Y' and resid 79 through 83 Processing helix chain 'Y' and resid 111 through 115 Processing helix chain 'Y' and resid 116 through 133 Processing helix chain 'Y' and resid 137 through 141 Processing helix chain 'Y' and resid 205 through 222 Processing helix chain 'Y' and resid 223 through 228 Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA B 196 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR B 147 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 30 Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AA5, first strand: chain 'A' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA A 196 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A 147 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 23 through 30 Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA8, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA9, first strand: chain 'C' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA C 196 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR C 147 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 23 through 30 Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 Processing sheet with id=AB3, first strand: chain 'C' and resid 98 through 100 Processing sheet with id=AB4, first strand: chain 'D' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA D 196 " --> pdb=" O GLY D 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR D 147 " --> pdb=" O ALA D 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 23 through 30 Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AB7, first strand: chain 'D' and resid 98 through 100 Processing sheet with id=AB8, first strand: chain 'E' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA E 196 " --> pdb=" O GLY E 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR E 147 " --> pdb=" O ALA E 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 23 through 30 Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 Processing sheet with id=AC2, first strand: chain 'E' and resid 98 through 100 Processing sheet with id=AC3, first strand: chain 'F' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA F 196 " --> pdb=" O GLY F 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR F 147 " --> pdb=" O ALA F 169 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 23 through 30 Processing sheet with id=AC5, first strand: chain 'F' and resid 76 through 78 Processing sheet with id=AC6, first strand: chain 'F' and resid 98 through 100 Processing sheet with id=AC7, first strand: chain 'G' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA G 196 " --> pdb=" O GLY G 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR G 147 " --> pdb=" O ALA G 169 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 23 through 30 Processing sheet with id=AC9, first strand: chain 'G' and resid 76 through 78 Processing sheet with id=AD1, first strand: chain 'G' and resid 98 through 100 Processing sheet with id=AD2, first strand: chain 'H' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA H 196 " --> pdb=" O GLY H 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR H 147 " --> pdb=" O ALA H 169 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 23 through 30 Processing sheet with id=AD4, first strand: chain 'H' and resid 76 through 78 Processing sheet with id=AD5, first strand: chain 'H' and resid 98 through 100 Processing sheet with id=AD6, first strand: chain 'I' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA I 196 " --> pdb=" O GLY I 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR I 147 " --> pdb=" O ALA I 169 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 23 through 30 Processing sheet with id=AD8, first strand: chain 'I' and resid 76 through 78 Processing sheet with id=AD9, first strand: chain 'I' and resid 98 through 100 Processing sheet with id=AE1, first strand: chain 'J' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA J 196 " --> pdb=" O GLY J 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR J 147 " --> pdb=" O ALA J 169 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 23 through 30 Processing sheet with id=AE3, first strand: chain 'J' and resid 76 through 78 Processing sheet with id=AE4, first strand: chain 'J' and resid 98 through 100 Processing sheet with id=AE5, first strand: chain 'K' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA K 196 " --> pdb=" O GLY K 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR K 147 " --> pdb=" O ALA K 169 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 23 through 30 Processing sheet with id=AE7, first strand: chain 'K' and resid 76 through 78 Processing sheet with id=AE8, first strand: chain 'K' and resid 98 through 100 Processing sheet with id=AE9, first strand: chain 'L' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA L 196 " --> pdb=" O GLY L 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR L 147 " --> pdb=" O ALA L 169 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 23 through 30 Processing sheet with id=AF2, first strand: chain 'L' and resid 76 through 78 Processing sheet with id=AF3, first strand: chain 'L' and resid 98 through 100 Processing sheet with id=AF4, first strand: chain 'M' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA M 196 " --> pdb=" O GLY M 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR M 147 " --> pdb=" O ALA M 169 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 23 through 30 Processing sheet with id=AF6, first strand: chain 'M' and resid 76 through 78 Processing sheet with id=AF7, first strand: chain 'M' and resid 98 through 100 Processing sheet with id=AF8, first strand: chain 'N' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA N 196 " --> pdb=" O GLY N 172 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR N 147 " --> pdb=" O ALA N 169 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 23 through 30 Processing sheet with id=AG1, first strand: chain 'N' and resid 76 through 78 Processing sheet with id=AG2, first strand: chain 'N' and resid 98 through 100 Processing sheet with id=AG3, first strand: chain 'O' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA O 196 " --> pdb=" O GLY O 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR O 147 " --> pdb=" O ALA O 169 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 23 through 30 Processing sheet with id=AG5, first strand: chain 'O' and resid 76 through 78 Processing sheet with id=AG6, first strand: chain 'O' and resid 98 through 100 Processing sheet with id=AG7, first strand: chain 'P' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA P 196 " --> pdb=" O GLY P 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR P 147 " --> pdb=" O ALA P 169 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 23 through 30 Processing sheet with id=AG9, first strand: chain 'P' and resid 76 through 78 Processing sheet with id=AH1, first strand: chain 'P' and resid 98 through 100 Processing sheet with id=AH2, first strand: chain 'Q' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA Q 196 " --> pdb=" O GLY Q 172 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR Q 147 " --> pdb=" O ALA Q 169 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 23 through 30 Processing sheet with id=AH4, first strand: chain 'Q' and resid 76 through 78 Processing sheet with id=AH5, first strand: chain 'Q' and resid 98 through 100 Processing sheet with id=AH6, first strand: chain 'R' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA R 196 " --> pdb=" O GLY R 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR R 147 " --> pdb=" O ALA R 169 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 23 through 30 Processing sheet with id=AH8, first strand: chain 'R' and resid 76 through 78 Processing sheet with id=AH9, first strand: chain 'R' and resid 98 through 100 Processing sheet with id=AI1, first strand: chain 'S' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA S 196 " --> pdb=" O GLY S 172 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR S 147 " --> pdb=" O ALA S 169 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'S' and resid 23 through 30 Processing sheet with id=AI3, first strand: chain 'S' and resid 76 through 78 Processing sheet with id=AI4, first strand: chain 'S' and resid 98 through 100 Processing sheet with id=AI5, first strand: chain 'T' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA T 196 " --> pdb=" O GLY T 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR T 147 " --> pdb=" O ALA T 169 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'T' and resid 23 through 30 Processing sheet with id=AI7, first strand: chain 'T' and resid 76 through 78 Processing sheet with id=AI8, first strand: chain 'T' and resid 98 through 100 Processing sheet with id=AI9, first strand: chain 'V' and resid 23 through 30 removed outlier: 3.520A pdb=" N ALA V 196 " --> pdb=" O GLY V 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR V 147 " --> pdb=" O ALA V 169 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'V' and resid 23 through 30 Processing sheet with id=AJ2, first strand: chain 'V' and resid 76 through 78 Processing sheet with id=AJ3, first strand: chain 'V' and resid 98 through 100 Processing sheet with id=AJ4, first strand: chain 'W' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA W 196 " --> pdb=" O GLY W 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR W 147 " --> pdb=" O ALA W 169 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'W' and resid 23 through 30 Processing sheet with id=AJ6, first strand: chain 'W' and resid 76 through 78 Processing sheet with id=AJ7, first strand: chain 'W' and resid 98 through 100 Processing sheet with id=AJ8, first strand: chain 'X' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA X 196 " --> pdb=" O GLY X 172 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR X 147 " --> pdb=" O ALA X 169 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'X' and resid 23 through 30 Processing sheet with id=AK1, first strand: chain 'X' and resid 76 through 78 Processing sheet with id=AK2, first strand: chain 'X' and resid 98 through 100 Processing sheet with id=AK3, first strand: chain 'Y' and resid 23 through 30 removed outlier: 3.521A pdb=" N ALA Y 196 " --> pdb=" O GLY Y 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR Y 147 " --> pdb=" O ALA Y 169 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'Y' and resid 23 through 30 Processing sheet with id=AK5, first strand: chain 'Y' and resid 76 through 78 Processing sheet with id=AK6, first strand: chain 'Y' and resid 98 through 100 2856 hydrogen bonds defined for protein. 