Starting phenix.real_space_refine on Fri Mar 6 21:50:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjt_54953/03_2026/9sjt_54953_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjt_54953/03_2026/9sjt_54953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sjt_54953/03_2026/9sjt_54953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjt_54953/03_2026/9sjt_54953.map" model { file = "/net/cci-nas-00/data/ceres_data/9sjt_54953/03_2026/9sjt_54953_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjt_54953/03_2026/9sjt_54953_neut.cif" } resolution = 1.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.318 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: 6 Type Number sf(0) Gaussians Fe 24 7.16 5 Mg 24 5.21 5 S 168 5.16 5 C 21312 2.51 5 N 5952 2.21 5 O 7824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35304 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Chain: "B" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' FE': 4, ' MG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "K" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "M" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "O" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "P" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "R" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "S" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "T" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "V" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "W" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "X" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "Y" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Restraints were copied for chains: D, F, I, J, R, C, E, G, H, K, L, M, N, O, P, Q, S, T, V, W, X, Y Residues with excluded nonbonded symmetry interactions: 72 residue: pdb="FE FE A 201 " occ=0.25 residue: pdb="FE FE A 203 " occ=0.25 residue: pdb="FE FE A 204 " occ=0.25 residue: pdb="FE FE A 205 " occ=0.25 residue: pdb="FE FE D 201 " occ=0.25 residue: pdb="FE FE D 203 " occ=0.25 residue: pdb="FE FE D 204 " occ=0.25 residue: pdb="FE FE D 205 " occ=0.25 residue: pdb="FE FE F 201 " occ=0.25 residue: pdb="FE FE F 203 " occ=0.25 residue: pdb="FE FE F 204 " occ=0.25 residue: pdb="FE FE F 205 " occ=0.25 ... (remaining 60 not shown) Time building chain proxies: 3.24, per 1000 atoms: 0.09 Number of scatterers: 35304 At special positions: 0 Unit cell: (136.752, 136.752, 136.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 24 26.01 S 168 16.00 Mg 24 11.99 O 7824 8.00 N 5952 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.4 seconds 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 78.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 Processing helix chain 'A' and resid 45 through 73 Processing helix chain 'A' and resid 92 through 121 Processing helix chain 'A' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU A 137 " --> pdb=" O HIS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.584A pdb=" N GLU A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 39 Processing helix chain 'B' and resid 45 through 73 Processing helix chain 'B' and resid 92 through 121 Processing helix chain 'B' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU B 137 " --> pdb=" O HIS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.584A pdb=" N GLU B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 39 Processing helix chain 'C' and resid 45 through 73 Processing helix chain 'C' and resid 92 through 121 Processing helix chain 'C' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU C 137 " --> pdb=" O HIS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.584A pdb=" N GLU C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 39 Processing helix chain 'D' and resid 45 through 73 Processing helix chain 'D' and resid 92 through 121 Processing helix chain 'D' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER D 136 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU D 137 " --> pdb=" O HIS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.583A pdb=" N GLU D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 39 Processing helix chain 'E' and resid 45 through 73 Processing helix chain 'E' and resid 92 through 121 Processing helix chain 'E' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER E 136 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU E 137 " --> pdb=" O HIS E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 171 removed outlier: 3.583A pdb=" N GLU E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 39 Processing helix chain 'F' and resid 45 through 73 Processing helix chain 'F' and resid 92 through 121 Processing helix chain 'F' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER F 136 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU F 137 " --> pdb=" O HIS F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 171 removed outlier: 3.584A pdb=" N GLU F 164 " --> pdb=" O SER F 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 39 Processing helix chain 'G' and resid 45 through 73 Processing helix chain 'G' and resid 92 through 121 Processing helix chain 'G' and resid 123 through 156 removed outlier: 5.789A pdb=" N SER G 136 " --> pdb=" O