Starting phenix.real_space_refine on Sun Jun 29 06:53:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o6e_12738/06_2025/7o6e_12738.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o6e_12738/06_2025/7o6e_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_12738/06_2025/7o6e_12738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o6e_12738/06_2025/7o6e_12738.map" model { file = "/net/cci-nas-00/data/ceres_data/7o6e_12738/06_2025/7o6e_12738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o6e_12738/06_2025/7o6e_12738.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, T, W, V, Y, X 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: 9.80, per 1000 atoms: 0.28 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: 9.28 Conformation dependent library (CDL) restraints added in 8.2 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: 2.95 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: 10.72 Time building geometry restraints manager: 10.82 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: 0.32 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.880 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: 0.040 Extract box with map and model: 1.490 Check model and map are aligned: 0.320 Set scattering table: 0.350 Process input model: 70.010 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.015 0.006 TRP T 127 HIS 0.016 0.005 HIS T 47 PHE 0.034 0.006 PHE N 128 TYR 0.024 0.006 TYR P 35 ARG 0.006 0.002 ARG S 144 Details of bonding type rmsd hydrogen bonds : bond 0.11494 ( 2664) hydrogen bonds : angle 4.69144 ( 7992) covalent geometry : bond 0.01712 (34584) covalent geometry : angle 1.09921 (46896) *********************** 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 : 4.123 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 694 average time/residue: 1.7084 time to fit residues: 1392.4691 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 : 4.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.9980 chunk 309 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 208 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 319 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 0.9990 chunk 370 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.106672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.096977 restraints weight = 169337.854| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.98 r_work: 0.2988 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34584 Z= 0.131 Angle : 0.450 3.846 46896 Z= 0.248 Chirality : 0.035 0.118 5136 Planarity : 0.006 0.065 6384 Dihedral : 3.567 12.929 4656 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.26 % Allowed : 12.67 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.12), residues: 4272 helix: 3.48 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.19 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 127 HIS 0.006 0.001 HIS B 47 PHE 0.013 0.002 PHE D 48 TYR 0.009 0.001 TYR W 49 ARG 0.004 0.000 ARG E 144 Details of bonding type rmsd hydrogen bonds : bond 0.05742 ( 2664) hydrogen bonds : angle 3.67605 ( 7992) covalent geometry : bond 0.00256 (34584) covalent geometry : angle 0.45040 (46896) *********************** 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 810 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 801 time to evaluate : 3.631 Fit side-chains REVERT: A 46 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8638 (ttpt) REVERT: F 46 LYS cc_start: 0.8876 (ttpp) cc_final: 0.8663 (ttpt) REVERT: K 46 LYS cc_start: 0.8855 (ttpp) cc_final: 0.8571 (ttpt) REVERT: Q 46 LYS cc_start: 0.8862 (ttpp) cc_final: 0.8628 (ttpt) REVERT: R 46 LYS cc_start: 0.8893 (ttpp) cc_final: 0.8678 (ttpt) REVERT: X 46 LYS cc_start: 0.8855 (ttpp) cc_final: 0.8592 (ttpt) REVERT: Y 46 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8565 (ttpt) outliers start: 9 outliers final: 0 residues processed: 804 average time/residue: 1.5486 time to fit residues: 1478.8077 Evaluate side-chains 766 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 766 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 401 optimal weight: 4.9990 chunk 382 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 255 optimal weight: 4.9990 chunk 373 optimal weight: 0.6980 chunk 169 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 360 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 76 optimal weight: 0.0870 overall best weight: 3.1564 ------------------------------------------------------------------------------- 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 E 152 ASN G 51 GLN G 132 GLN H 132 GLN ** I 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN J 51 GLN K 51 GLN ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN L 132 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 51 GLN P 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095721 restraints weight = 152081.277| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.00 r_work: 0.2916 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34584 Z= 0.181 Angle : 0.522 6.442 46896 Z= 0.282 Chirality : 0.036 0.129 5136 Planarity : 0.006 0.058 6384 Dihedral : 3.703 14.778 4656 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.50 % Allowed : 12.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.07 (0.12), residues: 4272 helix: 3.56 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.18 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 127 HIS 0.008 0.002 HIS B 47 PHE 0.019 0.002 PHE G 48 TYR 0.011 0.002 TYR B 35 ARG 0.003 0.001 ARG I 148 Details of bonding type rmsd hydrogen bonds : bond 0.06988 ( 2664) hydrogen bonds : angle 3.76247 ( 7992) covalent geometry : bond 0.00367 (34584) covalent geometry : angle 0.52176 (46896) *********************** 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 802 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 750 time to evaluate : 3.813 Fit side-chains REVERT: B 74 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: C 74 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: D 74 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8151 (mp0) REVERT: F 74 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: T 74 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: X 46 LYS cc_start: 0.8970 (ttpp) cc_final: 0.8689 (ttpt) REVERT: Y 46 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8550 (ttpt) REVERT: Y 74 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8052 (mp0) outliers start: 52 outliers final: 23 residues processed: 762 average time/residue: 1.5275 time to fit residues: 1381.6694 Evaluate side-chains 766 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 736 time to evaluate : 4.