7200 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: 11.98 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10436 1.33 - 1.45: 6700 1.45 - 1.57: 25248 1.57 - 1.69: 0 1.69 - 1.81: 480 Bond restraints: 42864 Sorted by residual: bond pdb=" CZ ARG V 6 " pdb=" NH2 ARG V 6 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.86e+00 bond pdb=" CZ ARG T 6 " pdb=" NH2 ARG T 6 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.84e+00 bond pdb=" CZ ARG Y 6 " pdb=" NH2 ARG Y 6 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.82e+00 bond pdb=" CZ ARG G 6 " pdb=" NH2 ARG G 6 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.75e+00 bond pdb=" CZ ARG O 6 " pdb=" NH2 ARG O 6 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.70e+00 ... (remaining 42859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 42205 1.44 - 2.89: 12613 2.89 - 4.33: 2416 4.33 - 5.77: 462 5.77 - 7.22: 72 Bond angle restraints: 57768 Sorted by residual: angle pdb=" C GLY M 206 " pdb=" N ARG M 207 " pdb=" CA ARG M 207 " ideal model delta sigma weight residual 120.79 125.79 -5.00 1.39e+00 5.18e-01 1.29e+01 angle pdb=" C GLY E 206 " pdb=" N ARG E 207 " pdb=" CA ARG E 207 " ideal model delta sigma weight residual 120.79 125.78 -4.99 1.39e+00 5.18e-01 1.29e+01 angle pdb=" C GLY Y 206 " pdb=" N ARG Y 207 " pdb=" CA ARG Y 207 " ideal model delta sigma weight residual 120.79 125.78 -4.99 1.39e+00 5.18e-01 1.29e+01 angle pdb=" C GLY J 206 " pdb=" N ARG J 207 " pdb=" CA ARG J 207 " ideal model delta sigma weight residual 120.79 125.78 -4.99 1.39e+00 5.18e-01 1.29e+01 angle pdb=" C GLY Q 206 " pdb=" N ARG Q 207 " pdb=" CA ARG Q 207 " ideal model delta sigma weight residual 120.79 125.77 -4.98 1.39e+00 5.18e-01 1.28e+01 ... (remaining 57763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.76: 23257 14.76 - 29.52: 2735 29.52 - 44.29: 441 44.29 - 59.05: 87 59.05 - 73.81: 72 Dihedral angle restraints: 26592 sinusoidal: 10872 harmonic: 15720 Sorted by residual: dihedral pdb=" CA ALA N 20 " pdb=" C ALA N 20 " pdb=" N ALA N 21 " pdb=" CA ALA N 21 " ideal model delta harmonic sigma weight residual 180.00 151.73 28.27 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ALA O 20 " pdb=" C ALA O 20 " pdb=" N ALA O 21 " pdb=" CA ALA O 21 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ALA D 20 " pdb=" C ALA D 20 " pdb=" N ALA D 21 " pdb=" CA ALA D 21 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 26589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4103 0.054 - 0.108: 2117 0.108 - 0.162: 620 0.162 - 0.216: 24 0.216 - 0.271: 24 Chirality restraints: 6888 Sorted by residual: chirality pdb=" CA LEU L 203 " pdb=" N LEU L 203 " pdb=" C LEU L 203 " pdb=" CB LEU L 203 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA LEU K 203 " pdb=" N LEU K 203 " pdb=" C LEU K 203 " pdb=" CB LEU K 203 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA LEU B 203 " pdb=" N LEU B 203 " pdb=" C LEU B 203 " pdb=" CB LEU B 203 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 6885 not shown) Planarity restraints: 7344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR V 41 " 0.071 2.00e-02 2.50e+03 3.77e-02 2.84e+01 pdb=" CG TYR V 41 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR V 41 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR V 41 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR V 41 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR V 41 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR V 41 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR V 41 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 41 " -0.071 2.00e-02 2.50e+03 3.77e-02 2.84e+01 pdb=" CG TYR Q 41 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 41 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 41 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 41 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 41 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR Q 41 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR Q 41 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 41 " -0.071 2.00e-02 2.50e+03 3.76e-02 2.83e+01 pdb=" CG TYR F 41 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR F 41 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR F 41 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR F 41 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR F 41 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR F 41 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR F 41 " -0.049 2.00e-02 2.50e+03 ... (remaining 7341 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 922 2.70 - 3.25: 45478 3.25 - 3.80: 70093 3.80 - 4.35: 88227 4.35 - 4.90: 140927 Nonbonded interactions: 345647 Sorted by model distance: nonbonded pdb=" O ASP C 84 " pdb=" N MET N 2 " model vdw 2.152 3.120 nonbonded pdb=" N MET L 2 " pdb=" O ASP O 84 " model vdw 2.255 3.120 nonbonded pdb=" O ASP F 84 " pdb=" N MET M 2 " model vdw 2.260 3.120 nonbonded pdb=" O ASP M 84 " pdb=" N MET V 2 " model vdw 2.344 3.120 nonbonded pdb=" NH2 ARG I 6 " pdb=" OD2 ASP R 205 " model vdw 2.360 3.120 ... (remaining 345642 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: 0.14 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 40.990 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 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 : 0.009 0.070 42864 Z= 0.537 Angle : 1.410 7.217 57768 Z= 0.870 Chirality : 0.067 0.271 6888 Planarity : 0.013 0.105 7344 Dihedral : 13.563 73.810 16464 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.08 % Allowed : 6.25 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: -1.58 (0.11), residues: 5424 helix: -1.83 (0.08), residues: 2160 sheet: -1.01 (0.13), residues: 1296 loop : 0.32 (0.16), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 110 TYR 0.071 0.014 TYR Q 41 PHE 0.040 0.011 PHE P 146 HIS 0.013 0.005 HIS I 174 Details of bonding type rmsd covalent geometry : bond 0.00912 (42864) covalent geometry : angle 1.40991 (57768) hydrogen bonds : bond 0.15176 ( 2664) hydrogen bonds : angle 7.32112 ( 7200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 545 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 193 MET cc_start: 0.8926 (ttm) cc_final: 0.8452 (ttp) REVERT: B 204 LEU cc_start: 0.9197 (mt) cc_final: 0.8810 (mt) REVERT: B 226 MET cc_start: 0.9209 (mmt) cc_final: 0.8894 (mmm) REVERT: A 193 MET cc_start: 0.8863 (ttm) cc_final: 0.8265 (ttp) REVERT: A 204 LEU cc_start: 0.9263 (mt) cc_final: 0.8957 (mt) REVERT: A 226 MET cc_start: 0.9256 (mmt) cc_final: 0.8921 (mmm) REVERT: C 56 MET cc_start: 0.9410 (mmm) cc_final: 0.8952 (mpp) REVERT: C 115 MET cc_start: 0.7686 (mtt) cc_final: 0.7087 (mtt) REVERT: C 193 MET cc_start: 0.9090 (ttm) cc_final: 0.8740 (ttp) REVERT: D 192 MET cc_start: 0.9025 (mmm) cc_final: 0.8711 (mmm) REVERT: D 193 MET cc_start: 0.8943 (ttm) cc_final: 0.8621 (ttp) REVERT: D 226 MET cc_start: 0.9338 (mmt) cc_final: 0.8907 (mmm) REVERT: E 5 MET cc_start: 0.9058 (tmt) cc_final: 0.8829 (tmm) REVERT: E 31 MET cc_start: 0.9119 (mmm) cc_final: 0.8849 (mmm) REVERT: E 193 MET cc_start: 0.8753 (ttm) cc_final: 0.8196 (ttp) REVERT: E 204 LEU cc_start: 0.9225 (mt) cc_final: 0.8918 (mt) REVERT: E 226 MET cc_start: 0.9109 (mmt) cc_final: 0.8896 (mmm) REVERT: F 192 MET cc_start: 0.9076 (mmm) cc_final: 0.8795 (mmm) REVERT: F 193 MET cc_start: 0.8953 (ttm) cc_final: 0.8576 (ttp) REVERT: F 226 MET cc_start: 0.9253 (mmt) cc_final: 0.9038 (mmt) REVERT: G 5 MET cc_start: 0.9079 (tmt) cc_final: 0.8839 (tmm) REVERT: G 31 MET cc_start: 0.9085 (mmm) cc_final: 0.8821 (mmm) REVERT: G 193 MET cc_start: 0.8767 (ttm) cc_final: 0.8194 (ttp) REVERT: G 204 LEU cc_start: 0.9143 (mt) cc_final: 0.8827 (mt) REVERT: G 226 MET cc_start: 0.9110 (mmt) cc_final: 0.8880 (mmm) REVERT: H 192 MET cc_start: 0.9015 (mmm) cc_final: 0.8793 (mmm) REVERT: H 193 MET cc_start: 0.8861 (ttm) cc_final: 0.8430 (ttp) REVERT: H 226 MET cc_start: 0.9249 (mmt) cc_final: 0.8931 (mmt) REVERT: I 192 MET cc_start: 0.8986 (mmm) cc_final: 0.8713 (mmm) REVERT: I 193 MET cc_start: 0.8860 (ttm) cc_final: 0.8539 (ttp) REVERT: I 226 MET cc_start: 0.9240 (mmt) cc_final: 0.8919 (mmt) REVERT: J 192 MET cc_start: 0.9030 (mmm) cc_final: 0.8687 (mmm) REVERT: J 193 MET cc_start: 0.8784 (ttm) cc_final: 0.8454 (ttp) REVERT: J 226 MET cc_start: 0.9117 (mmt) cc_final: 0.8889 (mmm) REVERT: K 56 MET cc_start: 0.9340 (mmm) cc_final: 0.8554 (mpp) REVERT: K 158 MET cc_start: 0.8988 (ttp) cc_final: 0.8723 (ptm) REVERT: K 192 MET cc_start: 0.9001 (mmm) cc_final: 0.8797 (mmm) REVERT: K 193 MET cc_start: 0.8765 (ttm) cc_final: 0.8379 (ttp) REVERT: K 226 MET cc_start: 0.9231 (mmt) cc_final: 0.8901 (mmt) REVERT: L 31 MET cc_start: 0.9146 (mmm) cc_final: 0.8851 (mmm) REVERT: L 52 LYS cc_start: 0.9427 (ptpp) cc_final: 0.9176 (tppt) REVERT: L 56 MET cc_start: 0.9444 (mmm) cc_final: 0.9048 (mpp) REVERT: L 193 MET cc_start: 0.9113 (ttm) cc_final: 0.8792 (ttp) REVERT: M 56 MET cc_start: 0.9386 (mmm) cc_final: 0.8939 (mpp) REVERT: M 115 MET cc_start: 0.7777 (mtt) cc_final: 0.7364 (mtt) REVERT: M 192 MET cc_start: 0.9123 (mmm) cc_final: 0.8881 (mmm) REVERT: M 193 MET cc_start: 0.9073 (ttm) cc_final: 0.8773 (ttp) REVERT: M 226 MET cc_start: 0.9056 (mmt) cc_final: 0.8850 (mmt) REVERT: N 193 MET cc_start: 0.8922 (ttm) cc_final: 0.8433 (ttp) REVERT: N 226 MET cc_start: 0.9325 (mmt) cc_final: 0.8918 (mmm) REVERT: O 31 MET cc_start: 0.9160 (mmm) cc_final: 0.8924 (mmm) REVERT: O 193 MET cc_start: 0.8785 (ttm) cc_final: 0.8394 (ttp) REVERT: P 158 MET cc_start: 0.9180 (ttp) cc_final: 0.8818 (ptm) REVERT: P 192 MET cc_start: 0.8954 (mmm) cc_final: 0.8709 (mmm) REVERT: P 193 MET cc_start: 0.8910 (ttm) cc_final: 0.8576 (ttp) REVERT: P 226 MET cc_start: 0.9276 (mmt) cc_final: 0.9038 (mmt) REVERT: Q 184 ASN cc_start: 0.9156 (m-40) cc_final: 0.8935 (m-40) REVERT: Q 193 MET cc_start: 0.8627 (ttm) cc_final: 0.8023 (ttp) REVERT: Q 204 LEU cc_start: 0.9261 (mt) cc_final: 0.8880 (mt) REVERT: R 5 MET cc_start: 0.9059 (tmt) cc_final: 0.8817 (tmm) REVERT: R 31 MET cc_start: 0.9136 (mmm) cc_final: 0.8909 (mmm) REVERT: R 193 MET cc_start: 0.8725 (ttm) cc_final: 0.8243 (ttp) REVERT: R 204 LEU cc_start: 0.9235 (mt) cc_final: 0.8855 (mt) REVERT: R 226 MET cc_start: 0.9111 (mmt) cc_final: 0.8814 (mmm) REVERT: S 31 MET cc_start: 0.9197 (mmm) cc_final: 0.8875 (mmm) REVERT: S 193 MET cc_start: 0.8796 (ttm) cc_final: 0.8352 (ttp) REVERT: S 204 LEU cc_start: 0.9254 (mt) cc_final: 0.8948 (mt) REVERT: T 31 MET cc_start: 0.9096 (mmm) cc_final: 0.8690 (mmm) REVERT: T 193 MET cc_start: 0.8554 (ttm) cc_final: 0.7909 (ttt) REVERT: T 204 LEU cc_start: 0.9206 (mt) cc_final: 0.8834 (mt) REVERT: V 192 MET cc_start: 0.9077 (mmm) cc_final: 0.8820 (mmm) REVERT: V 193 MET cc_start: 0.8914 (ttm) cc_final: 0.8503 (ttp) REVERT: V 226 MET cc_start: 0.9248 (mmt) cc_final: 0.9011 (mmt) REVERT: W 5 MET cc_start: 0.9069 (tmt) cc_final: 0.8839 (tmm) REVERT: W 31 MET cc_start: 0.9208 (mmm) cc_final: 0.8928 (mmm) REVERT: W 192 MET cc_start: 0.9033 (mmm) cc_final: 0.8831 (mmm) REVERT: W 193 MET cc_start: 0.8832 (ttm) cc_final: 0.8326 (ttp) REVERT: W 204 LEU cc_start: 0.9240 (mt) cc_final: 0.8893 (mt) REVERT: W 226 MET cc_start: 0.9127 (mmt) cc_final: 0.8879 (mmm) REVERT: X 193 MET cc_start: 0.8767 (ttm) cc_final: 0.8394 (ttp) REVERT: Y 192 MET cc_start: 0.9028 (mmm) cc_final: 0.8819 (mmm) REVERT: Y 193 MET cc_start: 0.8960 (ttm) cc_final: 0.8517 (ttp) REVERT: Y 226 MET cc_start: 0.9245 (mmt) cc_final: 0.8880 (mmt) outliers start: 96 outliers final: 36 residues processed: 641 average time/residue: 0.2816 time to fit residues: 286.2496 Evaluate side-chains 365 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 329 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 8.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 0.3980 chunk 223 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 184 ASN A 27 ASN A 184 ASN C 27 ASN C 184 ASN D 27 ASN E 27 ASN F 27 ASN G 27 ASN G 184 ASN H 27 ASN H 184 ASN I 27 ASN J 27 ASN J 184 ASN K 27 ASN K 184 ASN L 27 ASN L 184 ASN M 27 ASN M 184 ASN N 27 ASN O 27 ASN P 27 ASN Q 27 ASN Q 184 ASN R 27 ASN R 184 ASN S 18 ASN S 27 ASN T 27 ASN V 27 ASN V 184 ASN W 27 ASN W 184 ASN X 27 ASN Y 27 ASN Y 184 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.042099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.033580 restraints weight = 301034.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.034694 restraints weight = 185117.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.035489 restraints weight = 131093.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.036068 restraints weight = 102057.