THR G 132 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU G 137 " --> pdb=" O HIS G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 171 removed outlier: 3.584A pdb=" N GLU G 164 " --> pdb=" O SER G 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 39 Processing helix chain 'H' and resid 45 through 73 Processing helix chain 'H' and resid 92 through 121 Processing helix chain 'H' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER H 136 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU H 137 " --> pdb=" O HIS H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 171 removed outlier: 3.584A pdb=" N GLU H 164 " --> pdb=" O SER H 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 39 Processing helix chain 'I' and resid 45 through 73 Processing helix chain 'I' and resid 92 through 121 Processing helix chain 'I' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER I 136 " --> pdb=" O THR I 132 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU I 137 " --> pdb=" O HIS I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 171 removed outlier: 3.583A pdb=" N GLU I 164 " --> pdb=" O SER I 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 39 Processing helix chain 'J' and resid 45 through 73 Processing helix chain 'J' and resid 92 through 121 Processing helix chain 'J' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER J 136 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU J 137 " --> pdb=" O HIS J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 171 removed outlier: 3.584A pdb=" N GLU J 164 " --> pdb=" O SER J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 39 Processing helix chain 'K' and resid 45 through 73 Processing helix chain 'K' and resid 92 through 121 Processing helix chain 'K' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER K 136 " --> pdb=" O THR K 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU K 137 " --> pdb=" O HIS K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 171 removed outlier: 3.584A pdb=" N GLU K 164 " --> pdb=" O SER K 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 39 Processing helix chain 'L' and resid 45 through 73 Processing helix chain 'L' and resid 92 through 121 Processing helix chain 'L' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER L 136 " --> pdb=" O THR L 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU L 137 " --> pdb=" O HIS L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 171 removed outlier: 3.583A pdb=" N GLU L 164 " --> pdb=" O SER L 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 39 Processing helix chain 'M' and resid 45 through 73 Processing helix chain 'M' and resid 92 through 121 Processing helix chain 'M' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER M 136 " --> pdb=" O THR M 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU M 137 " --> pdb=" O HIS M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 171 removed outlier: 3.583A pdb=" N GLU M 164 " --> pdb=" O SER M 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 39 Processing helix chain 'N' and resid 45 through 73 Processing helix chain 'N' and resid 92 through 121 Processing helix chain 'N' and resid 123 through 156 removed outlier: 5.789A pdb=" N SER N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU N 137 " --> pdb=" O HIS N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 171 removed outlier: 3.584A pdb=" N GLU N 164 " --> pdb=" O SER N 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 39 Processing helix chain 'O' and resid 45 through 73 Processing helix chain 'O' and resid 92 through 121 Processing helix chain 'O' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER O 136 " --> pdb=" O THR O 132 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU O 137 " --> pdb=" O HIS O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 171 removed outlier: 3.584A pdb=" N GLU O 164 " --> pdb=" O SER O 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 39 Processing helix chain 'P' and resid 45 through 73 Processing helix chain 'P' and resid 92 through 121 Processing helix chain 'P' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER P 136 " --> pdb=" O THR P 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU P 137 " --> pdb=" O HIS P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 160 through 171 removed outlier: 3.584A pdb=" N GLU P 164 " --> pdb=" O SER P 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 39 Processing helix chain 'Q' and resid 45 through 73 Processing helix chain 'Q' and resid 92 through 121 Processing helix chain 'Q' and resid 123 through 156 removed outlier: 5.789A pdb=" N SER Q 136 " --> pdb=" O THR Q 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU Q 137 " --> pdb=" O HIS Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 171 removed outlier: 3.583A pdb=" N GLU Q 164 " --> pdb=" O SER Q 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 39 Processing helix chain 'R' and resid 45 through 73 Processing helix chain 'R' and resid 92 through 121 Processing helix chain 'R' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER R 136 " --> pdb=" O THR R 132 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU R 137 " --> pdb=" O HIS R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 171 removed outlier: 3.583A pdb=" N GLU R 164 " --> pdb=" O SER R 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 39 Processing helix chain 'S' and resid 45 through 73 Processing helix chain 'S' and resid 92 through 121 Processing helix chain 'S' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER S 136 " --> pdb=" O THR S 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU S 137 " --> pdb=" O HIS S 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 160 through 171 removed outlier: 3.584A pdb=" N GLU S 164 " --> pdb=" O SER S 160 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 39 Processing helix chain 'T' and resid 45 through 73 Processing helix chain 'T' and resid 92 through 121 Processing helix chain 'T' and resid 123 through 156 removed outlier: 5.789A pdb=" N SER T 136 " --> pdb=" O THR T 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU T 137 " --> pdb=" O HIS T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 160 through 171 removed outlier: 3.583A pdb=" N GLU T 164 " --> pdb=" O SER T 160 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 39 Processing helix chain 'V' and resid 45 through 73 Processing helix chain 'V' and resid 92 through 121 Processing helix chain 'V' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER V 136 " --> pdb=" O THR V 132 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU V 137 " --> pdb=" O HIS V 133 " (cutoff:3.500A) Processing helix chain 'V' and resid 160 through 171 removed outlier: 3.584A pdb=" N GLU V 164 " --> pdb=" O SER V 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 39 Processing helix chain 'W' and resid 45 through 73 Processing helix chain 'W' and resid 92 through 121 Processing helix chain 'W' and resid 123 through 156 removed outlier: 5.789A pdb=" N SER W 136 " --> pdb=" O THR W 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU W 137 " --> pdb=" O HIS W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 160 through 171 removed outlier: 3.584A pdb=" N GLU W 164 " --> pdb=" O SER W 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 39 Processing helix chain 'X' and resid 45 through 73 Processing helix chain 'X' and resid 92 through 121 Processing helix chain 'X' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER X 136 " --> pdb=" O THR X 132 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLU X 137 " --> pdb=" O HIS X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 160 through 171 removed outlier: 3.583A pdb=" N GLU X 164 " --> pdb=" O SER X 160 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 39 Processing helix chain 'Y' and resid 45 through 73 Processing helix chain 'Y' and resid 92 through 121 Processing helix chain 'Y' and resid 123 through 156 removed outlier: 5.790A pdb=" N SER Y 136 " --> pdb=" O THR Y 132 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLU Y 137 " --> pdb=" O HIS Y 133 " (cutoff:3.500A) Processing helix chain 'Y' and resid 160 through 171 removed outlier: 3.583A pdb=" N GLU Y 164 " --> pdb=" O SER Y 160 " (cutoff:3.500A) 2688 hydrogen bonds defined for protein. 8064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.92 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5976 1.30 - 1.43: 9168 1.43 - 1.55: 19296 1.55 - 1.68: 0 1.68 - 1.81: 264 Bond restraints: 34704 Sorted by residual: bond pdb=" C LEU S 69 " pdb=" O LEU S 69 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.15e-02 7.56e+03 2.93e+01 bond pdb=" C LEU V 69 " pdb=" O LEU V 69 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.15e-02 7.56e+03 2.93e+01 bond pdb=" C LEU X 69 " pdb=" O LEU X 69 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.15e-02 7.56e+03 2.93e+01 bond pdb=" C LEU L 69 " pdb=" O LEU L 69 " ideal model delta sigma weight residual 1.236 1.175 0.062 1.15e-02 7.56e+03 2.87e+01 bond pdb=" C LEU C 69 " pdb=" O LEU C 69 " ideal model delta sigma weight residual 1.236 1.175 0.062 1.15e-02 7.56e+03 2.87e+01 ... (remaining 34699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 44853 1.14 - 2.28: 1421 2.28 - 3.43: 333 3.43 - 4.57: 49 4.57 - 5.71: 72 Bond angle restraints: 46728 Sorted by residual: angle pdb=" O LEU O 69 " pdb=" C LEU O 69 " pdb=" N GLN O 70 " ideal model delta sigma weight residual 122.07 125.60 -3.53 1.03e+00 9.43e-01 1.18e+01 angle pdb=" O LEU Y 69 " pdb=" C LEU Y 69 " pdb=" N GLN Y 70 " ideal model delta sigma weight residual 122.07 125.58 -3.51 1.03e+00 9.43e-01 1.16e+01 angle pdb=" O LEU N 69 " pdb=" C LEU N 69 " pdb=" N GLN N 70 " ideal model delta sigma weight residual 122.07 125.58 -3.51 1.03e+00 9.43e-01 1.16e+01 angle pdb=" O LEU S 69 " pdb=" C LEU S 69 " pdb=" N GLN S 70 " ideal model delta sigma weight residual 122.07 125.54 -3.47 1.03e+00 9.43e-01 1.14e+01 angle pdb=" O LEU V 69 " pdb=" C LEU V 69 " pdb=" N GLN V 70 " ideal model delta sigma weight residual 122.07 125.54 -3.47 1.03e+00 9.43e-01 1.14e+01 ... (remaining 46723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 18188 16.53 - 33.06: 1889 33.06 - 49.60: 563 49.60 - 66.13: 216 66.13 - 82.66: 144 Dihedral angle restraints: 21000 sinusoidal: 8688 harmonic: 12312 Sorted by residual: