Starting phenix.real_space_refine on Fri Mar 6 20:11:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o6e_12738/03_2026/7o6e_12738.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o6e_12738/03_2026/7o6e_12738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7o6e_12738/03_2026/7o6e_12738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o6e_12738/03_2026/7o6e_12738.map" model { file = "/net/cci-nas-00/data/ceres_data/7o6e_12738/03_2026/7o6e_12738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o6e_12738/03_2026/7o6e_12738.cif" } resolution = 2.1 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= 0.410 sd= 1.618 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 120 5.16 5 C 21264 2.51 5 N 6096 2.21 5 O 7824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 192 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35304 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Conformer: "B" Number of residues, atoms: 177, 1403 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} bond proxies already assigned to first conformer: 1417 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "H" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "I" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "J" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "K" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "M" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "N" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "O" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "P" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "Q" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "S" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "T" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "V" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "W" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "X" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "Y" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, W, X, Y Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N AHIS A 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 175 " occ=0.50 residue: pdb=" N AHIS B 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 175 " occ=0.50 residue: pdb=" N AHIS C 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 175 " occ=0.50 residue: pdb=" N AHIS D 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 175 " occ=0.50 residue: pdb=" N AHIS E 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS E 175 " occ=0.50 residue: pdb=" N AHIS F 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS F 175 " occ=0.50 residue: pdb=" N AHIS G 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS G 175 " occ=0.50 residue: pdb=" N AHIS H 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS H 175 " occ=0.50 residue: pdb=" N AHIS I 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS I 175 " occ=0.50 residue: pdb=" N AHIS J 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS J 175 " occ=0.50 residue: pdb=" N AHIS K 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS K 175 " occ=0.50 residue: pdb=" N AHIS L 175 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS L 175 " occ=0.50 ... (remaining 12 not shown) Time building chain proxies: 3.67, per 1000 atoms: 0.10 Number of scatterers: 35304 At special positions: 0 Unit cell: (129.629, 129.629, 129.629, 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 120 16.00 O 7824 8.00 N 6096 7.00 C 21264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 2.6 seconds 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8112 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 76.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 Processing helix chain 'A' and resid 41 through 69 Processing helix chain 'A' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 38 Processing helix chain 'B' and resid 41 through 69 Processing helix chain 'B' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 134 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU B 156 " --> pdb=" O ASN B 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 38 Processing helix chain 'C' and resid 41 through 69 Processing helix chain 'C' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP C 127 " --> pdb=" O GLN C 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 38 Processing helix chain 'D' and resid 41 through 69 Processing helix chain 'D' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP D 127 " --> pdb=" O GLN D 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 38 Processing helix chain 'E' and resid 41 through 69 Processing helix chain 'E' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA E 91 " --> pdb=" O ARG E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP E 127 " --> pdb=" O GLN E 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE E 128 " --> pdb=" O PHE E 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU E 134 " --> pdb=" O GLN E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU E 156 " --> pdb=" O ASN E 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 38 Processing helix chain 'F' and resid 41 through 69 Processing helix chain 'F' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA F 91 " --> pdb=" O ARG F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP F 127 " --> pdb=" O GLN F 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE F 128 " --> pdb=" O PHE F 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU F 134 " --> pdb=" O GLN F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU F 156 " --> pdb=" O ASN F 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 38 Processing helix chain 'G' and resid 41 through 69 Processing helix chain 'G' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA G 91 " --> pdb=" O ARG G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE G 128 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU G 134 " --> pdb=" O GLN G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU G 156 " --> pdb=" O ASN G 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 