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 74 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 132 GLN 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 132 GLN Chi-restraints excluded: chain K residue 134 GLU Chi-restraints excluded: chain N residue 132 GLN Chi-restraints excluded: chain P residue 132 GLN 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 132 GLN 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 132 GLN Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 46 LYS Chi-restraints excluded: chain Y residue 74 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 268 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 291 optimal weight: 6.9990 chunk 306 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 383 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN I 51 GLN J 51 GLN ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Y 51 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.093401 restraints weight = 193465.156| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.15 r_work: 0.2918 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 34584 Z= 0.146 Angle : 0.475 6.222 46896 Z= 0.255 Chirality : 0.035 0.122 5136 Planarity : 0.005 0.054 6384 Dihedral : 3.478 13.321 4656 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.48 % Allowed : 12.85 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.25 (0.12), residues: 4272 helix: 3.68 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.08 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Y 127 HIS 0.007 0.001 HIS B 47 PHE 0.016 0.002 PHE N 48 TYR 0.008 0.002 TYR X 35 ARG 0.002 0.000 ARG H 144 Details of bonding type rmsd hydrogen bonds : bond 0.06245 ( 2664) hydrogen bonds : angle 3.61482 ( 7992) covalent geometry : bond 0.00285 (34584) covalent geometry : angle 0.47473 (46896) *********************** 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 822 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 771 time to evaluate : 3.834 Fit side-chains REVERT: A 74 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: B 74 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: C 74 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8220 (mp0) REVERT: D 74 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: F 46 LYS cc_start: 0.8963 (ttpp) cc_final: 0.8722 (ttpt) REVERT: F 74 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: K 74 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: N 74 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: P 74 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8228 (mp0) REVERT: Q 74 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: R 74 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8200 (mp0) REVERT: T 74 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: X 46 LYS cc_start: 0.8952 (ttpp) cc_final: 0.8693 (ttpt) REVERT: X 74 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: Y 74 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8187 (mp0) outliers start: 51 outliers final: 22 residues processed: 787 average time/residue: 2.0329 time to fit residues: 1896.2799 Evaluate side-chains 800 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 765 time to evaluate : 4.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 74 GLU 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 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 132 GLN 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 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 132 GLN 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 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 74 GLU Chi-restraints excluded: chain Y residue 132 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 40 optimal weight: 9.9990 chunk 390 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 288 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 D 132 GLN ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN I 51 GLN I 84 GLN J 51 GLN K 51 GLN ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN N 132 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN S 51 GLN T 51 GLN V 47 HIS W 51 GLN X 132 GLN ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.097718 restraints weight = 169781.763| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.98 r_work: 0.2922 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34584 Z= 0.168 Angle : 0.507 6.744 46896 Z= 0.271 Chirality : 0.035 0.124 5136 Planarity : 0.005 0.058 6384 Dihedral : 3.569 14.396 4656 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.56 % Allowed : 12.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.19 (0.12), residues: 4272 helix: 3.64 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.12 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 127 HIS 0.007 0.002 HIS B 47 PHE 0.017 0.002 PHE N 48 TYR 0.009 0.002 TYR X 35 ARG 0.002 0.000 ARG M 148 Details of bonding type rmsd hydrogen bonds : bond 0.06742 ( 2664) hydrogen bonds : angle 3.67087 ( 7992) covalent geometry : bond 0.00337 (34584) covalent geometry : angle 0.50741 (46896) *********************** 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 822 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 768 time to evaluate : 3.986 Fit side-chains REVERT: A 74 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: B 74 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: C 74 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: D 74 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: F 74 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: K 74 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8209 (mp0) REVERT: N 74 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: P 74 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: R 74 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: T 74 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: W 74 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: X 74 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: Y 46 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8538 (ttpt) REVERT: Y 74 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8118 (mp0) outliers start: 54 outliers final: 24 residues processed: 779 average time/residue: 1.5803 time to fit residues: 1462.3019 Evaluate side-chains 791 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 753 time to evaluate : 4.