dihedral pdb=" CA TRP F 90 " pdb=" C TRP F 90 " pdb=" N GLU F 91 " pdb=" CA GLU F 91 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA TRP D 90 " pdb=" C TRP D 90 " pdb=" N GLU D 91 " pdb=" CA GLU D 91 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA TRP S 90 " pdb=" C TRP S 90 " pdb=" N GLU S 91 " pdb=" CA GLU S 91 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3013 0.029 - 0.057: 1365 0.057 - 0.086: 231 0.086 - 0.115: 263 0.115 - 0.143: 48 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA TYR K 36 " pdb=" N TYR K 36 " pdb=" C TYR K 36 " pdb=" CB TYR K 36 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA TYR T 36 " pdb=" N TYR T 36 " pdb=" C TYR T 36 " pdb=" CB TYR T 36 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA TYR G 36 " pdb=" N TYR G 36 " pdb=" C TYR G 36 " pdb=" CB TYR G 36 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 4917 not shown) Planarity restraints: 6144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU L 131 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C GLU L 131 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU L 131 " 0.016 2.00e-02 2.50e+03 pdb=" N THR L 132 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 131 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C GLU F 131 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU F 131 " -0.016 2.00e-02 2.50e+03 pdb=" N THR F 132 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU J 131 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C GLU J 131 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU J 131 " 0.016 2.00e-02 2.50e+03 pdb=" N THR J 132 " 0.014 2.00e-02 2.50e+03 ... (remaining 6141 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 156 0.98 - 1.96: 132 1.96 - 2.94: 16684 2.94 - 3.92: 116593 3.92 - 4.90: 205867 Warning: very small nonbonded interaction distances. Nonbonded interactions: 339432 Sorted by model distance: nonbonded pdb=" O HOH G 351 " pdb=" O HOH G 352 " model vdw 0.004 3.040 nonbonded pdb=" O HOH X 351 " pdb=" O HOH X 352 " model vdw 0.004 3.040 nonbonded pdb="FE FE I 204 " pdb="FE FE I 205 " model vdw 0.004 1.480 nonbonded pdb="FE FE F 203 " pdb="FE FE F 204 " model vdw 0.005 1.480 nonbonded pdb=" O HOH F 348 " pdb=" O HOH F 349 " model vdw 0.005 3.040 ... (remaining 339427 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'R' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 24.960 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 : 0.003 0.062 34704 Z= 0.219 Angle : 0.554 5.710 46728 Z= 0.321 Chirality : 0.040 0.143 4920 Planarity : 0.004 0.036 6144 Dihedral : 17.206 82.659 13032 Min Nonbonded Distance : 0.004 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.95 % Allowed : 11.04 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.79 (0.13), residues: 4104 helix: 3.64 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.18 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG Q 60 TYR 0.021 0.002 TYR Y 36 PHE 0.026 0.003 PHE F 38 TRP 0.013 0.004 TRP K 90 HIS 0.004 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00343 (34704) covalent geometry : angle 0.55367 (46728) hydrogen bonds : bond 0.07025 ( 2688) hydrogen bonds : angle 3.81661 ( 8064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 791 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 24 residues processed: 815 average time/residue: 0.9519 time to fit residues: 887.2094 Evaluate side-chains 816 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 792 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain O residue 164 GLU Chi-restraints excluded: chain P residue 164 GLU Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain R residue 164 GLU Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain V residue 164 GLU Chi-restraints excluded: chain W residue 164 GLU Chi-restraints excluded: chain X residue 164 GLU Chi-restraints excluded: chain Y residue 164 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 102 HIS B 22 ASN B 102 HIS C 22 ASN C 102 HIS D 22 ASN D 102 HIS E 22 ASN E 102 HIS F 22 ASN F 102 HIS G 22 ASN G 102 HIS H 22 ASN H 102 HIS I 22 ASN I 102 HIS J 22 ASN J 102 HIS K 22 ASN K 102 HIS L 22 ASN L 102 HIS M 22 ASN M 102 HIS N 22 ASN N 102 HIS O 22 ASN O 102 HIS P 22 ASN P 102 HIS Q 22 ASN Q 102 HIS R 22 ASN R 72 GLN R 102 HIS S 22 ASN S 102 HIS T 22 ASN T 102 HIS V 22 ASN V 102 HIS W 22 ASN W 102 HIS X 22 ASN X 102 HIS Y 22 ASN Y 102 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.138231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.128580 restraints weight = 22493.385| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 0.46 r_work: 0.3215 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work: 0.2795 rms_B_bonded: 4.10 restraints_weight: 0.1250 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 34704 Z= 0.179 Angle : 0.605 5.892 46728 Z= 0.332 Chirality : 0.042 0.293 4920 Planarity : 0.005 0.039 6144 Dihedral : 6.704 48.793 4584 Min Nonbonded Distance : 0.982 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.24 % Allowed : 10.12 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.63 (0.13), residues: 4104 helix: 3.56 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.96 