Starting phenix.real_space_refine on Sat Aug 8 06:12:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uf0_42181/08_2026/8uf0_42181.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uf0_42181/08_2026/8uf0_42181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uf0_42181/08_2026/8uf0_42181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uf0_42181/08_2026/8uf0_42181.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uf0_42181/08_2026/8uf0_42181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uf0_42181/08_2026/8uf0_42181.map" } resolution = 2.02 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= 0.008 sd= 0.100 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 48 5.16 5 C 16776 2.51 5 N 4332 2.21 5 O 5844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27000 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 783 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "B" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "O" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "P" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "T" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "U" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "V" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "X" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, W, D, F, H, J, L, N, P, R, T, V, X Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" O HOH A 238 " occ=0.33 residue: pdb=" O HOH C 238 " occ=0.33 residue: pdb=" O HOH E 238 " occ=0.33 residue: pdb=" O HOH G 238 " occ=0.33 residue: pdb=" O HOH I 238 " occ=0.33 residue: pdb=" O HOH K 238 " occ=0.33 residue: pdb=" O HOH M 238 " occ=0.33 residue: pdb=" O HOH O 238 " occ=0.33 residue: pdb=" O HOH Q 238 " occ=0.33 residue: pdb=" O HOH S 238 " occ=0.33 residue: pdb=" O HOH U 238 " occ=0.33 residue: pdb=" O HOH W 238 " occ=0.33 Time building chain proxies: 3.38, per 1000 atoms: 0.13 Number of scatterers: 27000 At special positions: 0 Unit cell: (145.34, 141.04, 133.3, 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 48 16.00 O 5844 8.00 N 4332 7.00 C 16776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6552 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 36 sheets defined 43.1% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 26 through 40 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'B' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 143 Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 78 through 90 Processing helix chain 'C' and resid 106 through 117 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 82 removed outlier: 3.825A pdb=" N GLY D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 143 Processing helix chain 'D' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 203 removed outlier: 4.065A pdb=" N ILE D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 40 Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 90 Processing helix chain 'E' and resid 106 through 117 Processing helix chain 'F' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 82 removed outlier: 3.825A pdb=" N GLY F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 143 Processing helix chain 'F' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE F 200 " --> pdb=" O VAL F 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 40 Processing helix chain 'G' and resid 75 through 77 No H-bonds generated for 'chain 'G' and resid 75 through 77' Processing helix chain 'G' and resid 78 through 90 Processing helix chain 'G' and resid 106 through 117 Processing helix chain 'H' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 143 Processing helix chain 'H' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG H 176 " --> pdb=" O GLU H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 203 removed outlier: 4.065A pdb=" N ILE H 200 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 40 Processing helix chain 'I' and resid 75 through 77 No H-bonds generated for 'chain 'I' and resid 75 through 77' Processing helix chain 'I' and resid 78 through 90 Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'J' and resid 29 through 44 removed outlier: 3.778A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU J 105 " --> pdb=" O LEU J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 143 Processing helix chain 'J' and resid 167 through 183 removed outlier: 3.674A pdb=" N ARG J 176 " --> pdb=" O GLU J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 203 removed outlier: 4.067A pdb=" N ILE J 200 " --> pdb=" O VAL J 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 40 Processing helix chain 'K' and resid 75 through 77 No H-bonds generated for 'chain 'K' and resid 75 through 77' Processing helix chain 'K' and resid 78 through 90 Processing helix chain 'K' and resid 106 through 117 Processing helix chain 'L' and resid 29 through 44 removed outlier: 3.778A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 82 removed outlier: 3.825A pdb=" N GLY L 82 " --> pdb=" O LEU L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU L 105 " --> pdb=" O LEU L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 143 Processing helix chain 'L' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG L 176 " --> pdb=" O GLU L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 203 removed outlier: 4.065A pdb=" N ILE L 200 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 40 Processing helix chain 'M' and resid 75 through 77 No H-bonds generated for 'chain 'M' and resid 75 through 77' Processing helix chain 'M' and resid 78 through 90 Processing helix chain 'M' and resid 106 through 117 Processing helix chain 'N' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU N 105 " --> pdb=" O LEU N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 143 Processing helix chain 'N' and resid 167 through 183 removed outlier: 3.676A pdb=" N ARG N 176 " --> pdb=" O GLU N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE N 200 " --> pdb=" O VAL N 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 40 Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 78 through 90 Processing helix chain 'O' and resid 106 through 117 Processing helix chain 'P' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA P 44 " --> pdb=" O ALA P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY P 82 " --> pdb=" O LEU P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU P 105 " --> pdb=" O LEU P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 143 Processing helix chain 'P' and resid 167 through 183 removed outlier: 3.676A pdb=" N ARG P 176 " --> pdb=" O GLU P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE P 200 " --> pdb=" O VAL P 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 40 Processing helix chain 'Q' and resid 75 through 77 No H-bonds generated for 'chain 'Q' and resid 75 through 77' Processing helix chain 'Q' and resid 78 through 90 Processing helix chain 'Q' and resid 106 through 117 Processing helix chain 'R' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA R 44 " --> pdb=" O ALA R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY R 82 " --> pdb=" O LEU R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 143 Processing helix chain 'R' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG R 176 " --> pdb=" O GLU R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE R 200 " --> pdb=" O VAL R 196 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 40 Processing helix chain 'S' and resid 75 through 77 No H-bonds generated for 'chain 'S' and resid 75 through 77' Processing helix chain 'S' and resid 78 through 90 Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'T' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA T 44 " --> pdb=" O ALA T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY T 82 " --> pdb=" O LEU T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU T 105 " --> pdb=" O LEU T 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 128 through 143 Processing helix chain 'T' and resid 167 through 183 removed outlier: 3.674A pdb=" N ARG T 176 " --> pdb=" O GLU T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE T 200 " --> pdb=" O VAL T 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 40 Processing helix chain 'U' and resid 75 through 77 No H-bonds generated for 'chain 'U' and resid 75 through 77' Processing helix chain 'U' and resid 78 through 90 Processing helix chain 'U' and resid 106 through 117 Processing helix chain 'V' and resid 29 through 44 removed outlier: 3.778A pdb=" N ALA V 44 " --> pdb=" O ALA V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY V 82 " --> pdb=" O LEU V 78 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 107 removed outlier: 3.534A pdb=" N LEU V 105 " --> pdb=" O LEU V 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 128 through 143 Processing helix chain 'V' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG V 176 " --> pdb=" O GLU V 172 " (cutoff:3.500A) Processing helix chain 'V' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE V 200 " --> pdb=" O VAL V 196 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 40 Processing helix chain 'W' and