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 74 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 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 132 GLN 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 74 GLU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 132 GLN 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 132 GLN 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 132 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 105 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 chunk 315 optimal weight: 3.9990 chunk 292 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 194 optimal weight: 0.4980 chunk 369 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN J 51 GLN K 51 GLN ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN S 51 GLN T 51 GLN W 51 GLN ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.094248 restraints weight = 166212.121| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.02 r_work: 0.2940 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 34584 Z= 0.141 Angle : 0.469 6.608 46896 Z= 0.251 Chirality : 0.034 0.123 5136 Planarity : 0.005 0.054 6384 Dihedral : 3.409 13.118 4656 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.24 % Allowed : 13.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.29 (0.12), residues: 4272 helix: 3.70 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.05 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Y 127 HIS 0.006 0.001 HIS P 47 PHE 0.015 0.002 PHE N 48 TYR 0.007 0.001 TYR X 35 ARG 0.002 0.000 ARG F 72 Details of bonding type rmsd hydrogen bonds : bond 0.06137 ( 2664) hydrogen bonds : angle 3.56632 ( 7992) covalent geometry : bond 0.00275 (34584) covalent geometry : angle 0.46888 (46896) *********************** 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 818 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 775 time to evaluate : 4.059 Fit side-chains REVERT: A 74 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: B 74 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: C 74 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: D 74 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8212 (mp0) REVERT: F 46 LYS cc_start: 0.8940 (ttpp) cc_final: 0.8702 (ttpt) REVERT: K 74 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: N 74 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8234 (mp0) REVERT: P 74 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: R 74 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: T 74 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: W 74 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: X 46 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8667 (ttpt) REVERT: X 74 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: Y 46 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8538 (ttpt) REVERT: Y 74 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8144 (mp0) outliers start: 43 outliers final: 20 residues processed: 786 average time/residue: 1.5385 time to fit residues: 1440.0407 Evaluate side-chains 797 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 764 time to evaluate : 3.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 74 GLU 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 134 GLU 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 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 134 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 132 GLN 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 160 optimal weight: 10.0000 chunk 402 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 315 optimal weight: 0.8980 chunk 237 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 215 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 401 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN I 51 GLN J 51 GLN K 51 GLN K 132 GLN ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN M 51 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN S 51 GLN S 132 GLN T 51 GLN W 51 GLN X 152 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.098070 restraints weight = 178938.023| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.04 r_work: 0.2925 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 34584 Z= 0.160 Angle : 0.498 6.715 46896 Z= 0.266 Chirality : 0.035 0.125 5136 Planarity : 0.005 0.058 6384 Dihedral : 3.504 14.020 4656 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.24 % Allowed : 13.45 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.12), residues: 4272 helix: 3.66 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.08 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 127 HIS 0.007 0.002 HIS S 47 PHE 0.016 0.002 PHE N 48 TYR 0.009 0.002 TYR X 35 ARG 0.002 0.000 ARG H 148 Details of bonding type rmsd hydrogen bonds : bond 0.06581 ( 2664) hydrogen bonds : angle 3.62646 ( 7992) covalent geometry : bond 0.00319 (34584) covalent geometry : angle 0.49768 (46896) *********************** 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 804 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 761 time to evaluate : 4.183 Fit side-chains REVERT: A 74 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: C 74 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: D 74 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: K 74 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: N 74 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: P 74 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8159 (mp0) REVERT: R 74 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: T 74 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: W 74 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: X 74 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: Y 46 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8564 (ttpt) REVERT: Y 74 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8103 (mp0) outliers start: 43 outliers final: 22 residues processed: 772 average time/residue: 1.5915 time to fit residues: 1466.5766 Evaluate side-chains 792 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 758 time to evaluate : 3.