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.036480 restraints weight = 84794.368| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 42864 Z= 0.145 Angle : 0.632 5.515 57768 Z= 0.347 Chirality : 0.043 0.146 6888 Planarity : 0.004 0.040 7344 Dihedral : 6.199 21.699 5952 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: 0.86 (0.12), residues: 5424 helix: 0.83 (0.10), residues: 2160 sheet: -0.56 (0.13), residues: 1152 loop : 1.31 (0.16), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 68 TYR 0.018 0.002 TYR X 219 PHE 0.028 0.002 PHE T 154 HIS 0.007 0.002 HIS S 174 Details of bonding type rmsd covalent geometry : bond 0.00288 (42864) covalent geometry : angle 0.63180 (57768) hydrogen bonds : bond 0.04299 ( 2664) hydrogen bonds : angle 4.59205 ( 7200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.9345 (mmp) cc_final: 0.8935 (mmm) REVERT: B 192 MET cc_start: 0.9065 (mmm) cc_final: 0.8759 (mmm) REVERT: B 193 MET cc_start: 0.9144 (ttp) cc_final: 0.8263 (ttt) REVERT: B 204 LEU cc_start: 0.9186 (mt) cc_final: 0.8910 (mt) REVERT: A 31 MET cc_start: 0.9357 (mmp) cc_final: 0.9058 (mmm) REVERT: A 193 MET cc_start: 0.9234 (ttp) cc_final: 0.8221 (ttt) REVERT: A 204 LEU cc_start: 0.9165 (mt) cc_final: 0.8854 (mt) REVERT: A 226 MET cc_start: 0.9204 (mmt) cc_final: 0.8958 (mmt) REVERT: C 31 MET cc_start: 0.9382 (mmp) cc_final: 0.8797 (mmm) REVERT: C 193 MET cc_start: 0.9318 (ttp) cc_final: 0.8657 (ttt) REVERT: D 31 MET cc_start: 0.9487 (mmp) cc_final: 0.9055 (mmm) REVERT: D 193 MET cc_start: 0.9372 (ttp) cc_final: 0.8701 (ttt) REVERT: D 226 MET cc_start: 0.9099 (mmt) cc_final: 0.8834 (mmt) REVERT: E 31 MET cc_start: 0.8854 (mmm) cc_final: 0.8514 (mmm) REVERT: E 184 ASN cc_start: 0.9396 (m-40) cc_final: 0.9106 (m110) REVERT: E 193 MET cc_start: 0.8893 (ttp) cc_final: 0.8280 (ttt) REVERT: E 204 LEU cc_start: 0.9165 (mt) cc_final: 0.8907 (mt) REVERT: E 226 MET cc_start: 0.9219 (mmt) cc_final: 0.8901 (mmt) REVERT: F 31 MET cc_start: 0.9256 (mmp) cc_final: 0.8947 (mmm) REVERT: F 68 ARG cc_start: 0.9447 (ttm110) cc_final: 0.9174 (mtm110) REVERT: F 192 MET cc_start: 0.9205 (mmm) cc_final: 0.8912 (mmm) REVERT: F 193 MET cc_start: 0.9385 (ttp) cc_final: 0.8602 (ttt) REVERT: G 31 MET cc_start: 0.8764 (mmm) cc_final: 0.8456 (mmm) REVERT: G 193 MET cc_start: 0.8877 (ttp) cc_final: 0.8256 (ttt) REVERT: G 204 LEU cc_start: 0.9144 (mt) cc_final: 0.8888 (mt) REVERT: G 226 MET cc_start: 0.9203 (mmt) cc_final: 0.8909 (mmm) REVERT: H 31 MET cc_start: 0.9442 (mmp) cc_final: 0.9078 (mmm) REVERT: H 193 MET cc_start: 0.9382 (ttp) cc_final: 0.8744 (ttt) REVERT: H 226 MET cc_start: 0.9022 (mmt) cc_final: 0.8798 (mmt) REVERT: I 5 MET cc_start: 0.9160 (ptm) cc_final: 0.8809 (ppp) REVERT: I 28 GLU cc_start: 0.8893 (pt0) cc_final: 0.8611 (tt0) REVERT: I 31 MET cc_start: 0.9487 (mmp) cc_final: 0.9060 (mmm) REVERT: I 184 ASN cc_start: 0.9619 (m-40) cc_final: 0.9410 (m-40) REVERT: I 193 MET cc_start: 0.9256 (ttp) cc_final: 0.8299 (ttt) REVERT: J 31 MET cc_start: 0.9348 (mmp) cc_final: 0.9037 (mmm) REVERT: J 192 MET cc_start: 0.9077 (mmm) cc_final: 0.8738 (mmm) REVERT: J 193 MET cc_start: 0.9231 (ttp) cc_final: 0.8298 (ttt) REVERT: J 226 MET cc_start: 0.9121 (mmt) cc_final: 0.8826 (mmt) REVERT: K 31 MET cc_start: 0.9487 (mmp) cc_final: 0.9076 (mmm) REVERT: K 56 MET cc_start: 0.9211 (mmm) cc_final: 0.8910 (mpp) REVERT: K 158 MET cc_start: 0.9331 (ttp) cc_final: 0.8918 (ttm) REVERT: K 192 MET cc_start: 0.9078 (mmm) cc_final: 0.8831 (mmm) REVERT: K 193 MET cc_start: 0.9400 (ttp) cc_final: 0.8533 (ttt) REVERT: K 226 MET cc_start: 0.9024 (mmt) cc_final: 0.8785 (mmt) REVERT: L 5 MET cc_start: 0.9021 (ptm) cc_final: 0.8665 (ppp) REVERT: L 31 MET cc_start: 0.8884 (mmm) cc_final: 0.8638 (mmm) REVERT: L 46 LEU cc_start: 0.9867 (tp) cc_final: 0.9651 (mt) REVERT: L 193 MET cc_start: 0.9120 (ttp) cc_final: 0.8848 (ttt) REVERT: M 31 MET cc_start: 0.9457 (mmp) cc_final: 0.8975 (mmm) REVERT: M 193 MET cc_start: 0.9307 (ttp) cc_final: 0.8737 (ttt) REVERT: N 31 MET cc_start: 0.9375 (mmp) cc_final: 0.8938 (mmm) REVERT: N 158 MET cc_start: 0.9149 (ttm) cc_final: 0.8648 (ttm) REVERT: N 184 ASN cc_start: 0.9576 (m-40) cc_final: 0.9331 (m110) REVERT: N 192 MET cc_start: 0.9191 (mmm) cc_final: 0.8862 (mmm) REVERT: N 193 MET cc_start: 0.9327 (ttp) cc_final: 0.8563 (ttt) REVERT: N 226 MET cc_start: 0.9205 (mmt) cc_final: 0.8970 (mmt) REVERT: O 31 MET cc_start: 0.8968 (mmm) cc_final: 0.8746 (mmm) REVERT: O 184 ASN cc_start: 0.9544 (m-40) cc_final: 0.9287 (m110) REVERT: O 193 MET cc_start: 0.8934 (ttp) cc_final: 0.8305 (ttt) REVERT: P 31 MET cc_start: 0.9300 (mmp) cc_final: 0.8987 (mmm) REVERT: P 158 MET cc_start: 0.9364 (ttp) cc_final: 0.8933 (ttm) REVERT: P 193 MET cc_start: 0.9359 (ttp) cc_final: 0.8688 (ttt) REVERT: Q 31 MET cc_start: 0.9242 (mmp) cc_final: 0.8942 (mmm) REVERT: Q 192 MET cc_start: 0.9190 (mmm) cc_final: 0.8924 (mmm) REVERT: Q 193 MET cc_start: 0.9290 (ttp) cc_final: 0.8211 (ttt) REVERT: Q 204 LEU cc_start: 0.9217 (mt) cc_final: 0.8937 (mt) REVERT: Q 226 MET cc_start: 0.9139 (mmp) cc_final: 0.8903 (mmp) REVERT: R 31 MET cc_start: 0.8794 (mmm) cc_final: 0.8504 (mmm) REVERT: R 193 MET cc_start: 0.8883 (ttp) cc_final: 0.8256 (ttt) REVERT: R 204 LEU cc_start: 0.9192 (mt) cc_final: 0.8942 (mt) REVERT: R 226 MET cc_start: 0.9249 (mmt) cc_final: 0.8803 (mmt) REVERT: S 31 MET cc_start: 0.8869 (mmm) cc_final: 0.8644 (mmm) REVERT: S 184 ASN cc_start: 0.9444 (m-40) cc_final: 0.9177 (m110) REVERT: S 193 MET cc_start: 0.9037 (ttp) cc_final: 0.8447 (ttt) REVERT: S 204 LEU cc_start: 0.9169 (mt) cc_final: 0.8891 (mt) REVERT: T 31 MET cc_start: 0.8871 (mmm) cc_final: 0.8594 (mmm) REVERT: T 141 MET cc_start: 0.9055 (tmm) cc_final: 0.8787 (tmm) REVERT: T 154 PHE cc_start: 0.8919 (m-10) cc_final: 0.8592 (m-10) REVERT: T 184 ASN cc_start: 0.9328 (m-40) cc_final: 0.9049 (m110) REVERT: T 193 MET cc_start: 0.8891 (ttp) cc_final: 0.8154 (ttt) REVERT: T 204 LEU cc_start: 0.9209 (mt) cc_final: 0.8954 (mt) REVERT: V 31 MET cc_start: 0.9384 (mmp) cc_final: 0.8977 (mmm) REVERT: V 158 MET cc_start: 0.9169 (ttm) cc_final: 0.8737 (ttm) REVERT: V 193 MET cc_start: 0.9245 (ttp) cc_final: 0.8502 (ttt) REVERT: W 31 MET cc_start: 0.8808 (mmm) cc_final: 0.8499 (mmm) REVERT: W 193 MET cc_start: 0.8869 (ttp) cc_final: 0.8318 (ttt) REVERT: W 204 LEU cc_start: 0.9159 (mt) cc_final: 0.8926 (mt) REVERT: W 226 MET cc_start: 0.9232 (mmt) cc_final: 0.8923 (mmt) REVERT: X 31 MET cc_start: 0.9386 (mmp) cc_final: 0.9025 (mmm) REVERT: X 184 ASN cc_start: 0.9559 (m-40) cc_final: 0.9311 (m-40) REVERT: X 192 MET cc_start: 0.9064 (mmm) cc_final: 0.8775 (mmm) REVERT: X 193 MET cc_start: 0.9275 (ttp) cc_final: 0.8345 (ttt) REVERT: X 194 TYR cc_start: 0.9048 (m-10) cc_final: 0.8758 (m-10) REVERT: Y 31 MET cc_start: 0.9449 (mmp) cc_final: 0.9035 (mmm) REVERT: Y 192 MET cc_start: 0.9209 (mmm) cc_final: 0.8894 (mmm) REVERT: Y 193 MET cc_start: 0.9184 (ttp) cc_final: 0.8315 (ttt) REVERT: Y 226 MET cc_start: 0.9049 (mmt) cc_final: 0.8762 (mmt) outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.2335 time to fit residues: 185.2698 Evaluate side-chains 335 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 158 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 526 optimal weight: 0.9980 chunk 447 optimal weight: 0.7980 chunk 489 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 364 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 435 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.3014 r_free = 0.3014 target = 0.041389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.033021 restraints weight = 311227.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.034151 restraints weight = 186334.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.034976 restraints weight = 129341.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.035562 restraints weight = 98832.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.035981 restraints weight = 80876.674| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 42864 Z= 0.161 Angle : 0.597 5.700 57768 Z= 0.320 Chirality : 0.042 0.137 6888 Planarity : 0.003 0.022 7344 Dihedral : 5.462 19.756 5952 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: 1.60 (0.12), residues: 5424 helix: 1.63 (0.11), residues: 2160 sheet: -0.22 (0.14), residues: 1104 loop : 1.48 (0.16), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 68 TYR 0.010 0.001 TYR T 219 PHE 0.015 0.002 PHE Q 154 HIS 0.005 0.001 HIS L 174 Details of bonding type rmsd covalent geometry : bond 0.00313 (42864) covalent geometry : angle 0.59685 (57768) hydrogen bonds : bond 0.03774 ( 2664) hydrogen bonds : angle 4.30139 ( 7200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 MET cc_start: 0.8766 (ppp) cc_final: 0.8368 (ppp) REVERT: B 28 GLU cc_start: 0.9063 (pt0) cc_final: 0.8617 (tt0) REVERT: B 31 MET cc_start: 0.9397 (mmp) cc_final: 0.9065 (mmm) REVERT: B 193 MET cc_start: 0.9158 (ttp) cc_final: 0.8472 (ttt) REVERT: A 5 MET cc_start: 0.8775 (ppp) cc_final: 0.8435 (ppp) REVERT: A 31 MET cc_start: 0.9256 (mmp) cc_final: 0.8964 (mmm) REVERT: A 193 MET cc_start: 0.9297 (ttp) cc_final: 0.8352 (ttt) REVERT: A 226 MET cc_start: 0.9177 (mmt) cc_final: 0.8951 (mmt) REVERT: C 5 MET cc_start: 0.8683 (ppp) cc_final: 0.8408 (ppp) REVERT: C 31 MET cc_start: 0.9384 (mmp) cc_final: 0.8919 (mmm) REVERT: C 192 MET cc_start: 0.8965 (mmm) cc_final: 0.8755 (mmm) REVERT: C 193 MET cc_start: 0.9342 (ttp) cc_final: 0.8888 (ttt) REVERT: D 5 MET cc_start: 0.8579 (ppp) cc_final: 0.8370 (ppp) REVERT: D 31 MET cc_start: 0.9405 (mmp) cc_final: 0.8955 (mmm) REVERT: D 184 ASN cc_start: 0.9691 (m-40) cc_final: 0.9489 (m110) REVERT: D 192 MET cc_start: 0.9171 (mmp) cc_final: 0.8850 (mmm) REVERT: D 193 MET cc_start: 0.9252 (ttp) cc_final: 0.8239 (ttt) REVERT: D 226 MET cc_start: 0.9042 (mmt) cc_final: 0.8791 (mmt) REVERT: E 5 MET cc_start: 0.8721 (ppp) cc_final: 0.8488 (ppp) REVERT: E 31 MET cc_start: 0.8837 (mmm) cc_final: 0.8571 (mmm) REVERT: E 184 ASN cc_start: 0.9476 (m-40) cc_final: 0.9220 (m110) REVERT: E 193 MET cc_start: 0.9024 (ttp) cc_final: 0.8415 (ttt) REVERT: E 226 MET cc_start: 0.9262 (mmt) cc_final: 0.8896 (mmt) REVERT: F 5 MET cc_start: 0.8440 (ppp) cc_final: 0.8206 (ppp) REVERT: F 28 GLU cc_start: 0.8914 (pt0) cc_final: 0.8324 (tt0) REVERT: F 31 MET cc_start: 0.9451 (mmp) cc_final: 0.8986 (mmm) REVERT: F 184 ASN cc_start: 0.9693 (m-40) cc_final: 0.9479 (m110) REVERT: F 193 MET cc_start: 0.9317 (ttp) cc_final: 0.8297 (ttt) REVERT: G 5 MET cc_start: 0.8738 (ppp) cc_final: 0.8445 (ppp) REVERT: G 31 MET cc_start: 0.8748 (mmm) cc_final: 0.8483 (mmm) REVERT: G 193 MET cc_start: 0.9029 (ttp) cc_final: 0.8394 (ttt) REVERT: G 226 MET cc_start: 0.9181 (mmt) cc_final: 0.8835 (mmt) REVERT: H 5 MET cc_start: 0.8549 (ppp) cc_final: 0.8312 (ppp) REVERT: H 31 MET cc_start: 0.9271 (mmp) cc_final: 0.8843 (mmm) REVERT: H 192 MET cc_start: 0.9100 (mmp) cc_final: 0.8818 (mmm) REVERT: H 193 MET cc_start: 0.9259 (ttp) cc_final: 0.8326 (ttt) REVERT: I 5 MET cc_start: 0.9259 (ptm) cc_final: 0.8887 (ppp) REVERT: I 31 MET cc_start: 0.9416 (mmp) cc_final: 0.9030 (mmm) REVERT: I 184 ASN cc_start: 0.9654 (m-40) cc_final: 0.9437 (m110) REVERT: I 193 MET cc_start: 0.9290 (ttp) cc_final: 0.8110 (ttt) REVERT: J 5 MET cc_start: 0.8819 (ppp) cc_final: 0.8471 (ppp) REVERT: J 28 GLU cc_start: 0.9091 (pt0) cc_final: 0.8566 (tt0) REVERT: J 31 MET cc_start: 0.9321 (mmp) cc_final: 0.9022 (mmm) REVERT: J 193 MET cc_start: 0.9242 (ttp) cc_final: 0.8507 (ttt) REVERT: J 226 MET cc_start: 0.9021 (mmt) cc_final: 0.8771 (mmt) REVERT: K 5 MET cc_start: 0.8556 (ppp) cc_final: 0.8322 (ppp) REVERT: K 31 MET cc_start: 0.9438 (mmp) cc_final: 0.9040 (mmm) REVERT: K 158 MET cc_start: 0.9282 (ttp) cc_final: 0.8909 (ttm) REVERT: K 192 MET cc_start: 0.9193 (mmm) cc_final: 0.8875 (mmm) REVERT: K 193 MET cc_start: 0.9371 (ttp) cc_final: 0.8574 (ttt) REVERT: L 5 MET cc_start: 0.9154 (ptm) cc_final: 0.8810 (ppp) REVERT: L 31 MET cc_start: 0.8941 (mmm) cc_final: 0.8682 (mmm) REVERT: L 192 MET cc_start: 0.9040 (mmm) cc_final: 0.8792 (mmm) REVERT: L 194 TYR cc_start: 0.9314 (m-80) cc_final: 0.7837 (m-80) REVERT: M 5 MET cc_start: 0.8510 (ppp) cc_final: 0.8269 (ppp) REVERT: M 31 MET cc_start: 0.9409 (mmp) cc_final: 0.9000 (mmm) REVERT: M 192 MET cc_start: 0.9320 (mmp) cc_final: 0.9113 (mmm) REVERT: M 193 MET cc_start: 0.9353 (ttp) cc_final: 0.8609 (ttt) REVERT: N 5 MET cc_start: 0.8570 (ppp) cc_final: 0.8295 (ppp) REVERT: N 28 GLU cc_start: 0.8846 (pt0) cc_final: 0.8419 (tt0) REVERT: N 31 MET cc_start: 0.9453 (mmp) cc_final: 0.9007 (mmm) REVERT: N 158 MET cc_start: 0.9140 (ttm) cc_final: 0.8727 (ttm) REVERT: N 184 ASN cc_start: 0.9601 (m-40) cc_final: 0.9381 (m110) REVERT: N 193 MET cc_start: 0.9330 (ttp) cc_final: 0.8292 (ttt) REVERT: N 226 MET cc_start: 0.9170 (mmt) cc_final: 0.8926 (mmt) REVERT: O 5 MET cc_start: 0.8708 (ppp) cc_final: 0.8401 (ppp) REVERT: O 184 ASN cc_start: 0.9563 (m-40) cc_final: 0.9342 (m110) REVERT: O 192 MET cc_start: 0.9194 (mmp) cc_final: 0.8928 (mmm) REVERT: O 193 MET cc_start: 0.8849 (ttp) cc_final: 0.8359 (ttt) REVERT: O 226 MET cc_start: 0.9089 (mmp) cc_final: 0.8822 (mmp) REVERT: P 5 MET cc_start: 0.8581 (ppp) cc_final: 0.8301 (ppp) REVERT: P 31 MET cc_start: 0.9342 (mmp) cc_final: 0.8910 (mmm) REVERT: P 158 MET cc_start: 0.9408 (ttp) cc_final: 0.9021 (ttm) REVERT: P 192 MET cc_start: 0.9052 (mmp) cc_final: 0.8754 (mmm) REVERT: P 193 MET cc_start: 0.9292 (ttp) cc_final: 0.8437 (ttt) REVERT: Q 5 MET cc_start: 0.8907 (ppp) cc_final: 0.8546 (ppp) REVERT: Q 31 MET cc_start: 0.9253 (mmp) cc_final: 