resid 75 through 77 No H-bonds generated for 'chain 'W' and resid 75 through 77' Processing helix chain 'W' and resid 78 through 90 Processing helix chain 'W' and resid 106 through 117 Processing helix chain 'X' and resid 29 through 44 removed outlier: 3.777A pdb=" N ALA X 44 " --> pdb=" O ALA X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 82 removed outlier: 3.824A pdb=" N GLY X 82 " --> pdb=" O LEU X 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 107 removed outlier: 3.535A pdb=" N LEU X 105 " --> pdb=" O LEU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 143 Processing helix chain 'X' and resid 167 through 183 removed outlier: 3.675A pdb=" N ARG X 176 " --> pdb=" O GLU X 172 " (cutoff:3.500A) Processing helix chain 'X' and resid 196 through 203 removed outlier: 4.066A pdb=" N ILE X 200 " --> pdb=" O VAL X 196 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA A 46 " --> pdb=" O TYR A 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR A 73 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE A 48 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR A 71 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG A 69 " --> pdb=" O PRO A 50 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU B 48 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 64 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 50 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 22 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU B 93 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 24 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR B 91 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU B 26 " --> pdb=" O ILE B 89 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU B 147 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 165 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 149 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE B 121 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE B 191 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 123 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B 189 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU B 125 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'C' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA C 46 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR C 73 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE C 48 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR C 71 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG C 69 " --> pdb=" O PRO C 50 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'D' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU D 48 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU D 64 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS D 50 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU D 22 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU D 93 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE D 24 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR D 91 " --> pdb=" O ILE D 24 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU D 26 " --> pdb=" O ILE D 89 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'D' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU D 147 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 165 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER D 149 " --> pdb=" O THR D 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE D 121 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE D 191 " --> pdb=" O ILE D 121 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 123 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU D 189 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU D 125 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'E' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA E 46 " --> pdb=" O TYR E 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR E 73 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE E 48 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR E 71 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG E 69 " --> pdb=" O PRO E 50 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'F' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU F 48 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU F 64 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS F 50 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU F 22 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU F 93 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE F 24 " --> pdb=" O TYR F 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR F 91 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU F 26 " --> pdb=" O ILE F 89 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'F' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU F 147 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE F 165 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER F 149 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE F 121 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE F 191 " --> pdb=" O ILE F 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL F 123 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU F 189 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU F 125 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'G' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA G 46 " --> pdb=" O TYR G 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR G 73 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE G 48 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR G 71 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG G 69 " --> pdb=" O PRO G 50 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'H' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU H 48 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU H 64 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS H 50 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU H 22 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU H 93 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE H 24 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR H 91 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU H 26 " --> pdb=" O ILE H 89 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'H' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU H 147 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE H 165 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER H 149 " --> pdb=" O THR H 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE H 121 " --> pdb=" O ILE H 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE H 191 " --> pdb=" O ILE H 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL H 123 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU H 189 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU H 125 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'I' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA I 46 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR I 73 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE I 48 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR I 71 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG I 69 " --> pdb=" O PRO I 50 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'J' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU J 48 " --> pdb=" O LEU J 64 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU J 64 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS J 50 " --> pdb=" O MET J 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU J 22 " --> pdb=" O LEU J 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU J 93 " --> pdb=" O LEU J 22 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE J 24 " --> pdb=" O TYR J 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR J 91 " --> pdb=" O ILE J 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU J 26 " --> pdb=" O ILE J 89 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'J' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU J 147 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE J 165 " --> pdb=" O LEU J 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER J 149 " --> pdb=" O THR J 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE J 121 " --> pdb=" O ILE J 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE J 191 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL J 123 " --> pdb=" O LEU J 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU J 189 " --> pdb=" O VAL J 123 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU J 125 " --> pdb=" O LEU J 187 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'K' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA K 46 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR K 73 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE K 48 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR K 71 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG K 69 " --> pdb=" O PRO K 50 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'L' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU L 48 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU L 64 