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 132 GLN 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 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 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 134 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 132 GLN 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 173 optimal weight: 8.9990 chunk 363 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 356 optimal weight: 1.9990 chunk 331 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 278 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 288 optimal weight: 0.0870 chunk 140 optimal weight: 0.7980 overall best weight: 1.5762 ------------------------------------------------------------------------------- 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 E 51 GLN ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN G 132 GLN I 51 GLN J 51 GLN K 51 GLN ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN M 51 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN S 51 GLN T 51 GLN V 47 HIS V 51 GLN W 51 GLN ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.095099 restraints weight = 169833.420| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.08 r_work: 0.2949 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1855 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= 0.135 Angle : 0.460 7.010 46896 Z= 0.247 Chirality : 0.034 0.123 5136 Planarity : 0.005 0.055 6384 Dihedral : 3.342 13.290 4656 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.95 % Allowed : 13.66 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.34 (0.12), residues: 4272 helix: 3.74 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.01 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Y 127 HIS 0.006 0.001 HIS S 47 PHE 0.015 0.001 PHE N 48 TYR 0.006 0.001 TYR C 49 ARG 0.002 0.000 ARG Q 72 Details of bonding type rmsd hydrogen bonds : bond 0.05922 ( 2664) hydrogen bonds : angle 3.51779 ( 7992) covalent geometry : bond 0.00262 (34584) covalent geometry : angle 0.46043 (46896) *********************** 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 803 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 770 time to evaluate : 4.251 Fit side-chains REVERT: A 74 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: C 74 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: D 74 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: F 46 LYS cc_start: 0.8919 (ttpp) cc_final: 0.8694 (ttpt) REVERT: K 74 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: N 74 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: P 74 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: R 74 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: T 74 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: W 74 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: X 74 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: Y 74 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8166 (mp0) outliers start: 33 outliers final: 17 residues processed: 779 average time/residue: 1.6502 time to fit residues: 1530.9595 Evaluate side-chains 784 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 756 time to evaluate : 3.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 GLU 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 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 74 GLU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 132 GLN 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 356 optimal weight: 9.9990 chunk 101 optimal weight: 0.0040 chunk 224 optimal weight: 4.9990 chunk 309 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 276 optimal weight: 0.9990 chunk 353 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- 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 E 51 GLN ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN H 132 GLN I 51 GLN ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 GLN K 51 GLN ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN M 51 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 GLN V 47 HIS V 132 GLN W 51 GLN ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 132 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.096134 restraints weight = 171101.494| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.13 r_work: 0.2913 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1643 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= 0.178 Angle : 0.517 7.172 46896 Z= 0.276 Chirality : 0.035 0.126 5136 Planarity : 0.005 0.059 6384 Dihedral : 3.561 14.636 4656 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.98 % Allowed : 13.83 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.20 (0.12), residues: 4272 helix: 3.65 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.11 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 127 HIS 0.007 0.002 HIS B 47 PHE 0.017 0.002 PHE N 48 TYR 0.009 0.002 TYR X 35 ARG 0.003 0.000 ARG H 148 Details of bonding type rmsd hydrogen bonds : bond 0.06836 ( 2664) hydrogen bonds : angle 3.66423 ( 7992) covalent geometry : bond 0.00361 (34584) covalent geometry : angle 0.51694 (46896) *********************** 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 779 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 745 time to evaluate : 3.815 Fit side-chains REVERT: A 74 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: C 74 