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 76 TYR 0.026 0.003 TYR E 36 PHE 0.029 0.004 PHE I 38 TRP 0.013 0.004 TRP P 90 HIS 0.006 0.002 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00358 (34704) covalent geometry : angle 0.60543 (46728) hydrogen bonds : bond 0.04844 ( 2688) hydrogen bonds : angle 3.69409 ( 8064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 775 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 24 residues processed: 799 average time/residue: 0.9203 time to fit residues: 845.1978 Evaluate side-chains 772 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 748 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain Y residue 2 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 153 optimal weight: 30.0000 chunk 136 optimal weight: 30.0000 chunk 385 optimal weight: 9.9990 chunk 393 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 374 optimal weight: 20.0000 chunk 318 optimal weight: 9.9990 chunk 362 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS B 72 GLN B 102 HIS C 72 GLN C 102 HIS D 102 HIS E 102 HIS F 102 HIS G 72 GLN G 102 HIS H 72 GLN H 102 HIS I 102 HIS J 102 HIS J 122 ASN K 102 HIS K 122 ASN L 72 GLN L 102 HIS M 102 HIS N 72 GLN N 102 HIS O 102 HIS P 102 HIS Q 102 HIS R 102 HIS S 102 HIS S 122 ASN T 72 GLN T 102 HIS V 72 GLN V 102 HIS W 102 HIS W 122 ASN X 102 HIS X 122 ASN Y 72 GLN Y 102 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.135594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.125848 restraints weight = 22362.085| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 0.47 r_work: 0.3180 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work: 0.2768 rms_B_bonded: 4.01 restraints_weight: 0.1250 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 34704 Z= 0.229 Angle : 0.635 6.052 46728 Z= 0.353 Chirality : 0.044 0.208 4920 Planarity : 0.006 0.042 6144 Dihedral : 4.504 21.376 4512 Min Nonbonded Distance : 0.974 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.95 % Allowed : 8.44 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.48 (0.13), residues: 4104 helix: 3.43 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.97 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 60 TYR 0.028 0.003 TYR Y 36 PHE 0.032 0.004 PHE H 38 TRP 0.014 0.004 TRP Y 90 HIS 0.007 0.002 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00458 (34704) covalent geometry : angle 0.63525 (46728) hydrogen bonds : bond 0.05308 ( 2688) hydrogen bonds : angle 3.77284 ( 8064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 744 time to evaluate : 1.209 Fit side-chains outliers start: 72 outliers final: 24 residues processed: 792 average time/residue: 0.9261 time to fit residues: 844.0607 Evaluate side-chains 786 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 762 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain Y residue 2 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 320 optimal weight: 30.0000 chunk 369 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 283 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 232 optimal weight: 20.0000 chunk 152 optimal weight: 0.9990 chunk 290 optimal weight: 10.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 102 HIS B 57 HIS B 102 HIS C 57 HIS C 102 HIS D 57 HIS D 102 HIS E 57 HIS E 102 HIS F 57 HIS F 102 HIS G 57 HIS G 102 HIS H 57 HIS H 102 HIS I 57 HIS I 102 HIS J 57 HIS J 102 HIS K 57 HIS K 102 HIS K 122 ASN L 57 HIS L 102 HIS M 57 HIS M 102 HIS N 57 HIS N 102 HIS O 57 HIS O 102 HIS P 57 HIS P 102 HIS Q 57 HIS Q 102 HIS R 57 HIS R 102 HIS S 57 HIS S 102 HIS T 57 HIS T 102 HIS V 57 HIS V 102 HIS W 57 HIS W 102 HIS X 57 HIS X 102 HIS X 122 ASN Y 57 HIS Y 102 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.135207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.125420 restraints weight = 22377.592| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 0.46 r_work: 0.3179 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work: 0.2765 rms_B_bonded: 4.03 restraints_weight: 0.1250 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 34704 Z= 0.201 Angle : 0.594 6.006 46728 Z= 0.332 Chirality : 0.042 0.195 4920 Planarity : 0.005 0.037 6144 Dihedral : 4.497 21.178 4512 Min Nonbonded Distance : 0.974 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.78 % Allowed : 10.58 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.51 (0.13), residues: 4104 helix: 3.44 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.97 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 40 TYR 0.027 0.003 TYR M 36 PHE 0.030 0.004 PHE M 38 TRP 0.014 0.004 TRP Y 90 HIS 0.007 0.002 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00399 (34704) covalent geometry : angle 0.59397 (46728) hydrogen bonds : bond 0.05082 ( 2688) hydrogen bonds : angle 3.72177 ( 8064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 792 time to evaluate : 1.352 Fit side-chains REVERT: X 91 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7830 (pp20) outliers start: 29 outliers final: 24 residues processed: 816 average time/residue: 0.8993 time to fit residues: 846.9014 Evaluate side-chains 769 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 744 