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS L 50 " --> pdb=" O MET L 62 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU L 22 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU L 93 " --> pdb=" O LEU L 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE L 24 " --> pdb=" O TYR L 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR L 91 " --> pdb=" O ILE L 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU L 26 " --> pdb=" O ILE L 89 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'L' and resid 146 through 151 removed outlier: 5.655A pdb=" N LEU L 147 " --> pdb=" O ILE L 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE L 165 " --> pdb=" O LEU L 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER L 149 " --> pdb=" O THR L 163 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE L 121 " --> pdb=" O ILE L 191 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE L 191 " --> pdb=" O ILE L 121 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL L 123 " --> pdb=" O LEU L 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU L 189 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU L 125 " --> pdb=" O LEU L 187 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'M' and resid 45 through 58 removed outlier: 6.253A pdb=" N ALA M 46 " --> pdb=" O TYR M 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR M 73 " --> pdb=" O ALA M 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE M 48 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR M 71 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG M 69 " --> pdb=" O PRO M 50 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'N' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU N 48 " --> pdb=" O LEU N 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU N 64 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS N 50 " --> pdb=" O MET N 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU N 22 " --> pdb=" O LEU N 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU N 93 " --> pdb=" O LEU N 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE N 24 " --> pdb=" O TYR N 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR N 91 " --> pdb=" O ILE N 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU N 26 " --> pdb=" O ILE N 89 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'N' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU N 147 " --> pdb=" O ILE N 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE N 165 " --> pdb=" O LEU N 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER N 149 " --> pdb=" O THR N 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE N 121 " --> pdb=" O ILE N 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE N 191 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL N 123 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU N 189 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU N 125 " --> pdb=" O LEU N 187 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'O' and resid 45 through 58 removed outlier: 6.253A pdb=" N ALA O 46 " --> pdb=" O TYR O 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR O 73 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE O 48 " --> pdb=" O THR O 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR O 71 " --> pdb=" O ILE O 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG O 69 " --> pdb=" O PRO O 50 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'P' and resid 47 through 54 removed outlier: 5.671A pdb=" N LEU P 48 " --> pdb=" O LEU P 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU P 64 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS P 50 " --> pdb=" O MET P 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU P 22 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU P 93 " --> pdb=" O LEU P 22 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE P 24 " --> pdb=" O TYR P 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR P 91 " --> pdb=" O ILE P 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU P 26 " --> pdb=" O ILE P 89 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'P' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU P 147 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE P 165 " --> pdb=" O LEU P 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER P 149 " --> pdb=" O THR P 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE P 121 " --> pdb=" O ILE P 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE P 191 " --> pdb=" O ILE P 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL P 123 " --> pdb=" O LEU P 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU P 189 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU P 125 " --> pdb=" O LEU P 187 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'Q' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA Q 46 " --> pdb=" O TYR Q 73 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR Q 73 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE Q 48 " --> pdb=" O THR Q 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR Q 71 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG Q 69 " --> pdb=" O PRO Q 50 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'R' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU R 48 " --> pdb=" O LEU R 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU R 64 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS R 50 " --> pdb=" O MET R 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU R 22 " --> pdb=" O LEU R 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU R 93 " --> pdb=" O LEU R 22 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE R 24 " --> pdb=" O TYR R 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR R 91 " --> pdb=" O ILE R 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU R 26 " --> pdb=" O ILE R 89 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'R' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU R 147 " --> pdb=" O ILE R 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE R 165 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER R 149 " --> pdb=" O THR R 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE R 121 " --> pdb=" O ILE R 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE R 191 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL R 123 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU R 189 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU R 125 " --> pdb=" O LEU R 187 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'S' and resid 45 through 58 removed outlier: 6.253A pdb=" N ALA S 46 " --> pdb=" O TYR S 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR S 73 " --> pdb=" O ALA S 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE S 48 " --> pdb=" O THR S 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR S 71 " --> pdb=" O ILE S 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG S 69 " --> pdb=" O PRO S 50 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'T' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU T 48 " --> pdb=" O LEU T 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU T 64 " --> pdb=" O LEU T 48 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS T 50 " --> pdb=" O MET T 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU T 22 " --> pdb=" O LEU T 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU T 93 " --> pdb=" O LEU T 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE T 24 " --> pdb=" O TYR T 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR T 91 " --> pdb=" O ILE T 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU T 26 " --> pdb=" O ILE T 89 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'T' and resid 146 through 151 removed outlier: 5.653A pdb=" N LEU T 147 " --> pdb=" O ILE T 165 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE T 165 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER T 149 " --> pdb=" O THR T 163 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE T 121 " --> pdb=" O ILE T 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE T 191 " --> pdb=" O ILE T 121 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL T 123 " --> pdb=" O LEU T 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU T 189 " --> pdb=" O VAL T 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU T 125 " --> pdb=" O LEU T 187 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'U' and resid 45 through 58 removed outlier: 6.252A pdb=" N ALA U 46 " --> pdb=" O TYR U 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR U 73 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE U 48 " --> pdb=" O THR U 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR U 71 " --> pdb=" O ILE U 48 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG U 69 " --> pdb=" O PRO U 50 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'V' and resid 47 through 54 removed outlier: 5.672A pdb=" N LEU V 48 " --> pdb=" O LEU V 64 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU V 64 " --> pdb=" O LEU V 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS V 50 " --> pdb=" O MET V 62 