38 Processing helix chain 'H' and resid 41 through 69 Processing helix chain 'H' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP H 127 " --> pdb=" O GLN H 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE H 128 " --> pdb=" O PHE H 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU H 134 " --> pdb=" O GLN H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU H 156 " --> pdb=" O ASN H 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 38 Processing helix chain 'I' and resid 41 through 69 Processing helix chain 'I' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP I 127 " --> pdb=" O GLN I 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE I 128 " --> pdb=" O PHE I 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU I 134 " --> pdb=" O GLN I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU I 156 " --> pdb=" O ASN I 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 38 Processing helix chain 'J' and resid 41 through 69 Processing helix chain 'J' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA J 91 " --> pdb=" O ARG J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP J 127 " --> pdb=" O GLN J 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE J 128 " --> pdb=" O PHE J 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU J 134 " --> pdb=" O GLN J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU J 156 " --> pdb=" O ASN J 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 38 Processing helix chain 'K' and resid 41 through 69 Processing helix chain 'K' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA K 91 " --> pdb=" O ARG K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP K 127 " --> pdb=" O GLN K 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE K 128 " --> pdb=" O PHE K 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU K 134 " --> pdb=" O GLN K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU K 156 " --> pdb=" O ASN K 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 38 Processing helix chain 'L' and resid 41 through 69 Processing helix chain 'L' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP L 127 " --> pdb=" O GLN L 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU L 134 " --> pdb=" O GLN L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU L 156 " --> pdb=" O ASN L 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 38 Processing helix chain 'M' and resid 41 through 69 Processing helix chain 'M' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA M 91 " --> pdb=" O ARG M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP M 127 " --> pdb=" O GLN M 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE M 128 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU M 134 " --> pdb=" O GLN M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU M 156 " --> pdb=" O ASN M 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 38 Processing helix chain 'N' and resid 41 through 69 Processing helix chain 'N' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA N 91 " --> pdb=" O ARG N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP N 127 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE N 128 " --> pdb=" O PHE N 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU N 134 " --> pdb=" O GLN N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU N 156 " --> pdb=" O ASN N 152 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 38 Processing helix chain 'O' and resid 41 through 69 Processing helix chain 'O' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA O 91 " --> pdb=" O ARG O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP O 127 " --> pdb=" O GLN O 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE O 128 " --> pdb=" O PHE O 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU O 134 " --> pdb=" O GLN O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU O 156 " --> pdb=" O ASN O 152 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 38 Processing helix chain 'P' and resid 41 through 69 Processing helix chain 'P' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA P 91 " --> pdb=" O ARG P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP P 127 " --> pdb=" O GLN P 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE P 128 " --> pdb=" O PHE P 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU P 134 " --> pdb=" O GLN P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU P 156 " --> pdb=" O ASN P 152 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 38 Processing helix chain 'Q' and resid 41 through 69 Processing helix chain 'Q' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA Q 91 " --> pdb=" O ARG Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP Q 127 " --> pdb=" O GLN Q 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE Q 128 " --> pdb=" O PHE Q 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU Q 134 " --> pdb=" O GLN Q 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU Q 156 " --> pdb=" O ASN Q 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 38 Processing helix chain 'R' and resid 41 through 69 Processing helix chain 'R' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA R 91 " --> pdb=" O ARG R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP R 127 " --> pdb=" O GLN R 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE R 128 " --> pdb=" O PHE R 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU R 134 " --> pdb=" O GLN R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU R 156 " --> pdb=" O ASN R 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 38 Processing helix chain 'S' and resid 41 through 69 Processing helix chain 'S' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA S 91 " --> pdb=" O ARG S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP S 127 " --> pdb=" O GLN S 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE S 128 " --> pdb=" O PHE S 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU S 134 " --> pdb=" O GLN S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU S 156 " --> pdb=" O ASN S 152 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 38 Processing helix chain 'T' and resid 41 through 69 Processing helix chain 'T' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA T 91 " --> pdb=" O ARG T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP T 127 " --> pdb=" O GLN T 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE T 128 " --> pdb=" O PHE T 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU T 134 " --> pdb=" O GLN T 130 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU T 156 " --> pdb=" O ASN T 152 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 38 Processing helix chain 'V' and resid 41 through 69 Processing helix chain 'V' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA V 91 " --> pdb=" O ARG V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP V 127 " --> pdb=" O GLN V 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE V 128 " --> pdb=" O PHE V 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU V 134 " --> pdb=" O GLN V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU V 156 " --> pdb=" O ASN V 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 38 Processing helix chain 'W' and resid 41 through 69 Processing helix chain 'W' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA W 91 " --> pdb=" O ARG W 87 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP W 127 " --> pdb=" O GLN W 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE W 128 " --> pdb=" O PHE W 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU W 134 " --> pdb=" O GLN W 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU W 156 " --> pdb=" O ASN W 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 38 Processing helix chain 'X' and resid 41 through 69 Processing helix chain 'X' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA X 91 " --> pdb=" O ARG X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP X 127 " --> pdb=" O GLN X 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE X 128 " --> pdb=" O PHE X 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU X 134 " --> pdb=" O GLN X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU X 156 " --> pdb=" O ASN X 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 38 Processing helix chain 'Y' and resid 41 through 69 Processing helix chain 'Y' and resid 87 through 117 removed outlier: 3.636A pdb=" N ALA Y 91 " --> pdb=" O ARG Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 150 removed outlier: 4.389A pdb=" N TRP Y 127 " --> pdb=" O GLN Y 123 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE Y 128 " --> pdb=" O PHE Y 124 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU Y 134 " --> pdb=" O GLN Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 164 removed outlier: 3.876A pdb=" N LEU Y 156 " --> pdb=" O ASN Y 152 " (cutoff:3.500A) 2664 hydrogen bonds defined for protein. 7992 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: 5.92 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8952 1.32 - 1.44: 6576 1.44 - 1.56: 18816 1.56 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 34584 Sorted by residual: bond pdb=" C ASN H 57 " pdb=" O ASN H 57 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.93e+00 bond pdb=" C ASN D 57 " pdb=" O ASN D 57 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.93e+00 bond pdb=" C ASN J 57 " pdb=" O ASN J 57 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.93e+00 bond pdb=" C ASN K 57 " pdb=" O ASN K 57 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.93e+00 bond pdb=" C ASN R 57 " pdb=" O ASN R 57 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.93e+00 ... (remaining 34579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 40440 1.46 - 2.91: 5304 2.91 - 4.37: 792 4.37 - 5.83: 240 5.83 - 7.29: 120 Bond angle restraints: 46896 Sorted by residual: angle pdb=" CA PRO A 168 " pdb=" N PRO A 168 " pdb=" CD PRO A 168 " ideal model delta sigma weight residual 112.00 107.94 4.06 1.40e+00 5.10e-01 8.39e+00 angle pdb=" CA PRO H 168 " pdb=" N PRO H 168 " pdb=" CD PRO H 168 " ideal model delta sigma weight residual 112.00 107.94 4.06 1.40e+00 5.10e-01 8.39e+00 angle pdb=" CA PRO B 168 " pdb=" N PRO B 168 " pdb=" CD PRO B 168 " ideal model delta sigma weight residual 112.00 107.94 4.06 1.40e+00 5.10e-01 8.39e+00 angle pdb=" CA PRO X 168 " pdb=" N PRO X 168 " pdb=" CD PRO X 168 " ideal model delta sigma weight residual 112.00 107.94 4.06 1.40e+00 5.10e-01 8.39e+00 angle pdb=" CA PRO C 168 " pdb=" N PRO C 168 " pdb=" CD PRO C 168 " ideal model delta sigma weight residual 112.00 107.94 4.06 1.40e+00 5.10e-01 8.39e+00 ... (remaining 46891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 18120 17.72 - 35.43: 1920 35.43 - 53.15: 504 53.15 - 70.86: 144 70.86 - 88.58: 144 Dihedral angle restraints: 20832 sinusoidal: 8376 harmonic: 12456 Sorted by residual: dihedral pdb=" CA PRO R 76 " pdb=" C PRO R 76 " pdb=" N GLY R 77 " pdb=" CA GLY R 77 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PRO K 76 " pdb=" C PRO K 76 " pdb=" N GLY K 77 " pdb=" CA GLY K 77 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PRO H 76 " pdb=" C PRO H 76 " pdb=" N GLY H 77 " pdb=" CA GLY H 77 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 20829 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.049: 2400 0.049 - 0.096: 1848 0.096 - 0.143: 768 0.143 - 0.190: 72 0.190 - 0.237: 48 Chirality restraints: 5136 Sorted by residual: chirality pdb=" CA GLU O 74 " pdb=" N GLU O 74 " pdb=" C GLU O 74 " pdb=" CB GLU O 74 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA GLU L 74 " pdb=" N GLU L 74 " pdb=" C GLU L 74 " pdb=" CB GLU L 74 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA GLU W 74 " pdb=" N GLU W 74 " pdb=" C GLU W 74 " pdb=" CB GLU W 74 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 5133 not shown) Planarity restraints: 6384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA N 167 " -0.070 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO N 168 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO N 168 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO N 168 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA T 167 " -0.070 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO T 168 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO T 168 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO T 168 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 167 " -0.070 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 168 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 168 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 168 " -0.057 5.00e-02 4.00e+02 ... (remaining 6381 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1320 2.67 - 3.23: 36948 3.23 - 3.78: 68328 3.78 - 4.34: 81756 4.34 - 4.90: 128124 Nonbonded interactions: 316476 Sorted by model distance: nonbonded pdb=" O HOH B 212 " pdb=" O HOH B 250 " model vdw 2.110 3.040 nonbonded pdb=" O HOH N 212 " pdb=" O HOH N 250 " model vdw 2.110 3.040 nonbonded pdb=" O HOH T 212 " pdb=" O HOH T 250 " model vdw 2.110 3.040 nonbonded pdb=" O HOH V 212 " pdb=" O HOH V 250 " model vdw 2.110 3.040 nonbonded pdb=" O HOH C 212 " pdb=" O HOH C 250 " model vdw 2.110 3.040 ... (remaining 316471 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 2.660 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: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 28.920 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 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:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 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 : 0.017 0.078 34584 Z= 0.842 Angle : 1.099 7.286 46896 Z= 0.642 Chirality : 0.070 0.237 5136 Planarity : 0.010 0.103 6384 Dihedral : 18.129 88.578 12720 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.12), residues: 4272 helix: 2.05 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.59 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG S 144 TYR 0.024 0.006 TYR P 35 PHE 0.034 0.006 PHE N 128 TRP 0.015 0.006 TRP T 127 HIS 0.016 0.005 HIS T 47 Details of bonding type rmsd covalent geometry : bond 0.01712 (34584) covalent geometry : angle 1.09921 (46896) hydrogen bonds : bond 0.11494 ( 2664) hydrogen bonds : angle 4.69144 ( 7992) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 694 time to evaluate : 1.419 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 694 average time/residue: 0.8415 time to fit residues: 685.8070 Evaluate side-chains 621 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 621 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.094173 restraints weight = 177033.462| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.05 r_work: 0.2927 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34584 Z= 0.150 Angle : 0.483 5.144 46896 Z= 0.265 Chirality : 0.035 0.121 5136 Planarity : 0.006 0.067 6384 Dihedral : 3.736 13.801 4656 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.19 % Allowed : 11.72 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.85 (0.12), residues: 4272 helix: 3.40 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.26 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 144 TYR 0.009 0.002 TYR T 49 PHE 0.015 0.002 PHE G 48 TRP 0.003 0.001 TRP C 127 HIS 0.007 0.002 HIS P 47 Details of bonding type rmsd covalent geometry : bond 0.00295 (34584) covalent geometry : angle 0.48335 (46896) hydrogen bonds : bond 0.06418 ( 2664) hydrogen bonds : angle 3.77175 ( 7992) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 764 time to evaluate : 1.446 Fit side-chains REVERT: E 8 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7863 (mtmm) REVERT: O 8 LYS cc_start: 0.8047 (mtmm) cc_final: 0.7844 (mtmm) outliers start: 41 outliers final: 15 residues processed: 783 average time/residue: 0.8058 time to fit residues: 751.3415 Evaluate side-chains 760 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 745 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain G residue 132 GLN Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain I residue 132 GLN Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain V residue 132 GLN Chi-restraints excluded: chain X residue 134 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 87 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 chunk 385 optimal weight: 7.9990 chunk 393 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 374 optimal weight: 10.0000 chunk 318 optimal weight: 1.9990 chunk 362 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN B 51 GLN C 51 GLN D 132 GLN G 51 GLN J 51 GLN K 51 GLN K 132 GLN L 51 GLN N 132 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN P 132 GLN R 132 GLN S 51 GLN T 51 GLN V 51 GLN W 51 GLN X 132 GLN ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 132 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.106825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.096766 restraints weight = 161535.599| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.97 r_work: 0.2903 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 34584 Z= 0.195 Angle : 0.539 7.312 46896 Z= 0.289 Chirality : 0.036 0.129 5136 Planarity : 0.006 0.058 6384 Dihedral : 3.799 15.387 4656 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.33 % Allowed : 12.15 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.97 (0.12), residues: 4272 helix: 3.49 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.22 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 144 TYR 0.012 0.002 TYR B 35 PHE 0.019 0.002 PHE G 48 TRP 0.005 0.001 TRP Y 127 HIS 0.009 0.002 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00398 (34584) covalent geometry : angle 0.53948 (46896) hydrogen bonds : bond 0.07184 ( 2664) hydrogen bonds : angle 3.81331 ( 7992) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 741 time to evaluate : 1.191 Fit side-chains REVERT: D 74 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: K 74 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: N 74 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: Q 74 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: X 74 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: Y 46 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8574 (ttpt) REVERT: Y 74 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8113 (mp0) outliers start: 46 outliers final: 22 residues processed: 751 average time/residue: 0.7440 time to fit residues: 664.5528 Evaluate side-chains 761 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 732 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain G residue 132 GLN Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain I residue 132 GLN Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain P residue 134 GLU Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain S residue 132 GLN Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain V residue 132 GLN Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain X residue 74 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 74 GLU Chi-restraints excluded: chain Y residue 134 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 320 optimal weight: 10.0000 chunk 369 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 283 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 290 optimal weight: 0.9980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN C 51 GLN G 51 GLN J 51 GLN L 51 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN S 51 GLN T 51 GLN V 51 GLN W 51 GLN ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.095895 restraints weight = 155626.678| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.99 r_work: 0.2912 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 34584 Z= 0.186 Angle : 0.531 7.824 46896 Z= 0.282 Chirality : 0.036 0.127 5136 Planarity : 0.006 0.054 6384 Dihedral : 3.727 15.229 4656 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.39 % Allowed : 12.01 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.02 (0.12), residues: 4272 helix: 3.52 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.20 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 148 TYR 0.010 0.002 TYR B 35 PHE 0.018 0.002 PHE N 48 TRP 0.005 0.001 TRP Y 127 HIS 0.008 0.002 HIS P 47 Details of bonding type rmsd covalent geometry : bond 0.00380 (34584) covalent geometry : angle 0.53081 (46896) hydrogen bonds : bond 0.07010 ( 2664) hydrogen bonds : angle 3.74930 ( 7992) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 752 time to evaluate : 1.423 Fit side-chains REVERT: A 74 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: C 74 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: D 74 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8212 (mp0) REVERT: F 74 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: K 74 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: N 74 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: Q 74 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: T 74 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: X 74 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: Y 46 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8567 (ttpt) REVERT: Y 74 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8107 (mp0) outliers start: 48 outliers final: 23 residues processed: 764 average time/residue: 0.7626 time to fit residues: 693.0452 Evaluate side-chains 774 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 740 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain G residue 132 GLN Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain I residue 132 GLN Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain S residue 132 GLN Chi-restraints excluded: chain T residue 74 GLU Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain V residue 132 GLN Chi-restraints excluded: chain W residue 132 GLN Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain X residue 74 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 74 GLU Chi-restraints excluded: chain Y residue 134 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 363 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 296 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 338 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 291 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN C 51 GLN G 51 GLN I 84 GLN J 51 GLN L 51 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN S 51 GLN T 51 GLN V 51 GLN W 51 GLN ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.095817 restraints weight = 164820.042| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.07 r_work: 0.2904 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 34584 Z= 0.185 Angle : 0.530 7.383 46896 Z= 0.281 Chirality : 0.035 0.126 5136 Planarity : 0.006 0.057 6384 Dihedral : 3.703 14.933 4656 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.36 % Allowed : 12.27 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.03 (0.12), residues: 4272 helix: 3.53 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.19 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 148 TYR 0.010 0.002 TYR B 35 PHE 0.018 0.002 PHE G 48 TRP 0.005 0.001 TRP Y 127 HIS 0.008 0.002 HIS P 47 Details of bonding type rmsd covalent geometry : bond 0.00376 (34584) covalent geometry : angle 0.52969 (46896) hydrogen bonds : bond 0.07023 ( 2664) hydrogen bonds : angle 3.74201 ( 7992) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 746 time to evaluate : 1.340 Fit side-chains REVERT: A 74 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: C 74 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: D 74 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: F 74 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: K 74 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: N 74 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: P 74 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: Q 74 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: R 74 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: T 74 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: W 74 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: X 74 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8262 (mp0) REVERT: Y 46 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8568 (ttpt) REVERT: Y 74 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8125 (mp0) outliers start: 47 outliers final: 24 residues processed: 756 average time/residue: 0.7783 time to fit residues: 701.7190 Evaluate side-chains 778 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 740 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain G residue 132 GLN Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain H residue 132 GLN Chi-restraints excluded: chain I residue 132 GLN Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain S residue 132 GLN Chi-restraints excluded: chain T residue 74 GLU Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain V residue 132 GLN Chi-restraints excluded: chain W residue 74 GLU Chi-restraints excluded: chain W residue 132 GLN Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain X residue 74 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 74 GLU Chi-restraints excluded: chain Y residue 134 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 404 optimal weight: 2.9990 chunk 359 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 335 optimal weight: 0.7980 chunk 228 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 304 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN C 51 GLN G 51 GLN J 51 GLN L 51 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN S 51 GLN T 51 GLN V 51 GLN W 51 GLN X 152 ASN Y 51 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.095457 restraints weight = 175761.842| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.05 r_work: 0.2958 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34584 Z= 0.130 Angle : 0.450 6.653 46896 Z= 0.242 Chirality : 0.034 0.122 5136 Planarity : 0.005 0.053 6384 Dihedral : 3.353 12.728 4656 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.98 % Allowed : 12.56 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.31 (0.12), residues: 4272 helix: 3.73 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.07 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 144 TYR 0.007 0.001 TYR N 49 PHE 0.015 0.001 PHE N 48 TRP 0.004 0.001 TRP Y 127 HIS 0.006 0.001 HIS P 47 Details of bonding type rmsd covalent geometry : bond 0.00250 (34584) covalent geometry : angle 0.44985 (46896) hydrogen bonds : bond 0.05741 ( 2664) hydrogen bonds : angle 3.52111 ( 7992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 792 time to evaluate : 1.606 Fit side-chains REVERT: A 74 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8151 (mp0) REVERT: C 74 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: D 74 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: F 46 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8582 (ttpt) REVERT: F 74 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: K 74 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: N 74 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: Q 74 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: R 74 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: T 74 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: W 74 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: X 74 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: Y 74 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8155 (mp0) outliers start: 34 outliers final: 12 residues processed: 800 average time/residue: 0.7551 time to fit residues: 718.8487 Evaluate side-chains 789 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 765 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain T residue 74 GLU Chi-restraints excluded: chain T residue 132 GLN Chi-restraints excluded: chain W residue 74 GLU Chi-restraints excluded: chain W residue 132 GLN Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain X residue 74 GLU Chi-restraints excluded: chain Y residue 74 GLU Chi-restraints excluded: chain Y residue 134 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 126 optimal weight: 7.9990 chunk 308 optimal weight: 9.9990 chunk 348 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 396 optimal weight: 5.9990 chunk 15 optimal weight: 0.0060 chunk 325 optimal weight: 6.9990 chunk 361 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 340 optimal weight: 10.0000 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN B 51 GLN C 47 HIS D 51 GLN G 51 GLN G 132 GLN H 132 GLN J 51 GLN K 51 GLN L 51 GLN L 132 GLN M 51 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 51 GLN T 51 GLN V 47 HIS V 132 GLN W 51 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.095767 restraints weight = 174581.248| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.17 r_work: 0.2900 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 34584 Z= 0.209 Angle : 0.554 7.155 46896 Z= 0.294 Chirality : 0.036 0.132 5136 Planarity : 0.006 0.057 6384 Dihedral : 3.700 15.715 4656 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.04 % Allowed : 13.45 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.10 (0.12), residues: 4272 helix: 3.58 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.17 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 72 TYR 0.011 0.002 TYR S 35 PHE 0.019 0.002 PHE G 48 TRP 0.005 0.002 TRP C 127 HIS 0.008 0.002 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00435 (34584) covalent geometry : angle 0.55354 (46896) hydrogen bonds : bond 0.07254 ( 2664) hydrogen bonds : angle 3.75215 ( 7992) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 726 time to evaluate : 1.637 Fit side-chains REVERT: A 74 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: C 74 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: D 74 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: F 74 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: K 74 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: N 74 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: Q 74 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: R 74 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: T 74 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: W 74 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: X 74 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: Y 46 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8598 (ttpt) REVERT: Y 74 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8086 (mp0) outliers start: 36 outliers final: 16 residues processed: 729 average time/residue: 0.7522 time to fit residues: 655.6370 Evaluate side-chains 748 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 719 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain T residue 74 GLU Chi-restraints excluded: chain T residue 132 GLN Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain W residue 74 GLU Chi-restraints excluded: chain W residue 132 GLN Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain X residue 74 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 74 GLU Chi-restraints excluded: chain Y residue 134 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 368 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 349 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 396 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 283 optimal weight: 0.9980 chunk 245 optimal weight: 7.9990 chunk 320 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN G 51 GLN J 51 GLN K 51 GLN L 51 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN S 51 GLN T 51 GLN W 51 GLN Y 51 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.095972 restraints weight = 167712.124| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.09 r_work: 0.2900 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34584 Z= 0.197 Angle : 0.540 7.482 46896 Z= 0.287 Chirality : 0.036 0.128 5136 Planarity : 0.006 0.054 6384 Dihedral : 3.692 15.442 4656 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.22 % Allowed : 12.96 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.04 (0.12), residues: 4272 helix: 3.54 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.18 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 72 TYR 0.010 0.002 TYR S 35 PHE 0.018 0.002 PHE G 48 TRP 0.005 0.002 TRP C 127 HIS 0.008 0.002 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00406 (34584) covalent geometry : angle 0.54001 (46896) hydrogen bonds : bond 0.07113 ( 2664) hydrogen bonds : angle 3.73155 ( 7992) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 733 time to evaluate : 1.419 Fit side-chains REVERT: A 74 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: B 46 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8554 (ttpt) REVERT: C 74 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: D 74 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: K 74 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: N 74 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: P 46 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8581 (ttpt) REVERT: Q 74 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: R 74 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: S 46 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8565 (ttpt) REVERT: T 74 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: W 74 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: X 74 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: Y 46 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8583 (ttpt) REVERT: Y 74 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8126 (mp0) outliers start: 42 outliers final: 16 residues processed: 737 average time/residue: 0.7654 time to fit residues: 672.2582 Evaluate side-chains 758 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 727 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 132 GLN Chi-restraints excluded: chain T residue 74 GLU Chi-restraints excluded: chain T residue 132 GLN Chi-restraints excluded: chain W residue 74 GLU Chi-restraints excluded: chain W residue 132 GLN Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain X residue 74 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 74 GLU Chi-restraints excluded: chain Y residue 134 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 310 optimal weight: 5.9990 chunk 370 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 228 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 236 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 325 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN G 51 GLN J 51 GLN L 51 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN S 51 GLN T 51 GLN W 51 GLN Y 51 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095554 restraints weight = 170402.636| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.07 r_work: 0.2957 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34584 Z= 0.131 Angle : 0.458 7.208 46896 Z= 0.246 Chirality : 0.034 0.124 5136 Planarity : 0.005 0.057 6384 Dihedral : 3.365 12.772 4656 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.95 % Allowed : 13.28 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.32 (0.12), residues: 4272 helix: 3.72 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.02 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 72 TYR 0.007 0.001 TYR V 49 PHE 0.015 0.001 PHE N 48 TRP 0.004 0.001 TRP Y 127 HIS 0.006 0.001 HIS P 47 Details of bonding type rmsd covalent geometry : bond 0.00254 (34584) covalent geometry : angle 0.45760 (46896) hydrogen bonds : bond 0.05803 ( 2664) hydrogen bonds : angle 3.51171 ( 7992) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 765 time to evaluate : 1.220 Fit side-chains REVERT: A 74 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: B 46 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8481 (ttpt) REVERT: C 74 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: D 74 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: F 46 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8584 (ttpt) REVERT: K 