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 91 GLU Chi-restraints excluded: chain Y residue 2 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 363 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 chunk 40 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 338 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 202 optimal weight: 0.0370 chunk 111 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 102 HIS B 57 HIS B 102 HIS C 57 HIS C 102 HIS D 57 HIS D 102 HIS E 57 HIS E 102 HIS F 57 HIS F 102 HIS G 57 HIS G 102 HIS H 57 HIS H 102 HIS I 57 HIS I 102 HIS J 57 HIS J 102 HIS K 57 HIS K 102 HIS L 57 HIS L 102 HIS M 57 HIS M 102 HIS N 57 HIS N 102 HIS O 57 HIS O 102 HIS P 57 HIS P 102 HIS Q 57 HIS Q 102 HIS R 57 HIS R 102 HIS S 57 HIS S 102 HIS T 57 HIS T 102 HIS V 57 HIS V 102 HIS W 57 HIS W 102 HIS X 57 HIS X 102 HIS Y 57 HIS Y 102 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.136687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.126929 restraints weight = 22435.766| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 0.46 r_work: 0.3206 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work: 0.2790 rms_B_bonded: 4.12 restraints_weight: 0.1250 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 34704 Z= 0.150 Angle : 0.533 5.786 46728 Z= 0.297 Chirality : 0.040 0.168 4920 Planarity : 0.004 0.028 6144 Dihedral : 4.361 21.502 4512 Min Nonbonded Distance : 1.040 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.11 % Allowed : 11.26 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.83 (0.13), residues: 4104 helix: 3.74 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.87 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 60 TYR 0.024 0.002 TYR E 36 PHE 0.024 0.003 PHE Y 38 TRP 0.012 0.003 TRP Y 90 HIS 0.005 0.001 HIS W 125 Details of bonding type rmsd covalent geometry : bond 0.00293 (34704) covalent geometry : angle 0.53300 (46728) hydrogen bonds : bond 0.04534 ( 2688) hydrogen bonds : angle 3.58856 ( 8064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 768 time to evaluate : 1.381 Fit side-chains REVERT: Q 88 ASP cc_start: 0.7333 (m-30) cc_final: 0.7128 (m-30) outliers start: 4 outliers final: 0 residues processed: 768 average time/residue: 0.8990 time to fit residues: 797.3275 Evaluate side-chains 744 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 744 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 404 optimal weight: 9.9990 chunk 359 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 4 optimal weight: 30.0000 chunk 162 optimal weight: 5.9990 chunk 335 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 304 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 102 HIS B 57 HIS B 102 HIS C 57 HIS C 102 HIS D 57 HIS D 102 HIS E 57 HIS E 102 HIS F 57 HIS F 102 HIS G 57 HIS G 102 HIS H 57 HIS H 102 HIS I 57 HIS I 102 HIS J 57 HIS J 102 HIS K 57 HIS K 102 HIS L 57 HIS L 102 HIS M 57 HIS M 102 HIS N 57 HIS N 102 HIS O 57 HIS O 102 HIS P 57 HIS P 102 HIS Q 57 HIS Q 102 HIS R 57 HIS R 102 HIS S 57 HIS S 102 HIS T 57 HIS T 102 HIS V 57 HIS V 102 HIS W 57 HIS W 102 HIS X 57 HIS X 102 HIS Y 57 HIS Y 102 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.135578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.125906 restraints weight = 22318.868| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 0.46 r_work: 0.3201 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work: 0.2786 rms_B_bonded: 4.07 restraints_weight: 0.1250 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 34704 Z= 0.184 Angle : 0.578 5.975 46728 Z= 0.321 Chirality : 0.041 0.160 4920 Planarity : 0.004 0.033 6144 Dihedral : 4.440 21.879 4512 Min Nonbonded Distance : 1.003 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.43 % Allowed : 9.96 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.70 (0.13), residues: 4104 helix: 3.63 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.89 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG G 60 TYR 0.026 0.003 TYR I 36 PHE 0.028 0.004 PHE N 38 TRP 0.013 0.004 TRP O 90 HIS 0.006 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00365 (34704) covalent geometry : angle 0.57830 (46728) hydrogen bonds : bond 0.04928 ( 2688) hydrogen bonds : angle 3.67658 ( 8064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 768 time to evaluate : 1.439 Fit side-chains REVERT: E 88 ASP cc_start: 0.7347 (m-30) cc_final: 0.7135 (m-30) REVERT: F 88 ASP cc_start: 0.7344 (m-30) cc_final: 0.7135 (m-30) REVERT: G 88 ASP cc_start: 0.7347 (m-30) cc_final: 0.7122 (m-30) REVERT: J 88 ASP cc_start: 0.7356 (m-30) cc_final: 0.7144 (m-30) REVERT: L 88 ASP cc_start: 0.7358 (m-30) cc_final: 0.7152 (m-30) REVERT: R 88 ASP cc_start: 0.7356 (m-30) cc_final: 0.7143 (m-30) REVERT: S 88 ASP cc_start: 0.7353 (m-30) cc_final: 0.7146 (m-30) REVERT: T 88 ASP cc_start: 0.7353 (m-30) cc_final: 0.7139 (m-30) REVERT: V 88 ASP cc_start: 0.7359 (m-30) cc_final: 0.7139 (m-30) outliers start: 16 outliers final: 0 residues processed: 782 average time/residue: 0.9155 time to fit residues: 824.1034 Evaluate side-chains 744 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 744 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 126 optimal weight: 