0.8900 (mmm) REVERT: Q 154 PHE cc_start: 0.9139 (m-10) cc_final: 0.8799 (m-10) REVERT: Q 193 MET cc_start: 0.9287 (ttp) cc_final: 0.8301 (ttt) REVERT: R 5 MET cc_start: 0.8782 (ppp) cc_final: 0.8418 (ppp) REVERT: R 31 MET cc_start: 0.8799 (mmm) cc_final: 0.8558 (mmm) REVERT: R 141 MET cc_start: 0.8993 (tmm) cc_final: 0.8755 (mmm) REVERT: R 193 MET cc_start: 0.9007 (ttp) cc_final: 0.8348 (ttt) REVERT: R 226 MET cc_start: 0.9120 (mmt) cc_final: 0.8725 (mmt) REVERT: S 5 MET cc_start: 0.8805 (ppp) cc_final: 0.8537 (ppp) REVERT: S 184 ASN cc_start: 0.9505 (m-40) cc_final: 0.9295 (m110) REVERT: S 193 MET cc_start: 0.8988 (ttp) cc_final: 0.8341 (ttt) REVERT: S 204 LEU cc_start: 0.9248 (mt) cc_final: 0.9037 (mt) REVERT: S 226 MET cc_start: 0.9078 (mmp) cc_final: 0.8781 (mmp) REVERT: T 5 MET cc_start: 0.8847 (ppp) cc_final: 0.8554 (ppp) REVERT: T 31 MET cc_start: 0.8909 (mmm) cc_final: 0.8675 (mmm) REVERT: T 141 MET cc_start: 0.9038 (tmm) cc_final: 0.8738 (tmm) REVERT: T 154 PHE cc_start: 0.9233 (m-10) cc_final: 0.8856 (m-10) REVERT: T 184 ASN cc_start: 0.9397 (m-40) cc_final: 0.9159 (m110) REVERT: T 193 MET cc_start: 0.9101 (ttp) cc_final: 0.8417 (ttt) REVERT: T 226 MET cc_start: 0.9115 (mmp) cc_final: 0.8877 (mmp) REVERT: V 5 MET cc_start: 0.8624 (ppp) cc_final: 0.8317 (ppp) REVERT: V 31 MET cc_start: 0.9326 (mmp) cc_final: 0.8929 (mmm) REVERT: V 158 MET cc_start: 0.9205 (ttm) cc_final: 0.8840 (ttm) REVERT: V 192 MET cc_start: 0.9170 (mmp) cc_final: 0.8859 (mmm) REVERT: V 193 MET cc_start: 0.9198 (ttp) cc_final: 0.8220 (ttt) REVERT: W 5 MET cc_start: 0.8776 (ppp) cc_final: 0.8412 (ppp) REVERT: W 31 MET cc_start: 0.8819 (mmm) cc_final: 0.8555 (mmm) REVERT: W 141 MET cc_start: 0.8926 (tmm) cc_final: 0.8702 (mmm) REVERT: W 192 MET cc_start: 0.9279 (mmp) cc_final: 0.8817 (mmm) REVERT: W 193 MET cc_start: 0.9096 (ttp) cc_final: 0.8536 (ttt) REVERT: W 226 MET cc_start: 0.9256 (mmt) cc_final: 0.8890 (mmt) REVERT: X 5 MET cc_start: 0.8765 (ppp) cc_final: 0.8460 (ppp) REVERT: X 28 GLU cc_start: 0.9026 (pt0) cc_final: 0.8602 (tt0) REVERT: X 31 MET cc_start: 0.9259 (mmp) cc_final: 0.8979 (mmm) REVERT: X 184 ASN cc_start: 0.9563 (m-40) cc_final: 0.9336 (m110) REVERT: X 193 MET cc_start: 0.9339 (ttp) cc_final: 0.8541 (ttt) REVERT: X 226 MET cc_start: 0.9106 (mmp) cc_final: 0.8874 (mmp) REVERT: Y 5 MET cc_start: 0.8602 (ppp) cc_final: 0.8327 (ppp) REVERT: Y 31 MET cc_start: 0.9426 (mmp) cc_final: 0.9052 (mmm) REVERT: Y 193 MET cc_start: 0.9292 (ttp) cc_final: 0.8828 (ttt) REVERT: Y 226 MET cc_start: 0.9031 (mmt) cc_final: 0.8783 (mmt) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.2259 time to fit residues: 158.2357 Evaluate side-chains 311 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 154 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 429 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 211 optimal weight: 0.0170 chunk 188 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- 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 = 0.3007 r_free = 0.3007 target = 0.040942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.032630 restraints weight = 309946.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.033733 restraints weight = 188490.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.034546 restraints weight = 132522.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.035122 restraints weight = 101528.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.035535 restraints weight = 83266.658| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 42864 Z= 0.144 Angle : 0.555 6.519 57768 Z= 0.300 Chirality : 0.041 0.137 6888 Planarity : 0.003 0.022 7344 Dihedral : 5.049 18.810 5952 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: 1.78 (0.12), residues: 5424 helix: 1.79 (0.11), residues: 2160 sheet: -0.24 (0.14), residues: 1104 loop : 1.64 (0.16), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 68 TYR 0.030 0.001 TYR Y 194 PHE 0.013 0.001 PHE Q 154 HIS 0.005 0.002 HIS J 174 Details of bonding type rmsd covalent geometry : bond 0.00281 (42864) covalent geometry : angle 0.55507 (57768) hydrogen bonds : bond 0.03323 ( 2664) hydrogen bonds : angle 4.23981 ( 7200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 MET cc_start: 0.8865 (ppp) cc_final: 0.8472 (ppp) REVERT: B 31 MET cc_start: 0.9246 (mmp) cc_final: 0.9003 (mmm) REVERT: B 193 MET cc_start: 0.9312 (ttp) cc_final: 0.8346 (ttt) REVERT: A 5 MET cc_start: 0.8815 (ppp) cc_final: 0.8497 (ppp) REVERT: A 31 MET cc_start: 0.9210 (mmp) cc_final: 0.8998 (mmm) REVERT: A 184 ASN cc_start: 0.9624 (m-40) cc_final: 0.9402 (m110) REVERT: A 193 MET cc_start: 0.9154 (ttp) cc_final: 0.7875 (ttt) REVERT: A 226 MET cc_start: 0.9104 (mmt) cc_final: 0.8899 (mmt) REVERT: C 5 MET cc_start: 0.8764 (ppp) cc_final: 0.8479 (ppp) REVERT: C 31 MET cc_start: 0.9326 (mmp) cc_final: 0.8898 (mmm) REVERT: C 193 MET cc_start: 0.9251 (ttp) cc_final: 0.8459 (ttt) REVERT: C 226 MET cc_start: 0.8779 (mpp) cc_final: 0.8491 (mmt) REVERT: D 5 MET cc_start: 0.8666 (ppp) cc_final: 0.8444 (ppp) REVERT: D 31 MET cc_start: 0.9395 (mmp) cc_final: 0.8978 (mmm) REVERT: D 193 MET cc_start: 0.8727 (ttp) cc_final: 0.8449 (ttt) REVERT: E 5 MET cc_start: 0.8808 (ppp) cc_final: 0.8522 (ppp) REVERT: E 26 PHE cc_start: 0.8727 (m-80) cc_final: 0.8519 (m-80) REVERT: E 31 MET cc_start: 0.8832 (mmm) cc_final: 0.8560 (mmm) REVERT: E 184 ASN cc_start: 0.9536 (m-40) cc_final: 0.9294 (m110) REVERT: E 193 MET cc_start: 0.9045 (ttp) cc_final: 0.8432 (ttt) REVERT: E 226 MET cc_start: 0.9212 (mmt) cc_final: 0.8905 (mmt) REVERT: F 5 MET cc_start: 0.8558 (ppp) cc_final: 0.8255 (ppp) REVERT: F 31 MET cc_start: 0.9298 (mmp) cc_final: 0.8964 (mmm) REVERT: F 193 MET cc_start: 0.9377 (ttp) cc_final: 0.8370 (ttt) REVERT: G 5 MET cc_start: 0.8822 (ppp) cc_final: 0.8486 (ppp) REVERT: G 31 MET cc_start: 0.8744 (mmm) cc_final: 0.8442 (mmm) REVERT: G 158 MET cc_start: 0.9397 (ttp) cc_final: 0.9189 (ptm) REVERT: G 193 MET cc_start: 0.8981 (ttp) cc_final: 0.8300 (ttt) REVERT: G 226 MET cc_start: 0.9172 (mmt) cc_final: 0.8856 (mmt) REVERT: H 5 MET cc_start: 0.8677 (ppp) cc_final: 0.8444 (ppp) REVERT: H 31 MET cc_start: 0.9325 (mmp) cc_final: 0.9003 (mmm) REVERT: H 158 MET cc_start: 0.9523 (ptm) cc_final: 0.8995 (ptm) REVERT: H 192 MET cc_start: 0.9351 (mmp) cc_final: 0.8947 (mmm) REVERT: H 193 MET cc_start: 0.9233 (ttp) cc_final: 0.8677 (ttt) REVERT: I 5 MET cc_start: 0.9314 (ptm) cc_final: 0.9093 (ppp) REVERT: I 31 MET cc_start: 0.9394 (mmp) cc_final: 0.9033 (mmm) REVERT: I 184 ASN cc_start: 0.9677 (m-40) cc_final: 0.9472 (m110) REVERT: I 192 MET cc_start: 0.8719 (mmm) cc_final: 0.8382 (mmm) REVERT: I 193 MET cc_start: 0.9233 (ttp) cc_final: 0.8188 (ttt) REVERT: J 5 MET cc_start: 0.8855 (ppp) cc_final: 0.8515 (ppp) REVERT: J 31 MET cc_start: 0.9186 (mmp) cc_final: 0.8971 (mmm) REVERT: J 193 MET cc_start: 0.9341 (ttp) cc_final: 0.8475 (ttt) REVERT: J 226 MET cc_start: 0.9074 (mmt) cc_final: 0.8776 (mpp) REVERT: K 5 MET cc_start: 0.8672 (ppp) cc_final: 0.8445 (ppp) REVERT: K 28 GLU cc_start: 0.9004 (pt0) cc_final: 0.8469 (tt0) REVERT: K 31 MET cc_start: 0.9347 (mmp) cc_final: 0.8892 (mmm) REVERT: K 158 MET cc_start: 0.9347 (ttp) cc_final: 0.9020 (ttm) REVERT: K 193 MET cc_start: 0.9345 (ttp) cc_final: 0.8400 (ttt) REVERT: L 193 MET cc_start: 0.8195 (ttt) cc_final: 0.7592 (ttt) REVERT: L 194 TYR cc_start: 0.9179 (m-80) cc_final: 0.8910 (m-10) REVERT: M 5 MET cc_start: 0.8634 (ppp) cc_final: 0.8379 (ppp) REVERT: M 31 MET cc_start: 0.9392 (mmp) cc_final: 0.8919 (mmm) REVERT: M 46 LEU cc_start: 0.9857 (tp) cc_final: 0.9641 (mt) REVERT: M 193 MET cc_start: 0.9223 (ttp) cc_final: 0.8417 (ttt) REVERT: N 5 MET cc_start: 0.8696 (ppp) cc_final: 0.8382 (ppp) REVERT: N 31 MET cc_start: 0.9417 (mmp) cc_final: 0.8985 (mmm) REVERT: N 184 ASN cc_start: 0.9634 (m-40) cc_final: 0.9429 (m110) REVERT: N 193 MET cc_start: 0.9300 (ttp) cc_final: 0.8257 (ttt) REVERT: O 5 MET cc_start: 0.8806 (ppp) cc_final: 0.8449 (ppp) REVERT: O 31 MET cc_start: 0.9293 (mmp) cc_final: 0.8935 (mmm) REVERT: O 184 ASN cc_start: 0.9586 (m-40) cc_final: 0.9366 (m110) REVERT: O 193 MET cc_start: 0.9157 (ttp) cc_final: 0.8209 (ttt) REVERT: O 226 MET cc_start: 0.9054 (mmp) cc_final: 0.8774 (mmp) REVERT: P 5 MET cc_start: 0.8732 (ppp) cc_final: 0.8457 (ppp) REVERT: P 31 MET cc_start: 0.9303 (mmp) cc_final: 0.8963 (mmm) REVERT: P 158 MET cc_start: 0.9424 (ttp) cc_final: 0.9054 (ttm) REVERT: P 192 MET cc_start: 0.9298 (mmp) cc_final: 0.8897 (mmm) REVERT: P 193 MET cc_start: 0.9258 (ttp) cc_final: 0.8542 (ttt) REVERT: Q 5 MET cc_start: 0.8933 (ppp) cc_final: 0.8575 (ppp) REVERT: Q 31 MET cc_start: 0.9242 (mmp) cc_final: 0.8967 (mmm) REVERT: Q 184 ASN cc_start: 0.9531 (m-40) cc_final: 0.9325 (m110) REVERT: Q 193 MET cc_start: 0.9249 (ttp) cc_final: 0.7924 (ttt) REVERT: R 5 MET cc_start: 0.8787 (ppp) cc_final: 0.8511 (ppp) REVERT: R 26 PHE cc_start: 0.9054 (m-80) cc_final: 0.8685 (m-80) REVERT: R 31 MET cc_start: 0.8770 (mmm) cc_final: 0.8555 (mmm) REVERT: R 193 MET cc_start: 0.8967 (ttp) cc_final: 0.8326 (ttt) REVERT: R 226 MET cc_start: 0.9093 (mmt) cc_final: 0.8709 (mpp) REVERT: S 5 MET cc_start: 0.8838 (ppp) cc_final: 0.8560 (ppp) REVERT: S 31 MET cc_start: 0.9237 (mmp) cc_final: 0.8903 (mmm) REVERT: S 184 ASN cc_start: 0.9561 (m-40) cc_final: 0.9357 (m110) REVERT: S 192 MET cc_start: 0.9348 (mmm) cc_final: 0.9022 (mmm) REVERT: S 193 MET cc_start: 0.9289 (ttp) cc_final: 0.8240 (ttt) REVERT: S 204 LEU cc_start: 0.9238 (mt) cc_final: 0.9017 (mt) REVERT: S 226 MET cc_start: 0.9110 (mmp) cc_final: 0.8817 (mmp) REVERT: T 5 MET cc_start: 0.8953 (ppp) cc_final: 0.8611 (ppp) REVERT: T 31 MET cc_start: 0.8874 (mmm) cc_final: 0.8640 (mmm) REVERT: T 141 MET cc_start: 0.8989 (tmm) cc_final: 0.8603 (tmm) REVERT: T 154 PHE cc_start: 0.9308 (m-10) cc_final: 0.8891 (m-10) REVERT: T 184 ASN cc_start: 0.9484 (m-40) cc_final: 0.9275 (m110) REVERT: T 192 MET cc_start: 0.9355 (mmm) cc_final: 0.9152 (mmm) REVERT: T 193 MET cc_start: 0.8885 (ttp) cc_final: 0.8345 (ttt) REVERT: T 226 MET cc_start: 0.9119 (mmp) cc_final: 0.8903 (mmp) REVERT: V 5 MET cc_start: 0.8731 (ppp) cc_final: 0.8374 (ppp) REVERT: V 31 MET cc_start: 0.9377 (mmp) cc_final: 0.8965 (mmm) REVERT: V 193 MET cc_start: 0.8826 (ttp) cc_final: 0.8566 (ttt) REVERT: W 5 MET cc_start: 0.8770 (ppp) cc_final: 0.8495 (ppp) REVERT: W 31 MET cc_start: 0.8698 (mmm) cc_final: 0.8488 (mmm) REVERT: W 193 MET cc_start: 0.8961 (ttp) cc_final: 0.8573 (ttt) REVERT: W 226 MET cc_start: 0.9190 (mmt) cc_final: 0.8807 (mmt) REVERT: X 5 MET cc_start: 0.8801 (ppp) cc_final: 0.8486 (ppp) REVERT: X 31 MET cc_start: 0.9216 (mmp) cc_final: 0.9010 (mmm) REVERT: X 184 ASN cc_start: 0.9582 (m-40) cc_final: 0.9357 (m110) REVERT: X 193 MET cc_start: 0.9339 (ttp) cc_final: 0.8475 (ttt) REVERT: Y 5 MET cc_start: 0.8730 (ppp) cc_final: 0.8384 (ppp) REVERT: Y 31 MET cc_start: 0.9338 (mmp) cc_final: 0.9030 (mmm) REVERT: Y 192 MET cc_start: 0.9139 (mmp) cc_final: 0.8645 (mmm) REVERT: Y 193 MET cc_start: 0.9431 (ttp) cc_final: 0.8511 (ttt) REVERT: Y 194 TYR cc_start: 0.8917 (m-80) cc_final: 0.8530 (m-10) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.2251 time to fit residues: 153.0488 Evaluate side-chains 320 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 371 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 344 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 376 optimal weight: 10.0000 chunk 493 optimal weight: 4.9990 chunk 349 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 287 optimal weight: 4.9990 chunk 300 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.039742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031767 restraints weight = 317616.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.032854 restraints weight = 193012.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.033652 restraints weight = 135046.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.034207 restraints weight = 103159.