74 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: N 74 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: P 46 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8470 (ttpt) REVERT: Q 74 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: R 74 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: S 46 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8480 (ttpt) REVERT: T 74 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: W 74 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: X 74 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: Y 74 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8160 (mp0) outliers start: 33 outliers final: 16 residues processed: 769 average time/residue: 0.7650 time to fit residues: 702.4196 Evaluate side-chains 786 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 756 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 74 GLU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain T residue 74 GLU Chi-restraints excluded: chain T residue 132 GLN Chi-restraints excluded: chain W residue 74 GLU Chi-restraints excluded: chain W residue 132 GLN Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain X residue 74 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 74 GLU Chi-restraints excluded: chain Y residue 134 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 12 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 339 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 355 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 243 optimal weight: 5.9990 chunk 336 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 350 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN D 51 GLN G 51 GLN I 51 GLN J 51 GLN K 51 GLN L 51 GLN M 51 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 51 GLN S 132 GLN T 51 GLN W 51 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.096832 restraints weight = 179366.301| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.14 r_work: 0.2911 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34584 Z= 0.173 Angle : 0.511 7.201 46896 Z= 0.275 Chirality : 0.035 0.126 5136 Planarity : 0.005 0.059 6384 Dihedral : 3.548 14.605 4656 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.98 % Allowed : 13.45 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.19 (0.12), residues: 4272 helix: 3.63 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.08 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 72 TYR 0.009 0.002 TYR S 35 PHE 0.017 0.002 PHE X 48 TRP 0.004 0.001 TRP C 127 HIS 0.008 0.002 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00351 (34584) covalent geometry : angle 0.51089 (46896) hydrogen bonds : bond 0.06752 ( 2664) hydrogen bonds : angle 3.64331 ( 7992) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 744 time to evaluate : 1.513 Fit side-chains REVERT: A 74 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: B 46 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8542 (ttpt) REVERT: C 74 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: D 74 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: K 74 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: N 74 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: P 46 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8569 (ttpt) REVERT: P 74 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: R 74 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: S 46 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8568 (ttpt) REVERT: T 74 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: W 74 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: X 74 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8262 (mp0) REVERT: Y 74 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8139 (mp0) outliers start: 34 outliers final: 16 residues processed: 749 average time/residue: 0.7443 time to fit residues: 666.9669 Evaluate side-chains 771 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 741 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain J residue 132 GLN Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 134 GLU Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 74 GLU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 134 GLU Chi-restraints excluded: chain S residue 46 LYS Chi-restraints excluded: chain T residue 74 GLU Chi-restraints excluded: chain T residue 132 GLN Chi-restraints excluded: chain W residue 74 GLU Chi-restraints excluded: chain W residue 132 GLN Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain X residue 74 GLU Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 74 GLU Chi-restraints excluded: chain Y residue 134 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 292 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 367 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN G 51 GLN I 51 GLN I 84 GLN J 51 GLN K 51 GLN L 51 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN S 51 GLN T 51 GLN W 51 GLN Y 51 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.096171 restraints weight = 153209.414| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.01 r_work: 0.2921 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 34584 Z= 0.198 Angle : 0.541 7.169 46896 Z= 0.290 Chirality : 0.036 0.130 5136 Planarity : 0.006 0.060 6384 Dihedral : 3.676 15.484 4656 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.98 % Allowed : 13.51 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.08 (0.12), residues: 4272 helix: 3.56 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.15 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 72 TYR 0.010 0.002 TYR S 35 PHE 0.018 0.002 PHE X 48 TRP 0.005 0.001 TRP C 127 HIS 0.008 0.002 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00408 (34584) covalent geometry : angle 0.54123 (46896) hydrogen bonds : bond 0.07141 ( 2664) hydrogen bonds : angle 3.71976 ( 7992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18257.02 seconds wall clock time: 309 minutes 36.34 seconds (18576.34 seconds total)