20.0000 chunk 308 optimal weight: 0.9990 chunk 348 optimal weight: 20.0000 chunk 211 optimal weight: 20.0000 chunk 396 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 325 optimal weight: 0.9990 chunk 361 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 340 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 102 HIS B 57 HIS B 102 HIS C 57 HIS C 102 HIS D 57 HIS D 102 HIS E 57 HIS E 102 HIS F 57 HIS F 102 HIS G 57 HIS G 102 HIS H 57 HIS H 102 HIS I 57 HIS I 102 HIS J 57 HIS J 102 HIS K 57 HIS K 102 HIS L 57 HIS L 102 HIS M 57 HIS M 102 HIS N 57 HIS N 102 HIS O 57 HIS O 102 HIS P 57 HIS P 102 HIS Q 57 HIS Q 102 HIS R 57 HIS R 102 HIS S 57 HIS S 102 HIS T 57 HIS T 102 HIS V 57 HIS V 102 HIS W 57 HIS W 102 HIS X 57 HIS X 102 HIS Y 57 HIS Y 102 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.136107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.126343 restraints weight = 22451.993| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 0.47 r_work: 0.3198 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work: 0.2788 rms_B_bonded: 4.05 restraints_weight: 0.1250 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34704 Z= 0.163 Angle : 0.554 5.896 46728 Z= 0.307 Chirality : 0.040 0.155 4920 Planarity : 0.004 0.029 6144 Dihedral : 4.379 21.649 4512 Min Nonbonded Distance : 1.015 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.30 % Allowed : 10.36 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.78 (0.13), residues: 4104 helix: 3.69 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.90 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 60 TYR 0.024 0.002 TYR I 36 PHE 0.026 0.003 PHE C 38 TRP 0.013 0.004 TRP X 90 HIS 0.006 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00321 (34704) covalent geometry : angle 0.55414 (46728) hydrogen bonds : bond 0.04697 ( 2688) hydrogen bonds : angle 3.62647 ( 8064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 768 time to evaluate : 1.532 Fit side-chains REVERT: Q 88 ASP cc_start: 0.7351 (m-30) cc_final: 0.7130 (m-30) outliers start: 11 outliers final: 0 residues processed: 777 average time/residue: 0.9094 time to fit residues: 813.4131 Evaluate side-chains 743 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 743 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 368 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 294 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 349 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 396 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 102 HIS B 57 HIS C 57 HIS C 102 HIS D 57 HIS E 57 HIS E 102 HIS F 57 HIS G 57 HIS G 102 HIS H 57 HIS H 102 HIS I 57 HIS I 102 HIS J 57 HIS J 102 HIS K 57 HIS K 102 HIS L 57 HIS L 102 HIS M 57 HIS M 102 HIS N 57 HIS O 57 HIS O 102 HIS P 57 HIS Q 57 HIS R 57 HIS R 102 HIS S 57 HIS T 57 HIS T 102 HIS V 57 HIS V 102 HIS W 57 HIS W 102 HIS X 57 HIS X 102 HIS Y 57 HIS Y 122 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.139370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.129758 restraints weight = 22432.223| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 0.46 r_work: 0.3239 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 1.47 restraints_weight: 0.2500 r_work: 0.2830 rms_B_bonded: 4.11 restraints_weight: 0.1250 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 34704 Z= 0.114 Angle : 0.491 5.400 46728 Z= 0.268 Chirality : 0.037 0.147 4920 Planarity : 0.003 0.022 6144 Dihedral : 4.199 22.006 4512 Min Nonbonded Distance : 1.083 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.08 % Allowed : 10.58 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.15 (0.13), residues: 4104 helix: 3.99 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.87 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 60 TYR 0.019 0.002 TYR G 36 PHE 0.018 0.002 PHE Q 38 TRP 0.012 0.003 TRP F 90 HIS 0.004 0.001 HIS M 125 Details of bonding type rmsd covalent geometry : bond 0.00220 (34704) covalent geometry : angle 0.49092 (46728) hydrogen bonds : bond 0.03925 ( 2688) hydrogen bonds : angle 3.41392 ( 8064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 827 time to evaluate : 1.439 Fit side-chains REVERT: G 88 ASP cc_start: 0.7273 (m-30) cc_final: 0.7068 (m-30) REVERT: J 88 ASP cc_start: 0.7282 (m-30) cc_final: 0.7080 (m-30) REVERT: R 88 ASP cc_start: 0.7274 (m-30) cc_final: 0.7067 (m-30) outliers start: 3 outliers final: 0 residues processed: 828 average time/residue: 0.8524 time to fit residues: 820.3521 Evaluate side-chains 753 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 753 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 310 optimal weight: 3.9990 chunk 370 optimal weight: 9.9990 chunk 305 optimal weight: 8.9990 chunk 228 optimal weight: 0.9990 chunk 298 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 236 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 325 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 95 ASN A 102 HIS A 109 GLN B 57 HIS B 95 ASN B 102 HIS B 109 GLN C 57 HIS C 95 ASN C 102 HIS C 109 GLN D 57 HIS D 95 ASN D 102 HIS D 109 GLN E 57 HIS E 95 ASN E 102 HIS E 109 GLN F 57 HIS F 95 ASN F 102 HIS F 109 GLN G 57 HIS G 95 ASN G 102 HIS G 109 GLN H 57 HIS H 95 ASN