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU V 22 " --> pdb=" O LEU V 93 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU V 93 " --> pdb=" O LEU V 22 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE V 24 " --> pdb=" O TYR V 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR V 91 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU V 26 " --> pdb=" O ILE V 89 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'V' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU V 147 " --> pdb=" O ILE V 165 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE V 165 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER V 149 " --> pdb=" O THR V 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE V 121 " --> pdb=" O ILE V 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE V 191 " --> pdb=" O ILE V 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL V 123 " --> pdb=" O LEU V 189 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU V 189 " --> pdb=" O VAL V 123 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU V 125 " --> pdb=" O LEU V 187 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'W' and resid 45 through 58 removed outlier: 6.253A pdb=" N ALA W 46 " --> pdb=" O TYR W 73 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR W 73 " --> pdb=" O ALA W 46 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE W 48 " --> pdb=" O THR W 71 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR W 71 " --> pdb=" O ILE W 48 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG W 69 " --> pdb=" O PRO W 50 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'X' and resid 47 through 54 removed outlier: 5.671A pdb=" N LEU X 48 " --> pdb=" O LEU X 64 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU X 64 " --> pdb=" O LEU X 48 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS X 50 " --> pdb=" O MET X 62 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU X 22 " --> pdb=" O LEU X 93 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU X 93 " --> pdb=" O LEU X 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE X 24 " --> pdb=" O TYR X 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR X 91 " --> pdb=" O ILE X 24 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU X 26 " --> pdb=" O ILE X 89 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'X' and resid 146 through 151 removed outlier: 5.654A pdb=" N LEU X 147 " --> pdb=" O ILE X 165 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE X 165 " --> pdb=" O LEU X 147 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER X 149 " --> pdb=" O THR X 163 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE X 121 " --> pdb=" O ILE X 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE X 191 " --> pdb=" O ILE X 121 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL X 123 " --> pdb=" O LEU X 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU X 189 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU X 125 " --> pdb=" O LEU X 187 " (cutoff:3.500A) 1488 hydrogen bonds defined for protein. 4212 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: 5.35 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8679 1.34 - 1.46: 3461 1.46 - 1.58: 14380 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 26604 Sorted by residual: bond pdb=" CB GLU L 66 " pdb=" CG GLU L 66 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" CB GLU K 75 " pdb=" CG GLU K 75 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" CB GLU G 75 " pdb=" CG GLU G 75 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CB GLU E 75 " pdb=" CG GLU E 75 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CB GLU A 75 " pdb=" CG GLU A 75 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.73e+00 ... (remaining 26599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 34998 1.76 - 3.52: 1088 3.52 - 5.29: 106 5.29 - 7.05: 0 7.05 - 8.81: 24 Bond angle restraints: 36216 Sorted by residual: angle pdb=" CA LEU T 83 " pdb=" CB LEU T 83 " pdb=" CG LEU T 83 " ideal model delta sigma weight residual 116.30 124.87 -8.57 3.50e+00 8.16e-02 5.99e+00 angle pdb=" CA LEU J 83 " pdb=" CB LEU J 83 " pdb=" CG LEU J 83 " ideal model delta sigma weight residual 116.30 124.86 -8.56 3.50e+00 8.16e-02 5.98e+00 angle pdb=" CA LEU L 83 " pdb=" CB LEU L 83 " pdb=" CG LEU L 83 " ideal model delta sigma weight residual 116.30 124.86 -8.56 3.50e+00 8.16e-02 5.98e+00 angle pdb=" CA LEU R 83 " pdb=" CB LEU R 83 " pdb=" CG LEU R 83 " ideal model delta sigma weight residual 116.30 124.85 -8.55 3.50e+00 8.16e-02 5.97e+00 angle pdb=" CA LEU B 83 " pdb=" CB LEU B 83 " pdb=" CG LEU B 83 " ideal model delta sigma weight residual 116.30 124.85 -8.55 3.50e+00 8.16e-02 5.96e+00 ... (remaining 36211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 14313 16.89 - 33.77: 1671 33.77 - 50.66: 444 50.66 - 67.54: 216 67.54 - 84.43: 60 Dihedral angle restraints: 16704 sinusoidal: 6636 harmonic: 10068 Sorted by residual: dihedral pdb=" CA ASP R 137 " pdb=" CB ASP R 137 " pdb=" CG ASP R 137 " pdb=" OD1 ASP R 137 " ideal model delta sinusoidal sigma weight residual -30.00 -89.89 59.89 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP X 137 " pdb=" CB ASP X 137 " pdb=" CG ASP X 137 " pdb=" OD1 ASP X 137 " ideal model delta sinusoidal sigma weight residual -30.00 -89.87 59.87 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP T 137 " pdb=" CB ASP T 137 " pdb=" CG ASP T 137 " pdb=" OD1 ASP T 137 " ideal model delta sinusoidal sigma weight residual -30.00 -89.86 59.86 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 16701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1828 0.029 - 0.057: 1432 0.057 - 0.086: 652 0.086 - 0.115: 256 0.115 - 0.143: 272 Chirality restraints: 4440 Sorted by residual: chirality pdb=" CA PRO E 93 " pdb=" N PRO E 93 " pdb=" C PRO E 93 " pdb=" CB PRO E 93 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA PRO M 93 " pdb=" N PRO M 93 " pdb=" C PRO M 93 " pdb=" CB PRO M 93 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA PRO O 93 " pdb=" N PRO O 93 " pdb=" C PRO O 93 " pdb=" CB PRO O 93 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 4437 not shown) Planarity restraints: 4656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS G 90 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO G 91 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO G 91 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 91 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS K 90 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO K 91 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO K 91 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO K 91 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS W 90 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO W 91 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO W 91 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO W 91 " 0.023 5.00e-02 4.00e+02 ... (remaining 4653 not shown) Histogram of nonbonded interaction distances: 0.01 - 0.99: 12 0.99 - 1.97: 0 1.97 - 2.95: 10725 2.95 - 3.92: 68434 3.92 - 4.90: 124559 Warning: very small nonbonded interaction distances. Nonbonded interactions: 203730 Sorted by model distance: nonbonded pdb=" O HOH G 238 " pdb=" O HOH K 238 " model vdw 0.013 3.040 nonbonded pdb=" O HOH A 238 " pdb=" O HOH I 238 " model vdw 0.013 3.040 nonbonded pdb=" O HOH O 238 " pdb=" O HOH S 238 " model vdw 0.013 3.040 nonbonded pdb=" O HOH M 238 " pdb=" O HOH W 238 " model vdw 0.013 3.040 nonbonded pdb=" O HOH G 238 " pdb=" O HOH U 238 " model vdw 0.013 3.040 ... (remaining 203725 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } 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=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.090 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 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 : 0.007 0.045 26604 Z= 0.282 Angle : 0.756 8.812 36216 Z= 0.408 Chirality : 0.054 0.143 4440 Planarity : 0.006 0.041 4656 Dihedral : 17.495 84.429 10152 Min Nonbonded Distance : 0.013 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.54 % Allowed : 19.37 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.09 (0.14), residues: 3408 helix: 0.96 (0.14), residues: 1392 sheet: 1.42 (0.19), residues: 756 loop : -1.89 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG V 141 TYR 0.014 0.002 TYR L 91 PHE 0.018 0.003 PHE I 115 TRP 0.008 0.002 TRP E 112 HIS 0.005 0.002 HIS W 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.28 (26604) covalent geometry : angle 0.75612 / 0.41 (36216) hydrogen bonds : bond 0.27623 / 18.67 ( 1488) hydrogen bonds : angle 7.04476 / 4.93 ( 4212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 295 time to evaluate : 1.094 Fit side-chains REVERT: D 159 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7340 (mtt180) REVERT: N 83 LEU cc_start: 0.5196 (OUTLIER) cc_final: 0.4901 (tp) REVERT: V 83 LEU cc_start: 0.5207 (OUTLIER) cc_final: 0.4920 (tp) outliers start: 15 outliers final: 11 residues processed: 310 average time/residue: 0.9002 time to fit residues: 313.8480 Evaluate side-chains 279 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 