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: D 74 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: K 74 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: N 74 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: P 74 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8164 (mp0) REVERT: R 74 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: T 74 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: W 74 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: X 74 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: Y 46 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8551 (ttpt) REVERT: Y 74 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8120 (mp0) outliers start: 34 outliers final: 18 residues processed: 751 average time/residue: 1.9614 time to fit residues: 1765.8741 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 : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 GLU 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 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 74 GLU Chi-restraints excluded: chain Q residue 134 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 132 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 61 optimal weight: 7.9990 chunk 76 optimal weight: 0.4980 chunk 360 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 350 optimal weight: 3.9990 chunk 368 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 252 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 398 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN E 51 GLN ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN I 51 GLN ** I 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 GLN K 51 GLN ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN S 51 GLN T 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 = 0.3304 r_free = 0.3304 target = 0.103839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.093736 restraints weight = 171781.525| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.08 r_work: 0.2924 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1770 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= 0.148 Angle : 0.483 7.306 46896 Z= 0.258 Chirality : 0.034 0.124 5136 Planarity : 0.005 0.055 6384 Dihedral : 3.431 13.282 4656 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 0.90 % Allowed : 13.89 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.27 (0.12), residues: 4272 helix: 3.68 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.04 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 127 HIS 0.006 0.001 HIS B 47 PHE 0.015 0.002 PHE N 48 TYR 0.007 0.002 TYR X 35 ARG 0.002 0.000 ARG Q 72 Details of bonding type rmsd hydrogen bonds : bond 0.06295 ( 2664) hydrogen bonds : angle 3.57901 ( 7992) covalent geometry : bond 0.00294 (34584) covalent geometry : angle 0.48258 (46896) ********************** 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 786 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 755 time to evaluate : 4.256 Fit side-chains REVERT: A 74 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: C 74 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8209 (mp0) REVERT: D 74 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: F 46 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8714 (ttpt) REVERT: K 74 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: N 74 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8271 (mp0) REVERT: P 74 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: R 46 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8673 (ttpt) REVERT: R 74 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: T 74 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: W 74 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: X 74 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: Y 74 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8187 (mp0) outliers start: 31 outliers final: 17 residues processed: 762 average time/residue: 1.5330 time to fit residues: 1397.7118 Evaluate side-chains 779 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 751 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 134 GLU 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 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 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 134 GLU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 132 GLN 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 74 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 15 optimal weight: 9.9990 chunk 399 optimal weight: 9.9990 chunk 324 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 176 optimal weight: 8.9990 chunk 268 optimal weight: 2.9990 chunk 391 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 395 optimal weight: 6.9990 chunk 59 optimal weight: 0.0070 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN B 132 GLN ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN I 51 GLN J 51 GLN ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN M 51 GLN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 GLN S 51 GLN T 51 GLN W 51 GLN ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.097462 restraints weight = 156597.699| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.02 r_work: 0.2944 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34584 Z= 0.157 Angle : 0.489 8.097 46896 Z= 0.264 Chirality : 0.035 0.125 5136 Planarity : 0.005 0.059 6384 Dihedral : 3.467 13.638 4656 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.95 % Allowed : 13.86 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.24 (0.12), residues: 4272 helix: 3.67 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.07 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 127 HIS 0.007 0.001 HIS S 47 PHE 0.016 0.002 PHE X 48 TYR 0.008 0.002 TYR X 35 ARG 0.002 0.000 ARG I 148 Details of bonding type rmsd hydrogen bonds : bond 0.06464 ( 2664) hydrogen bonds : angle 3.59673 ( 7992) covalent geometry : bond 0.00313 (34584) covalent geometry : angle 0.48924 (46896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40558.23 seconds wall clock time: 707 minutes 3.37 seconds (42423.37 seconds total)