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.034585 restraints weight = 84205.347| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 42864 Z= 0.207 Angle : 0.612 5.891 57768 Z= 0.323 Chirality : 0.041 0.140 6888 Planarity : 0.003 0.025 7344 Dihedral : 5.009 19.312 5952 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: 1.66 (0.12), residues: 5424 helix: 1.78 (0.11), residues: 2160 sheet: -0.35 (0.14), residues: 1104 loop : 1.49 (0.16), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 6 TYR 0.013 0.002 TYR B 41 PHE 0.015 0.002 PHE S 26 HIS 0.006 0.001 HIS S 174 Details of bonding type rmsd covalent geometry : bond 0.00404 (42864) covalent geometry : angle 0.61196 (57768) hydrogen bonds : bond 0.03379 ( 2664) hydrogen bonds : angle 4.31577 ( 7200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 MET cc_start: 0.8907 (ppp) cc_final: 0.8508 (ppp) REVERT: B 31 MET cc_start: 0.9219 (mmp) cc_final: 0.8975 (mmm) REVERT: B 192 MET cc_start: 0.8978 (mmm) cc_final: 0.8676 (mmm) REVERT: B 193 MET cc_start: 0.9326 (ttp) cc_final: 0.8416 (ttt) REVERT: A 5 MET cc_start: 0.8881 (ppp) cc_final: 0.8525 (ppp) REVERT: A 31 MET cc_start: 0.9219 (mmp) cc_final: 0.9009 (mmm) REVERT: A 192 MET cc_start: 0.8983 (mmm) cc_final: 0.8634 (mmm) REVERT: A 193 MET cc_start: 0.9232 (ttp) cc_final: 0.8320 (ttt) REVERT: C 5 MET cc_start: 0.8850 (ppp) cc_final: 0.8513 (ppp) REVERT: C 31 MET cc_start: 0.9316 (mmp) cc_final: 0.8892 (mmm) REVERT: C 46 LEU cc_start: 0.9867 (tp) cc_final: 0.9658 (mt) REVERT: C 193 MET cc_start: 0.9263 (ttp) cc_final: 0.8382 (ttt) REVERT: D 5 MET cc_start: 0.8756 (ppp) cc_final: 0.8481 (ppp) REVERT: D 31 MET cc_start: 0.9330 (mmp) cc_final: 0.8917 (mmm) REVERT: E 5 MET cc_start: 0.8862 (ppp) cc_final: 0.8552 (ppp) REVERT: E 31 MET cc_start: 0.8818 (mmm) cc_final: 0.8576 (mmm) REVERT: E 184 ASN cc_start: 0.9535 (m-40) cc_final: 0.9329 (m110) REVERT: E 193 MET cc_start: 0.8976 (ttp) cc_final: 0.8221 (ttt) REVERT: E 226 MET cc_start: 0.9171 (mmt) cc_final: 0.8844 (mmt) REVERT: F 5 MET cc_start: 0.8700 (ppp) cc_final: 0.8340 (ppp) REVERT: F 31 MET cc_start: 0.9386 (mmp) cc_final: 0.9099 (mmm) REVERT: F 192 MET cc_start: 0.8864 (mmm) cc_final: 0.8509 (mmm) REVERT: F 193 MET cc_start: 0.9356 (ttp) cc_final: 0.8352 (ttt) REVERT: G 5 MET cc_start: 0.8862 (ppp) cc_final: 0.8503 (ppp) REVERT: G 31 MET cc_start: 0.8741 (mmm) cc_final: 0.8479 (mmm) REVERT: G 192 MET cc_start: 0.9416 (mmp) cc_final: 0.9030 (mmm) REVERT: G 193 MET cc_start: 0.8961 (ttp) cc_final: 0.8244 (ttt) REVERT: G 226 MET cc_start: 0.9060 (mmt) cc_final: 0.8703 (mmt) REVERT: H 5 MET cc_start: 0.8783 (ppp) cc_final: 0.8478 (ppp) REVERT: H 31 MET cc_start: 0.9298 (mmp) cc_final: 0.8987 (mmm) REVERT: H 158 MET cc_start: 0.9566 (ptm) cc_final: 0.9148 (ptm) REVERT: H 192 MET cc_start: 0.9287 (mmp) cc_final: 0.9006 (mmm) REVERT: I 31 MET cc_start: 0.9363 (mmp) cc_final: 0.9046 (mmm) REVERT: I 192 MET cc_start: 0.8989 (mmm) cc_final: 0.8623 (mmm) REVERT: I 193 MET cc_start: 0.9320 (ttp) cc_final: 0.8162 (ttt) REVERT: J 5 MET cc_start: 0.8905 (ppp) cc_final: 0.8552 (ppp) REVERT: J 31 MET cc_start: 0.9195 (mmp) cc_final: 0.8954 (mmm) REVERT: J 192 MET cc_start: 0.8912 (mmm) cc_final: 0.8627 (mmm) REVERT: J 193 MET cc_start: 0.9342 (ttp) cc_final: 0.8412 (ttt) REVERT: K 5 MET cc_start: 0.8754 (ppp) cc_final: 0.8462 (ppp) REVERT: K 31 MET cc_start: 0.9332 (mmp) cc_final: 0.9039 (mmm) REVERT: K 158 MET cc_start: 0.9333 (ttp) cc_final: 0.9109 (ttm) REVERT: K 192 MET cc_start: 0.9269 (mmp) cc_final: 0.9045 (mmm) REVERT: K 193 MET cc_start: 0.9369 (ttp) cc_final: 0.8306 (ttt) REVERT: L 31 MET cc_start: 0.9227 (mmp) cc_final: 0.8836 (mmm) REVERT: L 193 MET cc_start: 0.8460 (ttt) cc_final: 0.7740 (ttt) REVERT: M 5 MET cc_start: 0.8758 (ppp) cc_final: 0.8432 (ppp) REVERT: M 31 MET cc_start: 0.9332 (mmp) cc_final: 0.8920 (mmm) REVERT: M 192 MET cc_start: 0.8914 (mmm) cc_final: 0.8654 (mmm) REVERT: M 193 MET cc_start: 0.9224 (ttp) cc_final: 0.8402 (ttt) REVERT: N 5 MET cc_start: 0.8792 (ppp) cc_final: 0.8444 (ppp) REVERT: N 31 MET cc_start: 0.9275 (mmp) cc_final: 0.8995 (mmm) REVERT: N 192 MET cc_start: 0.8915 (mmm) cc_final: 0.8544 (mmm) REVERT: N 193 MET cc_start: 0.9334 (ttp) cc_final: 0.8293 (ttt) REVERT: O 5 MET cc_start: 0.8859 (ppp) cc_final: 0.8481 (ppp) REVERT: O 31 MET cc_start: 0.9177 (mmp) cc_final: 0.8915 (mmm) REVERT: O 193 MET cc_start: 0.9005 (ttp) cc_final: 0.8161 (ttt) REVERT: O 226 MET cc_start: 0.9082 (mmp) cc_final: 0.8848 (mmp) REVERT: P 5 MET cc_start: 0.8807 (ppp) cc_final: 0.8442 (ppp) REVERT: P 31 MET cc_start: 0.9300 (mmp) cc_final: 0.8983 (mmm) REVERT: P 158 MET cc_start: 0.9325 (ttp) cc_final: 0.9021 (ttm) REVERT: P 184 ASN cc_start: 0.9725 (m-40) cc_final: 0.9524 (m-40) REVERT: P 192 MET cc_start: 0.9197 (mmp) cc_final: 0.8865 (mmm) REVERT: P 193 MET cc_start: 0.9127 (ttp) cc_final: 0.8735 (ttt) REVERT: Q 5 MET cc_start: 0.8953 (ppp) cc_final: 0.8587 (ppp) REVERT: Q 31 MET cc_start: 0.9240 (mmp) cc_final: 0.8964 (mmm) REVERT: Q 154 PHE cc_start: 0.9215 (m-10) cc_final: 0.8893 (m-10) REVERT: Q 184 ASN cc_start: 0.9584 (m-40) cc_final: 0.9377 (m110) REVERT: Q 192 MET cc_start: 0.9357 (mmp) cc_final: 0.9136 (mmm) REVERT: Q 193 MET cc_start: 0.9286 (ttp) cc_final: 0.8075 (ttt) REVERT: R 5 MET cc_start: 0.8892 (ppp) cc_final: 0.8552 (ppp) REVERT: R 31 MET cc_start: 0.8778 (mmm) cc_final: 0.8569 (mmm) REVERT: R 193 MET cc_start: 0.9007 (ttp) cc_final: 0.8265 (ttt) REVERT: R 226 MET cc_start: 0.9069 (mmt) cc_final: 0.8806 (mmt) REVERT: S 5 MET cc_start: 0.8878 (ppp) cc_final: 0.8542 (ppp) REVERT: S 31 MET cc_start: 0.9232 (mmp) cc_final: 0.8966 (mmm) REVERT: S 184 ASN cc_start: 0.9557 (m-40) cc_final: 0.9344 (m110) REVERT: S 193 MET cc_start: 0.9350 (ttp) cc_final: 0.8324 (ttt) REVERT: S 204 LEU cc_start: 0.9222 (mt) cc_final: 0.8959 (mp) REVERT: T 5 MET cc_start: 0.8965 (ppp) cc_final: 0.8606 (ppp) REVERT: T 154 PHE cc_start: 0.9349 (m-10) cc_final: 0.8910 (m-10) REVERT: T 184 ASN cc_start: 0.9508 (m-40) cc_final: 0.9270 (m110) REVERT: T 192 MET cc_start: 0.9495 (mmm) cc_final: 0.9260 (mmm) REVERT: T 193 MET cc_start: 0.8798 (ttp) cc_final: 0.8057 (ttt) REVERT: V 5 MET cc_start: 0.8813 (ppp) cc_final: 0.8428 (ppp) REVERT: V 31 MET cc_start: 0.9320 (mmp) cc_final: 0.8962 (mmm) REVERT: V 193 MET cc_start: 0.8638 (ttp) cc_final: 0.8355 (ttt) REVERT: W 5 MET cc_start: 0.8878 (ppp) cc_final: 0.8546 (ppp) REVERT: W 193 MET cc_start: 0.8990 (ttp) cc_final: 0.8489 (ttt) REVERT: W 226 MET cc_start: 0.9122 (mmt) cc_final: 0.8739 (mmt) REVERT: X 5 MET cc_start: 0.8855 (ppp) cc_final: 0.8543 (ppp) REVERT: X 31 MET cc_start: 0.9225 (mmp) cc_final: 0.8995 (mmm) REVERT: X 192 MET cc_start: 0.8793 (mmm) cc_final: 0.8432 (mmm) REVERT: X 193 MET cc_start: 0.9331 (ttp) cc_final: 0.8513 (ttt) REVERT: X 226 MET cc_start: 0.9096 (mmp) cc_final: 0.8821 (mmp) REVERT: Y 5 MET cc_start: 0.8805 (ppp) cc_final: 0.8435 (ppp) REVERT: Y 31 MET cc_start: 0.9383 (mmp) cc_final: 0.9067 (mmm) REVERT: Y 192 MET cc_start: 0.9285 (mmp) cc_final: 0.9002 (mmm) REVERT: Y 193 MET cc_start: 0.9514 (ttp) cc_final: 0.8648 (ttt) REVERT: Y 194 TYR cc_start: 0.9159 (m-80) cc_final: 0.8761 (m-10) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.2225 time to fit residues: 145.1516 Evaluate side-chains 309 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 500 optimal weight: 2.9990 chunk 479 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 341 optimal weight: 2.9990 chunk 385 optimal weight: 6.9990 chunk 335 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.039826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031776 restraints weight = 312530.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.032885 restraints weight = 187586.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.033695 restraints weight = 130506.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.034263 restraints weight = 99365.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.034668 restraints weight = 80696.911| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 42864 Z= 0.156 Angle : 0.558 8.863 57768 Z= 0.299 Chirality : 0.041 0.140 6888 Planarity : 0.003 0.025 7344 Dihedral : 4.806 19.418 5952 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: 1.75 (0.12), residues: 5424 helix: 1.84 (0.11), residues: 2136 sheet: -0.33 (0.14), residues: 1104 loop : 1.57 (0.16), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 89 TYR 0.021 0.001 TYR P 194 PHE 0.010 0.001 PHE D 26 HIS 0.006 0.002 HIS S 174 Details of bonding type rmsd covalent geometry : bond 0.00304 (42864) covalent geometry : angle 0.55847 (57768) hydrogen bonds : bond 0.03136 ( 2664) hydrogen bonds : angle 4.28445 ( 7200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 MET cc_start: 0.8879 (ppp) cc_final: 0.8536 (ppp) REVERT: B 31 MET cc_start: 0.9366 (mmp) cc_final: 0.8976 (mmm) REVERT: B 193 MET cc_start: 0.9341 (ttp) cc_final: 0.8417 (ttt) REVERT: A 5 MET cc_start: 0.8926 (ppp) cc_final: 0.8557 (ppp) REVERT: A 31 MET cc_start: 0.9158 (mmp) cc_final: 0.8878 (mmm) REVERT: A 193 MET cc_start: 0.9251 (ttp) cc_final: 0.8105 (ttt) REVERT: C 5 MET cc_start: 0.8856 (ppp) cc_final: 0.8494 (ppp) REVERT: C 31 MET cc_start: 0.9364 (mmp) cc_final: 0.9025 (mmm) REVERT: C 192 MET cc_start: 0.9003 (mmm) cc_final: 0.8788 (mmm) REVERT: C 193 MET cc_start: 0.9230 (ttp) cc_final: 0.8389 (ttt) REVERT: C 226 MET cc_start: 0.8837 (mpp) cc_final: 0.8525 (mmt) REVERT: D 5 MET cc_start: 0.8823 (ppp) cc_final: 0.8535 (ppp) REVERT: D 31 MET cc_start: 0.9275 (mmp) cc_final: 0.8922 (mmm) REVERT: D 158 MET cc_start: 0.9499 (ptm) cc_final: 0.9015 (tmm) REVERT: D 193 MET cc_start: 0.8233 (ttt) cc_final: 0.7580 (ttt) REVERT: E 5 MET cc_start: 0.8871 (ppp) cc_final: 0.8537 (ppp) REVERT: E 193 MET cc_start: 0.8863 (ttp) cc_final: 0.8205 (ttt) REVERT: E 226 MET cc_start: 0.9171 (mmt) cc_final: 0.8763 (mmt) REVERT: F 5 MET cc_start: 0.8775 (ppp) cc_final: 0.8389 (ppp) REVERT: F 31 MET cc_start: 0.9375 (mmp) cc_final: 0.8952 (mmm) REVERT: F 193 MET cc_start: 0.9379 (ttp) cc_final: 0.8392 (ttt) REVERT: G 5 MET cc_start: 0.8884 (ppp) cc_final: 0.8517 (ppp) REVERT: G 31 MET cc_start: 0.8710 (mmm) cc_final: 0.8468 (mmm) REVERT: G 192 MET cc_start: 0.9356 (mmp) cc_final: 0.9011 (mmm) REVERT: G 193 MET cc_start: 0.8988 (ttp) cc_final: 0.8277 (ttt) REVERT: G 226 MET cc_start: 0.9017 (mmt) cc_final: 0.8667 (mpp) REVERT: H 5 MET cc_start: 0.8808 (ppp) cc_final: 0.8441 (ppp) REVERT: H 31 MET cc_start: 0.9261 (mmp) cc_final: 0.8979 (mmm) REVERT: H 193 MET cc_start: 0.8449 (ttt) cc_final: 0.7753 (ttt) REVERT: I 5 MET cc_start: 0.8768 (ppp) cc_final: 0.8567 (ppp) REVERT: I 31 MET cc_start: 0.9318 (mmp) cc_final: 0.8992 (mmm) REVERT: I 192 MET cc_start: 0.8995 (mmm) cc_final: 0.8643 (mmm) REVERT: I 193 MET cc_start: 0.9328 (ttp) cc_final: 0.8168 (ttt) REVERT: J 5 MET cc_start: 0.8897 (ppp) cc_final: 0.8534 (ppp) REVERT: J 28 GLU cc_start: 0.9514 (pp20) cc_final: 0.9300 (pm20) REVERT: J 31 MET cc_start: 0.9214 (mmp) cc_final: 0.8893 (mmm) REVERT: J 193 MET cc_start: 0.9364 (ttp) cc_final: 0.8449 (ttt) REVERT: K 5 MET cc_start: 0.8810 (ppp) cc_final: 0.8452 (ppp) REVERT: K 31 MET cc_start: 0.9315 (mmp) cc_final: 0.8978 (mmm) REVERT: K 192 MET cc_start: 0.9344 (mmp) cc_final: 0.9099 (mmm) REVERT: K 193 MET cc_start: 0.9351 (ttp) cc_final: 0.8364 (ttt) REVERT: L 31 MET cc_start: 0.9218 (mmp) cc_final: 0.8925 (mmm) REVERT: L 193 MET cc_start: 0.8502 (ttt) cc_final: 0.7708 (ttt) REVERT: M 5 MET cc_start: 0.8798 (ppp) cc_final: 0.8422 (ppp) REVERT: M 31 MET cc_start: 0.9371 (mmp) cc_final: 0.9022 (mmm) REVERT: M 193 MET cc_start: 0.9232 (ttp) cc_final: 0.8376 (ttt) REVERT: N 5 MET cc_start: 0.8833 (ppp) cc_final: 0.8430 (ppp) REVERT: N 31 MET cc_start: 0.9309 (mmp) cc_final: 0.8991 (mmm) REVERT: N 193 MET cc_start: 0.9348 (ttp) cc_final: 0.8316 (ttt) REVERT: O 5 MET cc_start: 0.8874 (ppp) cc_final: 0.8514 (ppp) REVERT: O 31 MET cc_start: 0.9232 (mmp) cc_final: 0.8944 (mmm) REVERT: O 193 MET cc_start: 0.8991 (ttp) cc_final: 0.8186 (ttt) REVERT: P 5 MET cc_start: 0.8821 (ppp) cc_final: 0.8424 (ppp) REVERT: P 31 MET cc_start: 0.9332 (mmp) cc_final: 0.9022 (mmm) REVERT: P 192 MET cc_start: 0.9189 (mmp) cc_final: 0.8911 (mmm) REVERT: P 193 MET cc_start: 0.9222 (ttp) cc_final: 0.8908 (ttt) REVERT: Q 5 MET cc_start: 0.8946 (ppp) cc_final: 0.8570 (ppp) REVERT: Q 31 MET cc_start: 0.9235 (mmp) cc_final: 0.8948 (mmm) REVERT: Q 193 MET cc_start: 0.9351 (ttp) cc_final: 0.8091 (ttt) REVERT: R 5 MET cc_start: 0.8880 (ppp) cc_final: 0.8546 (ppp) REVERT: R 26 