266 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain T residue 54 VAL Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 83 LEU Chi-restraints excluded: chain X residue 54 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.0970 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN B 118 ASN D 118 ASN F 87 ASN F 118 ASN H 87 ASN H 118 ASN L 118 ASN N 87 ASN P 118 ASN T 118 ASN X 118 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.140044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.101293 restraints weight = 26139.061| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.82 r_work: 0.3059 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26604 Z= 0.194 Angle : 0.648 9.247 36216 Z= 0.350 Chirality : 0.047 0.141 4440 Planarity : 0.006 0.046 4656 Dihedral : 5.848 70.980 3687 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.38 % Allowed : 17.03 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.96 (0.15), residues: 3408 helix: 2.06 (0.14), residues: 1392 sheet: 1.14 (0.19), residues: 840 loop : -1.58 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 185 TYR 0.007 0.001 TYR R 91 PHE 0.013 0.002 PHE V 162 TRP 0.006 0.001 TRP K 112 HIS 0.002 0.001 HIS X 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.19 (26604) covalent geometry : angle 0.64756 / 0.35 (36216) hydrogen bonds : bond 0.08761 / 5.91 ( 1488) hydrogen bonds : angle 5.64179 / 3.89 ( 4212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 286 time to evaluate : 1.144 Fit side-chains REVERT: C 81 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8597 (mtmm) REVERT: D 159 ARG cc_start: 0.7434 (mtt90) cc_final: 0.7107 (mtt180) REVERT: F 83 LEU cc_start: 0.5141 (OUTLIER) cc_final: 0.4852 (tp) REVERT: G 35 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8698 (tttt) REVERT: H 83 LEU cc_start: 0.4860 (OUTLIER) cc_final: 0.4655 (tp) REVERT: P 83 LEU cc_start: 0.5069 (OUTLIER) cc_final: 0.4849 (tp) REVERT: R 66 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: S 35 LYS cc_start: 0.8921 (mtpp) cc_final: 0.8696 (tttt) REVERT: V 66 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: W 35 LYS cc_start: 0.8895 (mtpp) cc_final: 0.8682 (tttt) outliers start: 66 outliers final: 4 residues processed: 346 average time/residue: 0.8563 time to fit residues: 333.2537 Evaluate side-chains 294 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 284 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain V residue 66 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 188 optimal weight: 1.9990 chunk 259 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 314 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 219 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN F 87 ASN N 87 ASN P 118 ASN R 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.139362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.100079 restraints weight = 26162.170| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.84 r_work: 0.3040 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26604 Z= 0.218 Angle : 0.668 9.466 36216 Z= 0.365 Chirality : 0.049 0.140 4440 Planarity : 0.006 0.048 4656 Dihedral : 5.757 75.202 3672 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.70 % Allowed : 17.93 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.00 (0.15), residues: 3408 helix: 2.06 (0.14), residues: 1392 sheet: 1.39 (0.19), residues: 816 loop : -1.66 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 185 TYR 0.010 0.001 TYR R 91 PHE 0.014 0.003 PHE Q 115 TRP 0.007 0.002 TRP K 112 HIS 0.004 0.001 HIS O 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.22 (26604) covalent geometry : angle 0.66777 / 0.36 (36216) hydrogen bonds : bond 0.09047 / 6.10 ( 1488) hydrogen bonds : angle 5.53954 / 3.81 ( 4212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 287 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: B 83 LEU cc_start: 0.5071 (OUTLIER) cc_final: 0.4833 (tp) REVERT: C 87 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8846 (mtpp) REVERT: D 150 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.7816 (tpp) REVERT: D 159 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7088 (mtt180) REVERT: F 83 LEU cc_start: 0.5097 (OUTLIER) cc_final: 0.4869 (tp) REVERT: G 28 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8300 (mp0) REVERT: G 35 LYS cc_start: 0.8929 (ttmm) cc_final: 0.8714 (tttm) REVERT: G 72 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9063 (mt) REVERT: H 66 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: H 83 LEU cc_start: 0.4876 (OUTLIER) cc_final: 0.4656 (tp) REVERT: J 50 LYS cc_start: 0.6375 (OUTLIER) cc_final: 0.5153 (mptt) REVERT: J 159 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7293 (mtt90) REVERT: L 165 ILE cc_start: 0.8881 (tt) cc_final: 0.8326 (pp) REVERT: N 66 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: N 159 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7123 (mtt90) REVERT: P 66 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: P 159 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7353 (mtt90) REVERT: Q 63 LYS cc_start: 0.8356 (ptmt) cc_final: 0.7931 (ptmm) REVERT: R 66 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: R 159 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7247 (mtt90) REVERT: S 54 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8824 (tttp) REVERT: T 66 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: T 150 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8004 (ttp) REVERT: T 165 ILE cc_start: 0.8964 (tt) cc_final: 0.8463 (pp) REVERT: V 66 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: V 159 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7294 (mtt90) REVERT: W 35 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8660 (tttt) REVERT: X 66 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7666 (mp0) outliers start: 47 outliers final: 9 residues processed: 330 average time/residue: 0.8350 time to fit residues: 310.2568 Evaluate side-chains 309 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 277 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 159 ARG Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain S residue 54 LYS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain T residue 66 GLU Chi-restraints excluded: chain T residue 150 MET Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain W residue 103 THR Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 299 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 0.0170 chunk 77 optimal weight: 0.0870 chunk 198 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN F 87 ASN N 87 ASN N 118 ASN P 118 ASN R 87 ASN T 118 ASN X 118 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108078 restraints weight = 26727.390| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.84 r_work: 0.3158 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26604 Z= 0.126 Angle : 0.523 8.044 36216 Z= 0.274 Chirality : 0.045 0.140 4440 Planarity : 0.005 0.046 4656 Dihedral : 5.423 70.469 3672 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.60 % Allowed : 17.64 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.30 (0.15), residues: 3408 helix: 2.52 (0.14), residues: 1380 sheet: 1.74 (0.19), residues: 768 loop : -1.78 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 19 TYR 0.006 0.001 TYR H 30 PHE 0.012 0.002 PHE V 162 TRP 0.006 0.001 TRP E 112 HIS 0.001 0.000 HIS X 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 (26604) covalent geometry : angle 0.52282 / 0.27 (36216) hydrogen bonds : bond 0.04975 / 3.35 ( 1488) hydrogen bonds : angle 4.88633 / 3.33 ( 4212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 284 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8895 (ttmm) cc_final: 0.8682 (tttm) REVERT: B 50 LYS cc_start: 0.6438 (OUTLIER) cc_final: 0.4981 (mmmt) REVERT: C 81 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8458 (mtmm) REVERT: D 118 ASN cc_start: 0.7651 (t0) cc_final: 0.7416 (t0) REVERT: E 28 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: G 28 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: G 63 LYS cc_start: 0.8399 (ptmt) cc_final: 0.7874 (ptmm) REVERT: H 66 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: H 74 MET cc_start: 0.9122 (mmm) cc_final: 0.8852 (mmm) REVERT: H 87 ASN cc_start: 0.8117 (m110) cc_final: 0.7898 (m-40) REVERT: I 28 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: J 159 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7233 (mtt90) REVERT: K 35 LYS cc_start: 0.8958 (ttmm) cc_final: 0.8728 (tttt) REVERT: M 28 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: O 28 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: P 159 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7321 (mtt90) REVERT: Q 63 LYS cc_start: 0.8328 (ptmt) cc_final: 0.7902 (ptmm) REVERT: R 66 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: R 159 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7194 (mtt90) REVERT: S 35 LYS cc_start: 0.8904 (ttmm) cc_final: 0.8701 (tttt) REVERT: T 50 LYS cc_start: 0.6252 (OUTLIER) cc_final: 0.5049 (mmtt) REVERT: T 165 ILE cc_start: 0.8855 (tt) cc_final: 0.8313 (pp) REVERT: U 28 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: U 63 LYS cc_start: 0.8351 (ptmt) cc_final: 0.7872 (ptmm) REVERT: V 159 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7290 (mtt90) REVERT: W 28 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: X 66 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7268 (mp0) outliers start: 72 outliers final: 11 residues processed: 346 average time/residue: 0.8823 time to fit residues: 343.5415 Evaluate side-chains 308 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain W residue 28 GLU Chi-restraints excluded: chain X residue 18 GLU Chi-restraints excluded: chain X residue 66 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 57 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 333 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN F 87 ASN N 87 ASN P 118 ASN R 87 ASN T 87 ASN X 118 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.137068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.097958 restraints weight = 25651.355| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.77 r_work: 0.3000 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 26604 Z= 0.316 Angle : 0.806 9.976 36216 Z= 0.448 Chirality : 0.055 0.163 4440 Planarity : 0.006 0.043 4656 Dihedral : 5.917 77.807 3672 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.13 % Allowed : 18.15 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.97 (0.15), residues: 3408 helix: 1.96 (0.13), residues: 1404 sheet: 1.73 (0.19), residues: 768 loop : -1.75 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 185 TYR 0.017 0.003 TYR R 91 PHE 0.020 0.003 PHE Q 115 TRP 0.009 0.003 TRP W 112 HIS 0.007 0.002 HIS G 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.32 (26604) covalent geometry : angle 0.80608 / 0.45 (36216) hydrogen bonds : bond 0.11551 / 7.78 ( 1488) hydrogen bonds : angle 5.77647 / 4.00 ( 4212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 285 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.6577 (OUTLIER) cc_final: 0.5381 (mptt) REVERT: D 50 LYS cc_start: 0.6447 (OUTLIER) cc_final: 0.5159 (mmtt) REVERT: H 66 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: H 74 MET cc_start: 0.9193 (mmm) cc_final: 0.8967 (mmm) REVERT: H 83 LEU cc_start: 0.5103 (OUTLIER) cc_final: 0.4840 (tp) REVERT: J 50 LYS cc_start: 0.6530 (OUTLIER) cc_final: 0.5351 (mptt) REVERT: J 159 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7354 (mtt90) REVERT: L 50 LYS cc_start: 0.6499 (OUTLIER) cc_final: 0.5223 (mmtt) REVERT: N 50 LYS cc_start: 0.6609 (OUTLIER) cc_final: 0.5065 (mmmt) REVERT: N 66 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: P 50 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.5375 (mmtt) REVERT: P 66 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: P 159 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7449 (mtt90) REVERT: P 184 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8504 (mp0) REVERT: Q 54 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8907 (tttp) REVERT: Q 63 LYS cc_start: 0.8397 (ptmt) cc_final: 0.8047 (ptmm) REVERT: R 66 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: R 159 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7285 (mtt90) REVERT: S 35 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8769 (tttt) REVERT: S 54 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8911 (tttp) REVERT: T 50 LYS cc_start: 0.6453 (OUTLIER) cc_final: 0.5244 (mmtt) REVERT: T 165 ILE cc_start: 0.9037 (tt) cc_final: 0.8565 (pp) REVERT: U 54 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8975 (ttpm) REVERT: U 63 LYS cc_start: 0.8432 (ptmt) cc_final: 0.7887 (ptmm) REVERT: V 50 LYS cc_start: 0.6611 (OUTLIER) cc_final: 0.4979 (mmmt) REVERT: V 66 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: V 159 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7322 (mtt90) REVERT: V 184 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: X 50 LYS cc_start: 0.6363 (OUTLIER) cc_final: 0.5158 (mmtm) REVERT: X 66 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7927 (mp0) outliers start: 59 outliers final: 11 residues processed: 337 average time/residue: 0.9120 time to fit residues: 344.6938 Evaluate side-chains 315 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 279 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 50 LYS Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 50 LYS Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain P residue 184 GLU Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain S residue 54 LYS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain U residue 54 LYS Chi-restraints excluded: chain V residue 50 LYS Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain V residue 184 GLU Chi-restraints excluded: chain W residue 103 THR Chi-restraints excluded: chain X residue 18 GLU Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 66 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 107 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 291 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 319 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN F 87 ASN N 87 ASN P 118 ASN X 118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.139094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099807 restraints weight = 26029.770| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.84 r_work: 0.3032 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26604 Z= 0.234 Angle : 0.687 9.261 36216 Z= 0.379 Chirality : 0.050 0.141 4440 Planarity : 0.006 0.047 4656 Dihedral : 5.845 76.878 3672 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.31 % Allowed : 17.78 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.00 (0.15), residues: 3408 helix: 2.06 (0.14), residues: 1404 sheet: 1.57 (0.19), residues: 780 loop : -1.75 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 185 TYR 0.010 0.002 TYR R 91 PHE 0.016 0.003 PHE Q 115 TRP 0.007 0.002 TRP K 112 HIS 0.005 0.001 HIS O 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.23 (26604) covalent geometry : angle 0.68684 / 0.38 (36216) hydrogen bonds : bond 0.09167 / 6.18 ( 1488) hydrogen bonds : angle 5.53194 / 3.81 ( 4212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 281 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.6430 (OUTLIER) cc_final: 0.5245 (mptt) REVERT: B 83 LEU cc_start: 0.4930 (OUTLIER) cc_final: 0.4705 (tp) REVERT: D 50 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.4997 (mmtt) REVERT: E 28 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: F 50 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.4798 (mmmt) REVERT: F 83 LEU cc_start: 0.5300 (OUTLIER) cc_final: 0.5062 (tp) REVERT: G 63 LYS cc_start: 0.8386 (ptmt) cc_final: 0.7860 (ptmm) REVERT: H 50 LYS cc_start: 0.6403 (OUTLIER) cc_final: 0.5167 (mmtt) REVERT: H 66 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: H 74 MET cc_start: 0.9155 (mmm) cc_final: 0.8879 (mmm) REVERT: H 83 LEU cc_start: 0.4977 (OUTLIER) cc_final: 0.4719 (tp) REVERT: J 50 LYS cc_start: 0.6374 (OUTLIER) cc_final: 0.5195 (mptt) REVERT: J 159 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7317 (mtt90) REVERT: J 170 ASP cc_start: 0.8409 (m-30) cc_final: 0.8181 (m-30) REVERT: L 50 LYS cc_start: 0.6278 (OUTLIER) cc_final: 0.4981 (mmtt) REVERT: M 28 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: N 50 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.4922 (mmmt) REVERT: N 66 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: P 50 LYS cc_start: 0.6478 (OUTLIER) cc_final: 0.5204 (mmtt) REVERT: P 66 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: P 159 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7401 (mtt90) REVERT: Q 54 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8841 (tttp) REVERT: Q 63 LYS cc_start: 0.8336 (ptmt) cc_final: 0.7959 (ptmm) REVERT: R 66 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: R 159 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7211 (mtt90) REVERT: S 35 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8637 (tttt) REVERT: S 54 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8829 (tttp) REVERT: T 50 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5078 (mmtt) REVERT: U 28 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: U 63 LYS cc_start: 0.8430 (ptmt) cc_final: 0.7847 (ptmm) REVERT: V 50 LYS cc_start: 0.6480 (OUTLIER) cc_final: 0.4806 (mmmt) REVERT: V 66 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: V 159 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7293 (mtt90) REVERT: W 54 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8990 (ttpp) REVERT: X 66 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7714 (mp0) outliers start: 64 outliers final: 9 residues processed: 339 average time/residue: 0.8998 time to fit residues: 342.4931 Evaluate side-chains 315 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 277 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 50 LYS Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 50 LYS Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain S residue 54 LYS Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain V residue 50 LYS Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain W residue 54 LYS Chi-restraints excluded: chain W residue 103 THR Chi-restraints excluded: chain X residue 18 GLU Chi-restraints excluded: chain X residue 66 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 66 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 chunk 181 optimal weight: 50.0000 chunk 223 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN F 87 ASN N 87 ASN P 87 ASN P 118 ASN X 118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.147970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108434 restraints weight = 27427.628| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.92 r_work: 0.3282 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26604 Z= 0.175 Angle : 0.593 8.529 36216 Z= 0.322 Chirality : 0.047 0.142 4440 Planarity : 0.005 0.049 4656 Dihedral : 5.666 74.851 3672 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.95 % Allowed : 18.15 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.21 (0.15), residues: 3408 helix: 2.48 (0.14), residues: 1368 sheet: 1.72 (0.19), residues: 768 loop : -1.83 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 19 TYR 0.007 0.001 TYR R 91 PHE 0.014 0.002 PHE V 162 TRP 0.007 0.001 TRP K 112 HIS 0.002 0.001 HIS U 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.18 (26604) covalent geometry : angle 0.59307 / 0.32 (36216) hydrogen bonds : bond 0.07145 / 4.81 ( 1488) hydrogen bonds : angle 5.21821 / 3.58 ( 4212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.6550 (OUTLIER) cc_final: 0.5080 (mmmt) REVERT: D 118 ASN cc_start: 0.7620 (t0) cc_final: 0.7357 (t0) REVERT: E 28 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: F 50 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.4985 (mmmt) REVERT: G 28 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8313 (mp0) REVERT: G 63 LYS cc_start: 0.8422 (ptmt) cc_final: 0.7959 (ptmm) REVERT: H 50 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.5388 (mmtt) REVERT: H 66 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: H 74 MET cc_start: 0.9225 (mmm) cc_final: 0.8958 (mmm) REVERT: H 83 LEU cc_start: 0.4969 (OUTLIER) cc_final: 0.4751 (tp) REVERT: J 50 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.5393 (mptt) REVERT: L 50 LYS cc_start: 0.6489 (OUTLIER) cc_final: 0.5307 (mmtt) REVERT: M 28 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: O 28 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: P 66 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: P 87 ASN cc_start: 0.8133 (m-40) cc_final: 0.7886 (m-40) REVERT: P 159 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7420 (mtt90) REVERT: Q 54 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8949 (tttp) REVERT: Q 63 LYS cc_start: 0.8374 (ptmt) cc_final: 0.8060 (ptmm) REVERT: R 66 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: R 159 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7257 (mtt90) REVERT: T 50 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.5257 (mmtt) REVERT: T 165 ILE cc_start: 0.8985 (tt) cc_final: 0.8482 (pp) REVERT: U 28 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: U 54 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8990 (ttpm) REVERT: U 63 LYS cc_start: 0.8464 (ptmt) cc_final: 0.7979 (ptmm) REVERT: V 66 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: V 159 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7292 (mtt90) REVERT: W 28 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: X 50 LYS cc_start: 0.6225 (OUTLIER) cc_final: 0.5129 (mmtm) REVERT: X 66 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7572 (mp0) outliers start: 54 outliers final: 9 residues processed: 335 average time/residue: 0.8271 time to fit residues: 312.1839 Evaluate side-chains 316 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 283 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain U residue 54 LYS Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain W residue 28 GLU Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 66 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 297 optimal weight: 1.9990 chunk 268 optimal weight: 10.0000 chunk 275 optimal weight: 20.0000 chunk 233 optimal weight: 0.9980 chunk 326 optimal weight: 0.9980 chunk 181 optimal weight: 30.0000 chunk 196 optimal weight: 9.9990 chunk 313 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN F 87 ASN L 87 ASN N 87 ASN P 118 ASN X 118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.147382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.107356 restraints weight = 27304.848| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.95 r_work: 0.3258 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26604 Z= 0.153 Angle : 0.553 8.281 36216 Z= 0.296 Chirality : 0.046 0.139 4440 Planarity : 0.005 0.049 4656 Dihedral : 5.549 71.863 3672 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.88 % Allowed : 18.29 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.31 (0.15), residues: 3408 helix: 2.59 (0.14), residues: 1380 sheet: 1.74 (0.19), residues: 768 loop : -1.84 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 19 TYR 0.006 0.001 TYR M 109 PHE 0.013 0.002 PHE V 162 TRP 0.006 0.001 TRP K 112 HIS 0.002 0.001 HIS S 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (26604) covalent geometry : angle 0.55310 / 0.30 (36216) hydrogen bonds : bond 0.06284 / 4.23 ( 1488) hydrogen bonds : angle 5.01880 / 3.44 ( 4212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 281 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8602 (tttm) REVERT: B 50 LYS cc_start: 0.6342 (OUTLIER) cc_final: 0.4861 (mmmt) REVERT: D 118 ASN cc_start: 0.7549 (t0) cc_final: 0.7308 (t0) REVERT: E 28 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: F 50 LYS cc_start: 0.6443 (OUTLIER) cc_final: 0.4833 (mmmt) REVERT: G 28 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: G 63 LYS cc_start: 0.8374 (ptmt) cc_final: 0.7950 (ptmm) REVERT: H 50 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.5166 (mmtt) REVERT: H 66 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: H 74 MET cc_start: 0.9151 (mmm) cc_final: 0.8875 (mmm) REVERT: J 50 LYS cc_start: 0.6249 (OUTLIER) cc_final: 0.5042 (mptt) REVERT: J 159 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7195 (mtt90) REVERT: L 50 LYS cc_start: 0.6277 (OUTLIER) cc_final: 0.5084 (mmtt) REVERT: M 28 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: N 66 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: O 28 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: P 66 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: P 87 ASN cc_start: 0.8018 (m-40) cc_final: 0.7788 (m-40) REVERT: P 159 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7329 (mtt90) REVERT: Q 54 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8834 (tttp) REVERT: Q 63 LYS cc_start: 0.8294 (ptmt) cc_final: 0.7891 (ptmm) REVERT: R 66 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: R 159 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7112 (mtt90) REVERT: T 50 LYS cc_start: 0.6192 (OUTLIER) cc_final: 0.4963 (mmtt) REVERT: T 165 ILE cc_start: 0.8871 (tt) cc_final: 0.8333 (pp) REVERT: U 28 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: U 63 LYS cc_start: 0.8390 (ptmt) cc_final: 0.7850 (ptmm) REVERT: V 50 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.4779 (mmmt) REVERT: V 66 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: V 159 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7197 (mtt90) REVERT: W 28 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: X 50 LYS cc_start: 0.6224 (OUTLIER) cc_final: 0.5103 (mmtm) REVERT: X 66 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7406 (mp0) outliers start: 52 outliers final: 7 residues processed: 327 average time/residue: 0.8270 time to fit residues: 304.6498 Evaluate side-chains 310 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain V residue 50 LYS Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain W residue 28 GLU Chi-restraints excluded: chain W residue 103 THR Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 66 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 86 optimal weight: 0.6980 chunk 254 optimal weight: 5.9990 chunk 270 optimal weight: 0.2980 chunk 256 optimal weight: 0.8980 chunk 193 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN N 87 ASN P 118 ASN T 87 ASN X 118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.148770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108985 restraints weight = 27497.649| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.96 r_work: 0.3285 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26604 Z= 0.137 Angle : 0.525 7.960 36216 Z= 0.278 Chirality : 0.045 0.138 4440 Planarity : 0.005 0.047 4656 Dihedral : 5.424 69.668 3672 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.55 % Allowed : 18.94 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.42 (0.15), residues: 3408 helix: 2.67 (0.14), residues: 1392 sheet: 1.79 (0.19), residues: 768 loop : -1.82 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 19 TYR 0.009 0.001 TYR E 56 PHE 0.012 0.002 PHE V 162 TRP 0.006 0.001 TRP E 112 HIS 0.001 0.000 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (26604) covalent geometry : angle 0.52525 / 0.28 (36216) hydrogen bonds : bond 0.05599 / 3.77 ( 1488) hydrogen bonds : angle 4.85462 / 3.32 ( 4212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 282 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8595 (tttm) REVERT: B 50 LYS cc_start: 0.6349 (OUTLIER) cc_final: 0.4867 (mmmt) REVERT: E 28 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: F 50 LYS cc_start: 0.6444 (OUTLIER) cc_final: 0.5146 (mmpt) REVERT: G 63 LYS cc_start: 0.8395 (ptmt) cc_final: 0.7947 (ptmm) REVERT: H 50 LYS cc_start: 0.6427 (OUTLIER) cc_final: 0.5261 (mmtt) REVERT: H 74 MET cc_start: 0.9152 (mmm) cc_final: 0.8872 (mmm) REVERT: J 50 LYS cc_start: 0.6242 (OUTLIER) cc_final: 0.4702 (mmmt) REVERT: J 159 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7182 (mtt90) REVERT: L 50 LYS cc_start: 0.6198 (OUTLIER) cc_final: 0.5023 (mmtt) REVERT: M 28 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: N 159 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7118 (mtt90) REVERT: O 28 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: P 66 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: P 87 ASN cc_start: 0.8072 (m-40) cc_final: 0.7835 (m-40) REVERT: P 159 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7332 (mtt90) REVERT: Q 63 LYS cc_start: 0.8288 (ptmt) cc_final: 0.7891 (ptmm) REVERT: R 66 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: R 159 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7084 (mtt90) REVERT: T 50 LYS cc_start: 0.6295 (OUTLIER) cc_final: 0.5065 (mmtt) REVERT: T 165 ILE cc_start: 0.8854 (tt) cc_final: 0.8319 (pp) REVERT: U 28 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: U 63 LYS cc_start: 0.8396 (ptmt) cc_final: 0.7864 (ptmm) REVERT: V 66 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: V 159 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7175 (mtt90) REVERT: W 28 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: X 50 LYS cc_start: 0.6213 (OUTLIER) cc_final: 0.5106 (mmtm) REVERT: X 66 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7292 (mp0) outliers start: 43 outliers final: 6 residues processed: 322 average time/residue: 0.8969 time to fit residues: 324.9290 Evaluate side-chains 305 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain N residue 159 ARG Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain W residue 28 GLU Chi-restraints excluded: chain W residue 103 THR Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 66 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 111 optimal weight: 0.6980 chunk 91 optimal weight: 0.0020 chunk 141 optimal weight: 10.0000 chunk 265 optimal weight: 40.0000 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 282 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 312 optimal weight: 6.9990 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 118 ASN F 87 ASN N 87 ASN P 118 ASN T 87 ASN T 118 ASN X 118 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.146930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106603 restraints weight = 27206.837| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.96 r_work: 0.3249 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26604 Z= 0.161 Angle : 0.562 8.323 36216 Z= 0.303 Chirality : 0.046 0.137 4440 Planarity : 0.005 0.046 4656 Dihedral : 5.502 71.160 3672 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.48 % Allowed : 19.34 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.37 (0.15), residues: 3408 helix: 2.61 (0.14), residues: 1392 sheet: 1.77 (0.19), residues: 768 loop : -1.82 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 185 TYR 0.009 0.001 TYR C 56 PHE 0.013 0.002 PHE V 162 TRP 0.006 0.001 TRP M 112 HIS 0.002 0.001 HIS G 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 (26604) covalent geometry : angle 0.56157 / 0.30 (36216) hydrogen bonds : bond 0.06676 / 4.49 ( 1488) hydrogen bonds : angle 4.98097 / 3.42 ( 4212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6816 Ramachandran restraints generated. 3408 Oldfield, 0 Emsley, 3408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 279 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8600 (tttm) REVERT: B 50 LYS cc_start: 0.6350 (OUTLIER) cc_final: 0.4859 (mmmt) REVERT: E 28 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: F 50 LYS cc_start: 0.6475 (OUTLIER) cc_final: 0.5176 (mmpt) REVERT: G 28 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8198 (mp0) REVERT: H 50 LYS cc_start: 0.6416 (OUTLIER) cc_final: 0.5236 (mmtt) REVERT: H 66 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: H 74 MET cc_start: 0.9153 (mmm) cc_final: 0.8877 (mmm) REVERT: J 50 LYS cc_start: 0.6248 (OUTLIER) cc_final: 0.5046 (mptt) REVERT: J 159 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7187 (mtt90) REVERT: L 50 LYS cc_start: 0.6165 (OUTLIER) cc_final: 0.5003 (mmtt) REVERT: M 28 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: N 50 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.5037 (mmmt) REVERT: N 66 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: N 159 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7131 (mtt90) REVERT: O 28 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: P 66 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: P 87 ASN cc_start: 0.8094 (m-40) cc_final: 0.7848 (m-40) REVERT: P 159 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7325 (mtt90) REVERT: Q 63 LYS cc_start: 0.8295 (ptmt) cc_final: 0.7886 (ptmm) REVERT: R 66 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: R 159 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7085 (mtt90) REVERT: S 77 GLU cc_start: 0.7596 (pm20) cc_final: 0.7163 (pm20) REVERT: T 50 LYS cc_start: 0.6310 (OUTLIER) cc_final: 0.5082 (mmtt) REVERT: T 165 ILE cc_start: 0.8883 (tt) cc_final: 0.8355 (pp) REVERT: U 28 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: U 63 LYS cc_start: 0.8390 (ptmt) cc_final: 0.7890 (ptmm) REVERT: V 50 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.4937 (mmmt) REVERT: V 66 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: V 159 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7178 (mtt90) REVERT: X 50 LYS cc_start: 0.6214 (OUTLIER) cc_final: 0.5182 (mmtm) REVERT: X 66 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7427 (mp0) outliers start: 41 outliers final: 7 residues processed: 317 average time/residue: 0.9032 time to fit residues: 321.9161 Evaluate side-chains 310 residues out of total 2772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain G residue 28 GLU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 159 ARG Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain N residue 50 LYS Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain N residue 159 ARG Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain P residue 66 GLU Chi-restraints excluded: chain P residue 159 ARG Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 159 ARG Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain T residue 50 LYS Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain V residue 50 LYS Chi-restraints excluded: chain V residue 66 GLU Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 103 THR Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 66 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 256 optimal weight: 2.9990 chunk 184 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 262 optimal weight: 0.0870 chunk 132 optimal weight: 0.6980 chunk 187 optimal weight: 8.9990 chunk 330 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 276 optimal weight: 9.9990 chunk 157 optimal weight: 0.5980 chunk 54 optimal weight: 20.0000 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 118 ASN F 87 ASN N 87 ASN T 87 ASN T 118 ASN X 118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.150057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110638 restraints weight = 27416.875| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.95 r_work: 0.3309 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26604 Z= 0.126 Angle : 0.509 7.675 36216 Z= 0.268 Chirality : 0.045 0.136 4440 Planarity : 0.005 0.046 4656 Dihedral : 5.316 68.196 3672 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.30 % Allowed : 19.62 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.51 (0.15), residues: 3408 helix: 2.79 (0.14), residues: 1392 sheet: 1.81 (0.19), residues: 768 loop : -1.80 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 141 TYR 0.006 0.001 TYR M 109 PHE 0.012 0.002 PHE V 162 TRP 0.007 0.001 TRP E 112 HIS 0.001 0.000 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (26604) covalent geometry : angle 0.50950 / 0.27 (36216) hydrogen bonds : bond 0.05017 / 3.38 ( 1488) hydrogen bonds : angle 4.71085 / 3.21 ( 4212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14905.12 seconds wall clock time: 252 minutes 56.65 seconds (15176.65 seconds total)