PHE cc_start: 0.9118 (m-80) cc_final: 0.8861 (m-80) REVERT: R 192 MET cc_start: 0.9364 (mmp) cc_final: 0.8979 (mmm) REVERT: R 193 MET cc_start: 0.9025 (ttp) cc_final: 0.8394 (ttt) REVERT: R 226 MET cc_start: 0.9106 (mmt) cc_final: 0.8866 (mmt) REVERT: S 5 MET cc_start: 0.8885 (ppp) cc_final: 0.8532 (ppp) REVERT: S 31 MET cc_start: 0.9269 (mmp) cc_final: 0.9030 (mmm) REVERT: S 192 MET cc_start: 0.9313 (mmp) cc_final: 0.9073 (mmm) REVERT: S 193 MET cc_start: 0.9425 (ttp) cc_final: 0.8293 (ttt) REVERT: S 226 MET cc_start: 0.9073 (mmp) cc_final: 0.8841 (mmp) REVERT: T 5 MET cc_start: 0.8958 (ppp) cc_final: 0.8591 (ppp) REVERT: T 26 PHE cc_start: 0.8745 (m-80) cc_final: 0.8173 (m-80) REVERT: T 31 MET cc_start: 0.9218 (mmp) cc_final: 0.8868 (mmm) REVERT: T 141 MET cc_start: 0.8761 (tmm) cc_final: 0.8273 (mmp) REVERT: T 184 ASN cc_start: 0.9528 (m-40) cc_final: 0.9317 (m110) REVERT: T 193 MET cc_start: 0.9126 (ttp) cc_final: 0.8080 (ttt) REVERT: T 226 MET cc_start: 0.9105 (mmp) cc_final: 0.8845 (mmp) REVERT: V 5 MET cc_start: 0.8915 (ppp) cc_final: 0.8480 (ppp) REVERT: V 31 MET cc_start: 0.9332 (mmp) cc_final: 0.8961 (mmm) REVERT: V 193 MET cc_start: 0.8599 (ttp) cc_final: 0.8371 (ttt) REVERT: W 5 MET cc_start: 0.8898 (ppp) cc_final: 0.8541 (ppp) REVERT: W 31 MET cc_start: 0.9248 (mmp) cc_final: 0.8976 (mmm) REVERT: W 193 MET cc_start: 0.9206 (ttp) cc_final: 0.8450 (ttt) REVERT: W 226 MET cc_start: 0.9053 (mmt) cc_final: 0.8739 (mpp) REVERT: X 5 MET cc_start: 0.8941 (ppp) cc_final: 0.8590 (ppp) REVERT: X 31 MET cc_start: 0.9245 (mmp) cc_final: 0.8985 (mmm) REVERT: X 192 MET cc_start: 0.8683 (mmm) cc_final: 0.8460 (mmm) REVERT: X 193 MET cc_start: 0.9340 (ttp) cc_final: 0.8247 (ttt) REVERT: X 226 MET cc_start: 0.9072 (mmp) cc_final: 0.8749 (mmp) REVERT: Y 5 MET cc_start: 0.8907 (ppp) cc_final: 0.8492 (ppp) REVERT: Y 31 MET cc_start: 0.9372 (mmp) cc_final: 0.9019 (mmm) REVERT: Y 192 MET cc_start: 0.9310 (mmp) cc_final: 0.8967 (mmm) REVERT: Y 193 MET cc_start: 0.9479 (ttp) cc_final: 0.8638 (ttt) REVERT: Y 194 TYR cc_start: 0.9175 (m-80) cc_final: 0.8755 (m-10) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.2236 time to fit residues: 151.1648 Evaluate side-chains 306 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 402 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 193 optimal weight: 20.0000 chunk 416 optimal weight: 3.9990 chunk 251 optimal weight: 7.9990 chunk 466 optimal weight: 7.9990 chunk 309 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 387 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 HIS A 18 ASN A 201 HIS G 27 ASN J 201 HIS P 18 ASN Q 201 HIS S 201 HIS X 27 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.038905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.031082 restraints weight = 320745.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.032138 restraints weight = 195211.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.032923 restraints weight = 136672.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.033456 restraints weight = 104350.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.033838 restraints weight = 85093.567| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 42864 Z= 0.223 Angle : 0.621 7.791 57768 Z= 0.328 Chirality : 0.041 0.139 6888 Planarity : 0.004 0.028 7344 Dihedral : 4.960 19.789 5952 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: 1.60 (0.12), residues: 5424 helix: 1.80 (0.11), residues: 2136 sheet: -0.49 (0.15), residues: 1056 loop : 1.40 (0.15), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 89 TYR 0.026 0.002 TYR P 194 PHE 0.017 0.002 PHE Q 154 HIS 0.007 0.001 HIS O 174 Details of bonding type rmsd covalent geometry : bond 0.00435 (42864) covalent geometry : angle 0.62077 (57768) hydrogen bonds : bond 0.03320 ( 2664) hydrogen bonds : angle 4.40287 ( 7200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 MET cc_start: 0.8943 (ppp) cc_final: 0.8546 (ppp) REVERT: B 31 MET cc_start: 0.9354 (mmp) cc_final: 0.8973 (mmm) REVERT: B 192 MET cc_start: 0.9303 (mmp) cc_final: 0.9029 (mmm) REVERT: B 193 MET cc_start: 0.9403 (ttp) cc_final: 0.8495 (ttt) REVERT: A 5 MET cc_start: 0.8969 (ppp) cc_final: 0.8595 (ppp) REVERT: A 31 MET cc_start: 0.9219 (mmp) cc_final: 0.9010 (mmm) REVERT: A 192 MET cc_start: 0.8820 (mmm) cc_final: 0.8460 (mmm) REVERT: A 193 MET cc_start: 0.9329 (ttp) cc_final: 0.8381 (ttt) REVERT: C 5 MET cc_start: 0.8919 (ppp) cc_final: 0.8567 (ppp) REVERT: C 31 MET cc_start: 0.9360 (mmp) cc_final: 0.9044 (mmm) REVERT: C 193 MET cc_start: 0.9341 (ttp) cc_final: 0.8447 (ttt) REVERT: D 5 MET cc_start: 0.8897 (ppp) cc_final: 0.8592 (ppp) REVERT: D 31 MET cc_start: 0.9283 (mmp) cc_final: 0.8938 (mmm) REVERT: D 193 MET cc_start: 0.8337 (ttt) cc_final: 0.7748 (ttt) REVERT: E 5 MET cc_start: 0.8894 (ppp) cc_final: 0.8524 (ppp) REVERT: E 31 MET cc_start: 0.9225 (mmp) cc_final: 0.8923 (mmm) REVERT: E 158 MET cc_start: 0.9469 (ptm) cc_final: 0.9207 (ptm) REVERT: E 193 MET cc_start: 0.9214 (ttp) cc_final: 0.8123 (ttt) REVERT: F 5 MET cc_start: 0.8866 (ppp) cc_final: 0.8453 (ppp) REVERT: F 31 MET cc_start: 0.9378 (mmp) cc_final: 0.8986 (mmm) REVERT: F 192 MET cc_start: 0.9333 (mmp) cc_final: 0.9077 (mmm) REVERT: F 193 MET cc_start: 0.9391 (ttp) cc_final: 0.8309 (ttt) REVERT: G 5 MET cc_start: 0.8906 (ppp) cc_final: 0.8513 (ppp) REVERT: G 31 MET cc_start: 0.8737 (mmm) cc_final: 0.8490 (mmm) REVERT: G 192 MET cc_start: 0.9399 (mmp) cc_final: 0.9125 (mmm) REVERT: G 193 MET cc_start: 0.9027 (ttp) cc_final: 0.8404 (ttt) REVERT: H 5 MET cc_start: 0.8877 (ppp) cc_final: 0.8529 (ppp) REVERT: H 31 MET cc_start: 0.9244 (mmp) cc_final: 0.8937 (mmm) REVERT: H 193 MET cc_start: 0.8470 (ttt) cc_final: 0.7829 (ttt) REVERT: I 31 MET cc_start: 0.9367 (mmp) cc_final: 0.8873 (mmm) REVERT: I 192 MET cc_start: 0.8946 (mmm) cc_final: 0.8627 (mmm) REVERT: I 193 MET cc_start: 0.9403 (ttp) cc_final: 0.8430 (ttt) REVERT: J 5 MET cc_start: 0.8916 (ppp) cc_final: 0.8569 (ppp) REVERT: J 31 MET cc_start: 0.9273 (mmp) cc_final: 0.8890 (mmm) REVERT: J 193 MET cc_start: 0.9445 (ttp) cc_final: 0.8563 (ttt) REVERT: K 5 MET cc_start: 0.8886 (ppp) cc_final: 0.8541 (ppp) REVERT: K 31 MET cc_start: 0.9314 (mmp) cc_final: 0.8942 (mmm) REVERT: K 158 MET cc_start: 0.9520 (ttm) cc_final: 0.9214 (tpp) REVERT: K 193 MET cc_start: 0.9375 (ttp) cc_final: 0.8318 (ttt) REVERT: L 31 MET cc_start: 0.9222 (mmp) cc_final: 0.8899 (mmm) REVERT: L 193 MET cc_start: 0.8509 (ttt) cc_final: 0.7666 (ttt) REVERT: M 5 MET cc_start: 0.8874 (ppp) cc_final: 0.8461 (ppp) REVERT: M 31 MET cc_start: 0.9384 (mmp) cc_final: 0.9050 (mmm) REVERT: M 192 MET cc_start: 0.8784 (mmm) cc_final: 0.8527 (mmm) REVERT: M 193 MET cc_start: 0.9334 (ttp) cc_final: 0.8431 (ttt) REVERT: M 226 MET cc_start: 0.8643 (mpp) cc_final: 0.8438 (mpp) REVERT: N 5 MET cc_start: 0.8898 (ppp) cc_final: 0.8489 (ppp) REVERT: N 31 MET cc_start: 0.9289 (mmp) cc_final: 0.9022 (mmm) REVERT: N 192 MET cc_start: 0.9445 (mmm) cc_final: 0.8913 (mmm) REVERT: N 193 MET cc_start: 0.9364 (ttp) cc_final: 0.8431 (ttt) REVERT: O 5 MET cc_start: 0.8892 (ppp) cc_final: 0.8534 (ppp) REVERT: O 31 MET cc_start: 0.9301 (mmp) cc_final: 0.8986 (mmm) REVERT: O 193 MET cc_start: 0.9146 (ttp) cc_final: 0.8235 (ttt) REVERT: O 226 MET cc_start: 0.9097 (mmp) cc_final: 0.8806 (mmp) REVERT: P 5 MET cc_start: 0.8881 (ppp) cc_final: 0.8512 (ppp) REVERT: P 31 MET cc_start: 0.9328 (mmp) cc_final: 0.8991 (mmm) REVERT: P 192 MET cc_start: 0.9224 (mmp) cc_final: 0.8991 (mmm) REVERT: P 193 MET cc_start: 0.9123 (ttp) cc_final: 0.8908 (ttt) REVERT: Q 5 MET cc_start: 0.8963 (ppp) cc_final: 0.8588 (ppp) REVERT: Q 28 GLU cc_start: 0.9504 (pp20) cc_final: 0.9046 (tm-30) REVERT: Q 31 MET cc_start: 0.9239 (mmp) cc_final: 0.8944 (mmm) REVERT: Q 192 MET cc_start: 0.8620 (mmm) cc_final: 0.8322 (mmm) REVERT: Q 193 MET cc_start: 0.9512 (ttp) cc_final: 0.8808 (ttt) REVERT: R 5 MET cc_start: 0.8905 (ppp) cc_final: 0.8580 (ppp) REVERT: R 28 GLU cc_start: 0.9252 (pp20) cc_final: 0.8935 (pp20) REVERT: R 31 MET cc_start: 0.9212 (mmp) cc_final: 0.8961 (mmm) REVERT: R 141 MET cc_start: 0.8792 (tpt) cc_final: 0.8444 (mmp) REVERT: R 192 MET cc_start: 0.9282 (mmp) cc_final: 0.9012 (mmm) REVERT: R 193 MET cc_start: 0.9362 (ttp) cc_final: 0.8335 (ttt) REVERT: R 226 MET cc_start: 0.8996 (mmt) cc_final: 0.8778 (mmt) REVERT: S 5 MET cc_start: 0.8898 (ppp) cc_final: 0.8549 (ppp) REVERT: S 26 PHE cc_start: 0.9119 (m-80) cc_final: 0.8777 (m-80) REVERT: S 31 MET cc_start: 0.9214 (mmp) cc_final: 0.8895 (mmm) REVERT: S 193 MET cc_start: 0.9504 (ttp) cc_final: 0.8585 (ttt) REVERT: S 226 MET cc_start: 0.9054 (mmp) cc_final: 0.8798 (mmp) REVERT: T 5 MET cc_start: 0.8967 (ppp) cc_final: 0.8604 (ppp) REVERT: T 31 MET cc_start: 0.9261 (mmp) cc_final: 0.8970 (mmm) REVERT: T 141 MET cc_start: 0.8881 (tmm) cc_final: 0.8319 (mmp) REVERT: T 193 MET cc_start: 0.9302 (ttp) cc_final: 0.8254 (ttt) REVERT: T 226 MET cc_start: 0.9163 (mmp) cc_final: 0.8889 (mmp) REVERT: V 5 MET cc_start: 0.8962 (ppp) cc_final: 0.8561 (ppp) REVERT: V 31 MET cc_start: 0.9314 (mmp) cc_final: 0.8933 (mmm) REVERT: V 193 MET cc_start: 0.8762 (ttp) cc_final: 0.8512 (ttt) REVERT: V 194 TYR cc_start: 0.9385 (m-10) cc_final: 0.8971 (m-10) REVERT: W 5 MET cc_start: 0.8934 (ppp) cc_final: 0.8585 (ppp) REVERT: W 31 MET cc_start: 0.9252 (mmp) cc_final: 0.8988 (mmm) REVERT: W 193 MET cc_start: 0.9306 (ttp) cc_final: 0.8574 (ttt) REVERT: X 5 MET cc_start: 0.8967 (ppp) cc_final: 0.8599 (ppp) REVERT: X 31 MET cc_start: 0.9224 (mmp) cc_final: 0.8959 (mmm) REVERT: X 158 MET cc_start: 0.9639 (ptm) cc_final: 0.9386 (ptm) REVERT: X 192 MET cc_start: 0.9006 (mmm) cc_final: 0.8637 (mmm) REVERT: X 193 MET cc_start: 0.9401 (ttp) cc_final: 0.8589 (ttt) REVERT: X 226 MET cc_start: 0.9058 (mmp) cc_final: 0.8766 (mmp) REVERT: Y 5 MET cc_start: 0.8958 (ppp) cc_final: 0.8562 (ppp) REVERT: Y 31 MET cc_start: 0.9348 (mmp) cc_final: 0.8980 (mmm) REVERT: Y 192 MET cc_start: 0.9379 (mmp) cc_final: 0.9080 (mmm) REVERT: Y 193 MET cc_start: 0.9493 (ttp) cc_final: 0.8609 (ttt) REVERT: Y 194 TYR cc_start: 0.9196 (m-80) cc_final: 0.8849 (m-10) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.2242 time to fit residues: 142.1330 Evaluate side-chains 304 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 98 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 466 optimal weight: 2.9990 chunk 326 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 371 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 336 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 386 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 201 HIS R 201 HIS W 201 HIS X 201 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.039886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.031769 restraints weight = 312278.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.032869 restraints weight = 187992.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.033670 restraints weight = 131402.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.034231 restraints weight = 100557.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.034604 restraints weight = 82142.009| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 42864 Z= 0.122 Angle : 0.529 8.594 57768 Z= 0.281 Chirality : 0.041 0.141 6888 Planarity : 0.003 0.028 7344 Dihedral : 4.668 18.944 5952 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: 1.90 (0.12), residues: 5424 helix: 1.99 (0.11), residues: 2136 sheet: -0.38 (0.15), residues: 1056 loop : 1.66 (0.16), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 224 TYR 0.015 0.001 TYR P 194 PHE 0.016 0.001 PHE Q 154 HIS 0.007 0.001 HIS D 174 Details of bonding type rmsd covalent geometry : bond 0.00245 (42864) covalent geometry : angle 0.52916 (57768) hydrogen bonds : bond 0.02974 ( 2664) hydrogen bonds : angle 4.17532 ( 7200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 MET cc_start: 0.8967 (ppp) cc_final: 0.8646 (ppp) REVERT: B 31 MET cc_start: 0.9285 (mmp) cc_final: 0.8914 (mmm) REVERT: B 78 GLU cc_start: 0.9226 (mt-10) cc_final: 0.9000 (mp0) REVERT: B 192 MET cc_start: 0.9210 (mmp) cc_final: 0.8965 (mmm) REVERT: B 193 MET cc_start: 0.9363 (ttp) cc_final: 0.8597 (ttt) REVERT: A 5 MET cc_start: 0.8959 (ppp) cc_final: 0.8563 (ppp) REVERT: A 31 MET cc_start: 0.9227 (mmp) cc_final: 0.8996 (mmm) REVERT: A 193 MET cc_start: 0.9295 (ttp) cc_final: 0.8173 (ttt) REVERT: C 5 MET cc_start: 0.8850 (ppp) cc_final: 0.8472 (ppp) REVERT: C 26 PHE cc_start: 0.9206 (m-80) cc_final: 0.8779 (m-80) REVERT: C 31 MET cc_start: 0.9344 (mmp) cc_final: 0.9032 (mmm) REVERT: C 193 MET cc_start: 0.9284 (ttp) cc_final: 0.8447 (ttt) REVERT: D 5 MET cc_start: 0.8902 (ppp) cc_final: 0.8552 (ppp) REVERT: D 31 MET cc_start: 0.9258 (mmp) cc_final: 0.8889 (mmm) REVERT: D 193 MET cc_start: 0.8195 (ttt) cc_final: 0.7478 (ttt) REVERT: E 5 MET cc_start: 0.8884 (ppp) cc_final: 0.8537 (ppp) REVERT: E 31 MET cc_start: 0.9290 (mmp) cc_final: 0.8987 (mmm) REVERT: E 158 MET cc_start: 0.9418 (ptm) cc_final: 0.9201 (ptm) REVERT: E 192 MET cc_start: 0.9269 (mmp) cc_final: 0.8991 (mmm) REVERT: E 193 MET cc_start: 0.9175 (ttp) cc_final: 0.8418 (ttt) REVERT: F 5 MET cc_start: 0.8860 (ppp) cc_final: 0.8428 (ppp) REVERT: F 31 MET cc_start: 0.9368 (mmp) cc_final: 0.8955 (mmm) REVERT: F 193 MET cc_start: 0.9352 (ttp) cc_final: 0.8312 (ttt) REVERT: G 5 MET cc_start: 0.8898 (ppp) cc_final: 0.8499 (ppp) REVERT: G 31 MET cc_start: 0.8708 (mmm) cc_final: 0.8437 (mmm) REVERT: G 193 MET cc_start: 0.8899 (ttp) cc_final: 0.8503 (ttt) REVERT: H 5 MET cc_start: 0.8824 (ppp) cc_final: 0.8450 (ppp) REVERT: H 31 MET cc_start: 0.9248 (mmp) cc_final: 0.8915 (mmm) REVERT: H 193 MET cc_start: 0.8452 (ttt) cc_final: 0.7866 (ttt) REVERT: I 31 MET cc_start: 0.9317 (mmp) cc_final: 0.8940 (mmm) REVERT: I 158 MET cc_start: 0.9491 (ptm) cc_final: 0.9248 (tmm) REVERT: I 192 MET cc_start: 0.8950 (mmm) cc_final: 0.8684 (mmm) REVERT: I 193 MET cc_start: 0.9355 (ttp) cc_final: 0.8464 (ttt) REVERT: J 5 MET cc_start: 0.8969 (ppp) cc_final: 0.8601 (ppp) REVERT: J 31 MET cc_start: 0.9309 (mmp) cc_final: 0.9000 (mmm) REVERT: J 193 MET cc_start: 0.9409 (ttp) cc_final: 0.8676 (ttt) REVERT: K 5 MET cc_start: 0.8826 (ppp) cc_final: 0.8454 (ppp) REVERT: K 31 MET cc_start: 0.9320 (mmp) cc_final: 0.8954 (mmm) REVERT: K 158 MET cc_start: 0.9535 (ttm) cc_final: 0.9147 (tpp) REVERT: K 193 MET cc_start: 0.9363 (ttp) cc_final: 0.8337 (ttt) REVERT: L 31 MET cc_start: 0.9251 (mmp) cc_final: 0.8886 (mmm) REVERT: L 193 MET cc_start: 0.8477 (ttt) cc_final: 0.7640 (ttt) REVERT: M 5 MET cc_start: 0.8881 (ppp) cc_final: 0.8438 (ppp) REVERT: M 31 MET cc_start: 0.9371 (mmp) cc_final: 0.9017 (mmm) REVERT: M 193 MET cc_start: 0.9293 (ttp) cc_final: 0.8418 (ttt) REVERT: N 5 MET cc_start: 0.8903 (ppp) cc_final: 0.8501 (ppp) REVERT: N 28 GLU cc_start: 0.9491 (pp20) cc_final: 0.9162 (pm20) REVERT: N 31 MET cc_start: 0.9369 (mmp) cc_final: 0.8907 (mmm) REVERT: N 158 MET cc_start: 0.9294 (ttm) cc_final: 0.8577 (ttt) REVERT: N 193 MET cc_start: 0.9307 (ttp) cc_final: 0.8144 (ttt) REVERT: O 5 MET cc_start: 0.8954 (ppp) cc_final: 0.8579 (ppp) REVERT: O 31 MET cc_start: 0.9167 (mmp) cc_final: 0.8945 (mmm) REVERT: O 193 MET cc_start: 0.9079 (ttp) cc_final: 0.8250 (ttt) REVERT: P 5 MET cc_start: 0.8811 (ppp) cc_final: 0.8424 (ppp) REVERT: P 31 MET cc_start: 0.9344 (mmp) cc_final: 0.8980 (mmm) REVERT: P 192 MET cc_start: 0.9182 (mmp) cc_final: 0.8961 (mmm) REVERT: P 194 TYR cc_start: 0.9460 (m-80) cc_final: 0.9089 (m-80) REVERT: Q 5 MET cc_start: 0.8951 (ppp) cc_final: 0.8591 (ppp) REVERT: Q 31 MET cc_start: 0.9258 (mmp) cc_final: 0.8958 (mmm) REVERT: Q 192 MET cc_start: 0.8509 (mmm) cc_final: 0.8281 (mmm) REVERT: Q 193 MET cc_start: 0.9484 (ttp) cc_final: 0.8398 (ttt) REVERT: R 5 MET cc_start: 0.8916 (ppp) cc_final: 0.8574 (ppp) REVERT: R 26 PHE cc_start: 0.9078 (m-80) cc_final: 0.8133 (m-80) REVERT: R 31 MET cc_start: 0.9197 (mmp) cc_final: 0.8942 (mmm) REVERT: R 141 MET cc_start: 0.8756 (tpt) cc_final: 0.8417 (mmp) REVERT: R 158 MET cc_start: 0.9412 (ptm) cc_final: 0.9170 (ptm) REVERT: R 193 MET cc_start: 0.9326 (ttp) cc_final: 0.7919 (ttt) REVERT: S 5 MET cc_start: 0.8968 (ppp) cc_final: 0.8605 (ppp) REVERT: S 31 MET cc_start: 0.9203 (mmp) cc_final: 0.8999 (mmm) REVERT: S 193 MET cc_start: 0.9462 (ttp) cc_final: 0.8299 (ttt) REVERT: S 226 MET cc_start: 0.9103 (mmp) cc_final: 0.8854 (mmp) REVERT: T 5 MET cc_start: 0.8936 (ppp) cc_final: 0.8568 (ppp) REVERT: T 31 MET cc_start: 0.9297 (mmp) cc_final: 0.8989 (mmm) REVERT: T 141 MET cc_start: 0.8846 (tmm) cc_final: 0.8143 (mmp) REVERT: T 192 MET cc_start: 0.9385 (mmp) cc_final: 0.9083 (mmm) REVERT: T 193 MET cc_start: 0.9193 (ttp) cc_final: 0.8383 (ttt) REVERT: V 5 MET cc_start: 0.8917 (ppp) cc_final: 0.8551 (ppp) REVERT: V 31 MET cc_start: 0.9303 (mmp) cc_final: 0.8890 (mmm) REVERT: V 193 MET cc_start: 0.8817 (ttp) cc_final: 0.8582 (ttt) REVERT: W 5 MET cc_start: 0.8933 (ppp) cc_final: 0.8575 (ppp) REVERT: W 31 MET cc_start: 0.9266 (mmp) cc_final: 0.8972 (mmm) REVERT: W 193 MET cc_start: 0.9143 (ttp) cc_final: 0.8504 (ttt) REVERT: X 5 MET cc_start: 0.8961 (ppp) cc_final: 0.8584 (ppp) REVERT: X 26 PHE cc_start: 0.9207 (m-80) cc_final: 0.8850 (m-80) REVERT: X 31 MET cc_start: 0.9198 (mmp) cc_final: 0.8841 (mmm) REVERT: X 192 MET cc_start: 0.8477 (mmm) cc_final: 0.8249 (mmm) REVERT: X 193 MET cc_start: 0.9378 (ttp) cc_final: 0.8168 (ttt) REVERT: X 226 MET cc_start: 0.9044 (mmp) cc_final: 0.8755 (mmp) REVERT: Y 5 MET cc_start: 0.8953 (ppp) cc_final: 0.8545 (ppp) REVERT: Y 31 MET cc_start: 0.9367 (mmp) cc_final: 0.8954 (mmm) REVERT: Y 192 MET cc_start: 0.9362 (mmp) cc_final: 0.9022 (mmm) REVERT: Y 193 MET cc_start: 0.9437 (ttp) cc_final: 0.8556 (ttt) REVERT: Y 194 TYR cc_start: 0.9172 (m-80) cc_final: 0.8823 (m-10) REVERT: Y 226 MET cc_start: 0.8985 (mpp) cc_final: 0.8736 (mmt) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.2225 time to fit residues: 156.2586 Evaluate side-chains 312 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 454 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 272 optimal weight: 7.9990 chunk 499 optimal weight: 9.9990 chunk 179 optimal weight: 0.0170 chunk 398 optimal weight: 7.9990 chunk 172 optimal weight: 0.6980 chunk 267 optimal weight: 8.9990 overall best weight: 2.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 201 HIS G 201 HIS P 201 HIS S 27 ASN T 201 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.039753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.031633 restraints weight = 311751.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.032724 restraints weight = 189367.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.033506 restraints weight = 132515.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.034046 restraints weight = 101552.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.034431 restraints weight = 83547.920| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 42864 Z= 0.134 Angle : 0.558 16.499 57768 Z= 0.292 Chirality : 0.041 0.142 6888 Planarity : 0.003 0.028 7344 Dihedral : 4.610 19.057 5952 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: 1.89 (0.12), residues: 5424 helix: 1.99 (0.11), residues: 2136 sheet: -0.66 (0.15), residues: 1104 loop : 1.87 (0.16), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 6 TYR 0.015 0.001 TYR P 41 PHE 0.015 0.001 PHE B 26 HIS 0.006 0.001 HIS O 174 Details of bonding type rmsd covalent geometry : bond 0.00272 (42864) covalent geometry : angle 0.55810 (57768) hydrogen bonds : bond 0.02995 ( 2664) hydrogen bonds : angle 4.24911 ( 7200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 MET cc_start: 0.8971 (ppp) cc_final: 0.8637 (ppp) REVERT: B 26 PHE cc_start: 0.9268 (m-80) cc_final: 0.8627 (m-80) REVERT: B 31 MET cc_start: 0.9291 (mmp) cc_final: 0.8922 (mmm) REVERT: B 78 GLU cc_start: 0.9248 (mt-10) cc_final: 0.9008 (mp0) REVERT: B 192 MET cc_start: 0.9242 (mmp) cc_final: 0.8992 (mmm) REVERT: B 193 MET cc_start: 0.9358 (ttp) cc_final: 0.8592 (ttt) REVERT: A 5 MET cc_start: 0.8976 (ppp) cc_final: 0.8603 (ppp) REVERT: A 31 MET cc_start: 0.9289 (mmp) cc_final: 0.9029 (mmm) REVERT: A 192 MET cc_start: 0.8620 (mmm) cc_final: 0.8151 (mmm) REVERT: A 193 MET cc_start: 0.9310 (ttp) cc_final: 0.8199 (ttt) REVERT: C 5 MET cc_start: 0.8893 (ppp) cc_final: 0.8528 (ppp) REVERT: C 31 MET cc_start: 0.9312 (mmp) cc_final: 0.8972 (mmm) REVERT: C 192 MET cc_start: 0.8663 (mmm) cc_final: 0.8339 (mmm) REVERT: C 193 MET cc_start: 0.9307 (ttp) cc_final: 0.8448 (ttt) REVERT: D 5 MET cc_start: 0.8930 (ppp) cc_final: 0.8602 (ppp) REVERT: D 31 MET cc_start: 0.9254 (mmp) cc_final: 0.8889 (mmm) REVERT: D 158 MET cc_start: 0.9666 (ppp) cc_final: 0.8799 (ppp) REVERT: D 193 MET cc_start: 0.8208 (ttt) cc_final: 0.7487 (ttt) REVERT: E 5 MET cc_start: 0.8886 (ppp) cc_final: 0.8499 (ppp) REVERT: E 31 MET cc_start: 0.9300 (mmp) cc_final: 0.8970 (mmm) REVERT: E 141 MET cc_start: 0.9069 (tpp) cc_final: 0.8712 (tpp) REVERT: E 192 MET cc_start: 0.9510 (mmp) cc_final: 0.9224 (mmm) REVERT: E 193 MET cc_start: 0.9343 (ttp) cc_final: 0.8542 (ttt) REVERT: F 5 MET cc_start: 0.8864 (ppp) cc_final: 0.8517 (ppp) REVERT: F 31 MET cc_start: 0.9302 (mmp) cc_final: 0.8923 (mmm) REVERT: F 193 MET cc_start: 0.9393 (ttp) cc_final: 0.8320 (ttt) REVERT: G 5 MET cc_start: 0.8919 (ppp) cc_final: 0.8537 (ppp) REVERT: G 141 MET cc_start: 0.9061 (tpp) cc_final: 0.8683 (tpp) REVERT: G 192 MET cc_start: 0.8574 (mmm) cc_final: 0.8222 (mmm) REVERT: G 193 MET cc_start: 0.9113 (ttp) cc_final: 0.8612 (ttt) REVERT: H 5 MET cc_start: 0.8876 (ppp) cc_final: 0.8524 (ppp) REVERT: H 31 MET cc_start: 0.9264 (mmp) cc_final: 0.8948 (mmm) REVERT: H 193 MET cc_start: 0.8446 (ttt) cc_final: 0.7857 (ttt) REVERT: I 31 MET cc_start: 0.9311 (mmp) cc_final: 0.8931 (mmm) REVERT: I 192 MET cc_start: 0.8955 (mmm) cc_final: 0.8694 (mmm) REVERT: I 193 MET cc_start: 0.9352 (ttp) cc_final: 0.8466 (ttt) REVERT: J 5 MET cc_start: 0.8996 (ppp) cc_final: 0.8656 (ppp) REVERT: J 26 PHE cc_start: 0.8989 (m-80) cc_final: 0.8767 (m-80) REVERT: J 31 MET cc_start: 0.9319 (mmp) cc_final: 0.9013 (mmm) REVERT: J 78 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8968 (mp0) REVERT: J 158 MET cc_start: 0.9597 (ptm) cc_final: 0.9191 (tmm) REVERT: J 192 MET cc_start: 0.9211 (mmp) cc_final: 0.8946 (mmm) REVERT: J 193 MET cc_start: 0.9451 (ttp) cc_final: 0.8683 (ttt) REVERT: K 5 MET cc_start: 0.8856 (ppp) cc_final: 0.8555 (ppp) REVERT: K 31 MET cc_start: 0.9257 (mmp) cc_final: 0.9013 (mmm) REVERT: K 158 MET cc_start: 0.9510 (ttm) cc_final: 0.9082 (tpp) REVERT: K 193 MET cc_start: 0.9426 (ttp) cc_final: 0.8574 (ttt) REVERT: K 226 MET cc_start: 0.8977 (mpp) cc_final: 0.8734 (mmm) REVERT: L 31 MET cc_start: 0.9295 (mmp) cc_final: 0.8960 (mmm) REVERT: L 193 MET cc_start: 0.8482 (ttt) cc_final: 0.7625 (ttt) REVERT: M 5 MET cc_start: 0.8836 (ppp) cc_final: 0.8505 (ppp) REVERT: M 31 MET cc_start: 0.9374 (mmp) cc_final: 0.9035 (mmm) REVERT: M 193 MET cc_start: 0.9333 (ttp) cc_final: 0.8588 (ttt) REVERT: N 5 MET cc_start: 0.8916 (ppp) cc_final: 0.8581 (ppp) REVERT: N 31 MET cc_start: 0.9248 (mmp) cc_final: 0.8907 (mmm) REVERT: N 193 MET cc_start: 0.9442 (ttp) cc_final: 0.8397 (ttt) REVERT: O 5 MET cc_start: 0.8980 (ppp) cc_final: 0.8612 (ppp) REVERT: O 31 MET cc_start: 0.9199 (mmp) cc_final: 0.8960 (mmm) REVERT: O 158 MET cc_start: 0.9616 (ptm) cc_final: 0.9355 (ppp) REVERT: O 193 MET cc_start: 0.9061 (ttp) cc_final: 0.8256 (ttt) REVERT: O 226 MET cc_start: 0.9197 (mmp) cc_final: 0.8994 (mmp) REVERT: P 5 MET cc_start: 0.8843 (ppp) cc_final: 0.8523 (ppp) REVERT: P 31 MET cc_start: 0.9291 (mmp) cc_final: 0.8945 (mmm) REVERT: P 193 MET cc_start: 0.8609 (ttt) cc_final: 0.8040 (ttt) REVERT: P 194 TYR cc_start: 0.9401 (m-80) cc_final: 0.9011 (m-80) REVERT: Q 5 MET cc_start: 0.8928 (ppp) cc_final: 0.8616 (ppp) REVERT: Q 28 GLU cc_start: 0.9569 (pp20) cc_final: 0.9006 (tm-30) REVERT: Q 31 MET cc_start: 0.9266 (mmp) cc_final: 0.8937 (mmm) REVERT: Q 78 GLU cc_start: 0.9260 (mt-10) cc_final: 0.9041 (mp0) REVERT: Q 193 MET cc_start: 0.9495 (ttp) cc_final: 0.8730 (ttt) REVERT: R 5 MET cc_start: 0.8901 (ppp) cc_final: 0.8508 (ppp) REVERT: R 31 MET cc_start: 0.9245 (mmp) cc_final: 0.8991 (mmm) REVERT: R 141 MET cc_start: 0.8792 (tpt) cc_final: 0.8418 (mmp) REVERT: R 158 MET cc_start: 0.9411 (ptm) cc_final: 0.9165 (ptm) REVERT: R 193 MET cc_start: 0.9307 (ttp) cc_final: 0.8534 (ttt) REVERT: S 5 MET cc_start: 0.8981 (ppp) cc_final: 0.8603 (ppp) REVERT: S 26 PHE cc_start: 0.8892 (m-80) cc_final: 0.8023 (m-80) REVERT: S 31 MET cc_start: 0.9204 (mmp) cc_final: 0.8999 (mmm) REVERT: S 141 MET cc_start: 0.9048 (tpp) cc_final: 0.8617 (tpp) REVERT: S 158 MET cc_start: 0.9710 (ppp) cc_final: 0.9219 (ppp) REVERT: S 193 MET cc_start: 0.9462 (ttp) cc_final: 0.8310 (ttt) REVERT: T 5 MET cc_start: 0.8926 (ppp) cc_final: 0.8530 (ppp) REVERT: T 26 PHE cc_start: 0.8735 (m-80) cc_final: 0.8357 (m-80) REVERT: T 31 MET cc_start: 0.9264 (mmp) cc_final: 0.8976 (mmm) REVERT: T 141 MET cc_start: 0.8854 (tmm) cc_final: 0.8108 (mmp) REVERT: T 193 MET cc_start: 0.9173 (ttp) cc_final: 0.7942 (ttt) REVERT: V 5 MET cc_start: 0.8955 (ppp) cc_final: 0.8620 (ppp) REVERT: V 31 MET cc_start: 0.9300 (mmp) cc_final: 0.8888 (mmm) REVERT: W 5 MET cc_start: 0.8940 (ppp) cc_final: 0.8548 (ppp) REVERT: W 31 MET cc_start: 0.9246 (mmp) cc_final: 0.8973 (mmm) REVERT: W 193 MET cc_start: 0.9261 (ttp) cc_final: 0.8552 (ttt) REVERT: W 226 MET cc_start: 0.9118 (mmt) cc_final: 0.8887 (mmt) REVERT: X 5 MET cc_start: 0.8923 (ppp) cc_final: 0.8566 (ppp) REVERT: X 31 MET cc_start: 0.9179 (mmp) cc_final: 0.8836 (mmm) REVERT: X 158 MET cc_start: 0.9598 (ptm) cc_final: 0.9241 (ptm) REVERT: X 192 MET cc_start: 0.8660 (mmm) cc_final: 0.8420 (mmm) REVERT: X 193 MET cc_start: 0.9340 (ttp) cc_final: 0.8152 (ttt) REVERT: X 226 MET cc_start: 0.9048 (mmp) cc_final: 0.8753 (mmp) REVERT: Y 5 MET cc_start: 0.8960 (ppp) cc_final: 0.8620 (ppp) REVERT: Y 31 MET cc_start: 0.9339 (mmp) cc_final: 0.8954 (mmm) REVERT: Y 192 MET cc_start: 0.9380 (mmp) cc_final: 0.9044 (mmm) REVERT: Y 193 MET cc_start: 0.9441 (ttp) cc_final: 0.8564 (ttt) REVERT: Y 194 TYR cc_start: 0.9155 (m-80) cc_final: 0.8823 (m-10) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.2271 time to fit residues: 160.7250 Evaluate side-chains 304 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 2 optimal weight: 10.0000 chunk 437 optimal weight: 5.9990 chunk 460 optimal weight: 10.0000 chunk 444 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 390 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 478 optimal weight: 7.9990 chunk 316 optimal weight: 3.9990 chunk 213 optimal weight: 0.0980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.040528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.032281 restraints weight = 304795.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.033378 restraints weight = 184371.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.034178 restraints weight = 129720.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.034743 restraints weight = 99549.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.035124 restraints weight = 81484.628| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 42864 Z= 0.105 Angle : 0.542 13.827 57768 Z= 0.284 Chirality : 0.042 0.145 6888 Planarity : 0.003 0.031 7344 Dihedral : 4.429 18.628 5952 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: 2.08 (0.12), residues: 5424 helix: 2.17 (0.11), residues: 2136 sheet: -0.59 (0.14), residues: 1104 loop : 1.97 (0.16), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 202 TYR 0.015 0.001 TYR E 194 PHE 0.019 0.001 PHE T 26 HIS 0.005 0.001 HIS O 174 Details of bonding type rmsd covalent geometry : bond 0.00213 (42864) covalent geometry : angle 0.54173 (57768) hydrogen bonds : bond 0.02894 ( 2664) hydrogen bonds : angle 4.18723 ( 7200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 MET cc_start: 0.8911 (ppp) cc_final: 0.8571 (ppp) REVERT: B 26 PHE cc_start: 0.9350 (m-80) cc_final: 0.8089 (m-80) REVERT: B 31 MET cc_start: 0.9281 (mmp) cc_final: 0.8895 (mmm) REVERT: B 78 GLU cc_start: 0.9235 (mt-10) cc_final: 0.9001 (mp0) REVERT: B 192 MET cc_start: 0.9201 (mmp) cc_final: 0.8979 (mmm) REVERT: B 193 MET cc_start: 0.9309 (ttp) cc_final: 0.8569 (tmm) REVERT: A 5 MET cc_start: 0.8888 (ppp) cc_final: 0.8552 (ppp) REVERT: A 26 PHE cc_start: 0.9222 (m-80) cc_final: 0.8885 (m-80) REVERT: A 31 MET cc_start: 0.9277 (mmp) cc_final: 0.9021 (mmm) REVERT: A 158 MET cc_start: 0.9289 (ttm) cc_final: 0.8914 (ttt) REVERT: A 193 MET cc_start: 0.9190 (ttp) cc_final: 0.7935 (ttt) REVERT: C 5 MET cc_start: 0.8873 (ppp) cc_final: 0.8547 (ppp) REVERT: C 26 PHE cc_start: 0.9365 (m-10) cc_final: 0.8940 (m-10) REVERT: C 31 MET cc_start: 0.9308 (mmp) cc_final: 0.9015 (mmm) REVERT: C 192 MET cc_start: 0.8625 (mmm) cc_final: 0.8337 (mmm) REVERT: C 193 MET cc_start: 0.9185 (ttp) cc_final: 0.8576 (tmm) REVERT: D 5 MET cc_start: 0.8859 (ppp) cc_final: 0.8555 (ppp) REVERT: D 31 MET cc_start: 0.9242 (mmp) cc_final: 0.8867 (mmm) REVERT: D 158 MET cc_start: 0.9564 (ppp) cc_final: 0.9206 (ppp) REVERT: D 193 MET cc_start: 0.8194 (ttt) cc_final: 0.7547 (ttt) REVERT: E 5 MET cc_start: 0.8910 (ppp) cc_final: 0.8565 (ppp) REVERT: E 31 MET cc_start: 0.9298 (mmp) cc_final: 0.8954 (mmm) REVERT: E 141 MET cc_start: 0.8933 (tpp) cc_final: 0.8725 (tpp) REVERT: E 193 MET cc_start: 0.9107 (ttp) cc_final: 0.8558 (ttt) REVERT: F 5 MET cc_start: 0.8914 (ppp) cc_final: 0.8572 (ppp) REVERT: F 26 PHE cc_start: 0.9230 (m-80) cc_final: 0.9020 (m-80) REVERT: F 31 MET cc_start: 0.9262 (mmp) cc_final: 0.9006 (mmm) REVERT: F 193 MET cc_start: 0.9272 (ttp) cc_final: 0.8516 (tmm) REVERT: G 5 MET cc_start: 0.8867 (ppp) cc_final: 0.8508 (ppp) REVERT: G 31 MET cc_start: 0.9264 (mmp) cc_final: 0.8969 (mmm) REVERT: G 141 MET cc_start: 0.9064 (tpp) cc_final: 0.8689 (tpp) REVERT: G 192 MET cc_start: 0.8421 (mmm) cc_final: 0.8080 (mmm) REVERT: G 193 MET cc_start: 0.9146 (ttp) cc_final: 0.8912 (ttt) REVERT: G 226 MET cc_start: 0.9152 (mmt) cc_final: 0.8837 (mpp) REVERT: H 5 MET cc_start: 0.8869 (ppp) cc_final: 0.8547 (ppp) REVERT: H 31 MET cc_start: 0.9257 (mmp) cc_final: 0.8920 (mmm) REVERT: H 193 MET cc_start: 0.8442 (ttt) cc_final: 0.7819 (ttt) REVERT: I 31 MET cc_start: 0.9288 (mmp) cc_final: 0.8951 (mmm) REVERT: I 158 MET cc_start: 0.9523 (ptm) cc_final: 0.8868 (tmm) REVERT: I 193 MET cc_start: 0.9177 (ttp) cc_final: 0.7900 (ttt) REVERT: J 5 MET cc_start: 0.8924 (ppp) cc_final: 0.8619 (ppp) REVERT: J 31 MET cc_start: 0.9288 (mmp) cc_final: 0.8996 (mmm) REVERT: J 78 GLU cc_start: 0.9227 (mt-10) cc_final: 0.9011 (mp0) REVERT: J 158 MET cc_start: 0.9615 (ptm) cc_final: 0.9256 (tmm) REVERT: J 192 MET cc_start: 0.9202 (mmp) cc_final: 0.8935 (mmm) REVERT: J 193 MET cc_start: 0.9362 (ttp) cc_final: 0.8783 (ttt) REVERT: K 5 MET cc_start: 0.8868 (ppp) cc_final: 0.8543 (ppp) REVERT: K 26 PHE cc_start: 0.9281 (m-80) cc_final: 0.8746 (m-80) REVERT: K 31 MET cc_start: 0.9255 (mmp) cc_final: 0.8990 (mmm) REVERT: K 193 MET cc_start: 0.9372 (ttp) cc_final: 0.8516 (ttt) REVERT: K 226 MET cc_start: 0.8981 (mpp) cc_final: 0.8710 (mmt) REVERT: L 31 MET cc_start: 0.9281 (mmp) cc_final: 0.8943 (mmm) REVERT: L 193 MET cc_start: 0.8577 (ttt) cc_final: 0.7657 (ttt) REVERT: M 5 MET cc_start: 0.8849 (ppp) cc_final: 0.8512 (ppp) REVERT: M 31 MET cc_start: 0.9269 (mmp) cc_final: 0.9020 (mmm) REVERT: M 193 MET cc_start: 0.9204 (ttp) cc_final: 0.8486 (ttt) REVERT: N 5 MET cc_start: 0.8847 (ppp) cc_final: 0.8500 (ppp) REVERT: N 31 MET cc_start: 0.9194 (mmp) cc_final: 0.8866 (mmm) REVERT: N 193 MET cc_start: 0.9287 (ttp) cc_final: 0.8176 (ttt) REVERT: O 5 MET cc_start: 0.8909 (ppp) cc_final: 0.8579 (ppp) REVERT: O 26 PHE cc_start: 0.9301 (m-80) cc_final: 0.9071 (m-80) REVERT: O 31 MET cc_start: 0.9164 (mmp) cc_final: 0.8919 (mmm) REVERT: O 158 MET cc_start: 0.9614 (ptm) cc_final: 0.9370 (ppp) REVERT: O 193 MET cc_start: 0.9031 (ttp) cc_final: 0.8344 (ttt) REVERT: P 5 MET cc_start: 0.8869 (ppp) cc_final: 0.8525 (ppp) REVERT: P 31 MET cc_start: 0.9309 (mmp) cc_final: 0.8980 (mmm) REVERT: P 193 MET cc_start: 0.8639 (ttt) cc_final: 0.8108 (ttt) REVERT: Q 5 MET cc_start: 0.8968 (ppp) cc_final: 0.8636 (ppp) REVERT: Q 26 PHE cc_start: 0.9131 (m-80) cc_final: 0.8826 (m-80) REVERT: Q 31 MET cc_start: 0.9224 (mmp) cc_final: 0.8937 (mmm) REVERT: Q 154 PHE cc_start: 0.9196 (m-10) cc_final: 0.8929 (m-80) REVERT: Q 193 MET cc_start: 0.9218 (ttp) cc_final: 0.8278 (tmm) REVERT: Q 195 LEU cc_start: 0.9673 (mp) cc_final: 0.9249 (mp) REVERT: R 5 MET cc_start: 0.8913 (ppp) cc_final: 0.8546 (ppp) REVERT: R 26 PHE cc_start: 0.9075 (m-80) cc_final: 0.8153 (m-80) REVERT: R 31 MET cc_start: 0.9181 (mmp) cc_final: 0.8959 (mmm) REVERT: R 141 MET cc_start: 0.8856 (tpt) cc_final: 0.8441 (mmp) REVERT: R 193 MET cc_start: 0.9231 (ttp) cc_final: 0.8402 (ttt) REVERT: S 5 MET cc_start: 0.8970 (ppp) cc_final: 0.8672 (ppp) REVERT: S 26 PHE cc_start: 0.8866 (m-80) cc_final: 0.8094 (m-80) REVERT: S 31 MET cc_start: 0.9263 (mmp) cc_final: 0.8946 (mmm) REVERT: S 141 MET cc_start: 0.8925 (tpp) cc_final: 0.8638 (tpp) REVERT: S 158 MET cc_start: 0.9493 (ppp) cc_final: 0.8761 (ppp) REVERT: S 193 MET cc_start: 0.9321 (ttp) cc_final: 0.8299 (tmm) REVERT: T 5 MET cc_start: 0.8916 (ppp) cc_final: 0.8592 (ppp) REVERT: T 26 PHE cc_start: 0.9082 (m-80) cc_final: 0.8512 (m-80) REVERT: T 31 MET cc_start: 0.9229 (mmp) cc_final: 0.8933 (mmm) REVERT: T 141 MET cc_start: 0.8553 (tmm) cc_final: 0.7898 (mmp) REVERT: T 192 MET cc_start: 0.9370 (mmp) cc_final: 0.9001 (mmm) REVERT: T 193 MET cc_start: 0.9079 (ttp) cc_final: 0.8422 (tmm) REVERT: V 5 MET cc_start: 0.8957 (ppp) cc_final: 0.8601 (ppp) REVERT: V 31 MET cc_start: 0.9196 (mmp) cc_final: 0.8857 (mmm) REVERT: V 158 MET cc_start: 0.9304 (ttm) cc_final: 0.8668 (ttm) REVERT: V 193 MET cc_start: 0.8021 (ttt) cc_final: 0.7537 (ttt) REVERT: W 5 MET cc_start: 0.8905 (ppp) cc_final: 0.8560 (ppp) REVERT: W 31 MET cc_start: 0.9241 (mmp) cc_final: 0.8973 (mmm) REVERT: W 193 MET cc_start: 0.9036 (ttp) cc_final: 0.8518 (ttt) REVERT: W 226 MET cc_start: 0.9165 (mmt) cc_final: 0.8887 (mmt) REVERT: X 5 MET cc_start: 0.8902 (ppp) cc_final: 0.8579 (ppp) REVERT: X 26 PHE cc_start: 0.8958 (m-80) cc_final: 0.8658 (m-80) REVERT: X 31 MET cc_start: 0.9147 (mmp) cc_final: 0.8822 (mmm) REVERT: X 158 MET cc_start: 0.9562 (ptm) cc_final: 0.9299 (ttp) REVERT: X 193 MET cc_start: 0.9280 (ttp) cc_final: 0.8340 (ttt) REVERT: Y 5 MET cc_start: 0.8895 (ppp) cc_final: 0.8536 (ppp) REVERT: Y 31 MET cc_start: 0.9270 (mmp) cc_final: 0.8951 (mmm) REVERT: Y 192 MET cc_start: 0.9329 (mmp) cc_final: 0.8996 (mmm) REVERT: Y 193 MET cc_start: 0.9349 (ttp) cc_final: 0.8397 (ttt) REVERT: Y 194 TYR cc_start: 0.9085 (m-80) cc_final: 0.8734 (m-10) REVERT: Y 226 MET cc_start: 0.9003 (mpp) cc_final: 0.8763 (mpp) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.2207 time to fit residues: 167.9982 Evaluate side-chains 318 residues out of total 4608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 312 optimal weight: 6.9990 chunk 273 optimal weight: 9.9990 chunk 417 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 270 optimal weight: 8.9990 chunk 348 optimal weight: 0.1980 chunk 318 optimal weight: 7.9990 chunk 363 optimal weight: 8.9990 chunk 277 optimal weight: 0.3980 chunk 293 optimal weight: 7.9990 chunk 388 optimal weight: 10.0000 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 201 HIS Q 27 ASN X 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.038938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.031085 restraints weight = 324854.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.032134 restraints weight = 196695.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.032900 restraints weight = 137443.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.033424 restraints weight = 105174.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.033799 restraints weight = 86244.286| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 42864 Z= 0.205 Angle : 0.624 14.770 57768 Z= 0.326 Chirality : 0.042 0.166 6888 Planarity : 0.004 0.034 7344 Dihedral : 4.716 20.137 5952 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: 1.79 (0.12), residues: 5424 helix: 1.85 (0.11), residues: 2136 sheet: -0.46 (0.15), residues: 1056 loop : 1.67 (0.16), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 6 TYR 0.030 0.002 TYR E 194 PHE 0.024 0.002 PHE C 26 HIS 0.007 0.001 HIS O 174 Details of bonding type rmsd covalent geometry : bond 0.00407 (42864) covalent geometry : angle 0.62367 (57768) hydrogen bonds : bond 0.03246 ( 2664) hydrogen bonds : angle 4.42141 ( 7200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5369.48 seconds wall clock time: 95 minutes 16.93 seconds (5716.93 seconds total)