H 102 HIS H 109 GLN I 57 HIS I 95 ASN I 102 HIS I 109 GLN J 57 HIS J 95 ASN J 102 HIS J 109 GLN K 57 HIS K 95 ASN K 102 HIS K 109 GLN L 57 HIS L 95 ASN L 102 HIS L 109 GLN M 57 HIS M 95 ASN M 102 HIS M 109 GLN N 57 HIS N 95 ASN N 102 HIS N 109 GLN O 57 HIS O 95 ASN O 102 HIS O 109 GLN P 57 HIS P 95 ASN P 109 GLN Q 57 HIS Q 95 ASN Q 109 GLN R 57 HIS R 95 ASN R 102 HIS R 109 GLN S 57 HIS S 95 ASN S 102 HIS S 109 GLN T 57 HIS T 95 ASN T 102 HIS T 109 GLN V 57 HIS V 95 ASN V 102 HIS V 109 GLN W 57 HIS W 95 ASN W 102 HIS W 109 GLN X 57 HIS X 95 ASN X 102 HIS X 109 GLN Y 57 HIS Y 95 ASN Y 109 GLN Total number of N/Q/H flips: 93 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.138125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.128400 restraints weight = 22274.314| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 0.46 r_work: 0.3224 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work: 0.2816 rms_B_bonded: 4.09 restraints_weight: 0.1250 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 34704 Z= 0.127 Angle : 0.513 5.540 46728 Z= 0.281 Chirality : 0.037 0.144 4920 Planarity : 0.003 0.023 6144 Dihedral : 4.248 22.469 4512 Min Nonbonded Distance : 1.063 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.03 % Allowed : 10.63 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.04 (0.13), residues: 4104 helix: 3.91 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.82 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 60 TYR 0.020 0.002 TYR J 36 PHE 0.021 0.002 PHE V 38 TRP 0.011 0.003 TRP X 90 HIS 0.004 0.001 HIS L 125 Details of bonding type rmsd covalent geometry : bond 0.00248 (34704) covalent geometry : angle 0.51267 (46728) hydrogen bonds : bond 0.04145 ( 2688) hydrogen bonds : angle 3.45767 ( 8064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 787 time to evaluate : 0.910 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 788 average time/residue: 0.9437 time to fit residues: 853.0908 Evaluate side-chains 766 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 766 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 12 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 339 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 355 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 336 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 350 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 102 HIS B 57 HIS B 102 HIS C 57 HIS C 102 HIS D 57 HIS D 102 HIS E 57 HIS E 102 HIS F 57 HIS G 57 HIS G 102 HIS H 57 HIS H 102 HIS I 57 HIS I 102 HIS J 57 HIS J 102 HIS K 57 HIS K 102 HIS L 57 HIS L 102 HIS M 57 HIS M 102 HIS N 57 HIS N 102 HIS O 57 HIS O 102 HIS P 57 HIS Q 57 HIS R 57 HIS R 102 HIS S 57 HIS S 102 HIS T 57 HIS T 102 HIS V 57 HIS V 102 HIS W 57 HIS W 102 HIS X 57 HIS X 102 HIS Y 57 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.137777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.127994 restraints weight = 22389.744| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 0.47 r_work: 0.3219 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 1.47 restraints_weight: 0.2500 r_work: 0.2810 rms_B_bonded: 4.11 restraints_weight: 0.1250 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34704 Z= 0.136 Angle : 0.526 5.626 46728 Z= 0.290 Chirality : 0.038 0.142 4920 Planarity : 0.004 0.023 6144 Dihedral : 4.292 22.493 4512 Min Nonbonded Distance : 1.058 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.03 % Allowed : 10.85 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.98 (0.13), residues: 4104 helix: 3.86 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.85 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 60 TYR 0.021 0.002 TYR E 36 PHE 0.021 0.003 PHE V 38 TRP 0.011 0.003 TRP F 90 HIS 0.005 0.001 HIS N 125 Details of bonding type rmsd covalent geometry : bond 0.00268 (34704) covalent geometry : angle 0.52641 (46728) hydrogen bonds : bond 0.04281 ( 2688) hydrogen bonds : angle 3.48873 ( 8064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 792 time to evaluate : 1.450 Fit side-chains REVERT: G 88 ASP cc_start: 0.7298 (m-30) cc_final: 0.7097 (m-30) REVERT: R 88 ASP cc_start: 0.7293 (m-30) cc_final: 0.7092 (m-30) outliers start: 1 outliers final: 1 residues processed: 793 average time/residue: 0.9452 time to fit residues: 859.6350 Evaluate side-chains 773 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 772 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 164 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 292 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 102 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 281 optimal weight: 5.9990 chunk 367 optimal weight: 8.9990 chunk 242 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 102 HIS A 109 GLN B 57 HIS B 102 HIS B 109 GLN C 57 HIS C 102 HIS C 109 GLN D 57 HIS D 102 HIS D 109 GLN E 57 HIS E 102 HIS E 109 GLN F 55 GLN F 57 HIS F 102 HIS F 109 GLN G 57 HIS G 102 HIS G 109 GLN H 57 HIS H 102 HIS H 109 GLN I 57 HIS I 102 HIS I 109 GLN J 57 HIS J 102 HIS J 109 GLN K 57 HIS K 102 HIS K 109 GLN L 57 HIS L 102 HIS L 109 GLN M 57 HIS M 102 HIS M 109 GLN N 57 HIS N 102 HIS N 109 GLN O 57 HIS O 102 HIS O 109 GLN P 57 HIS P 102 HIS P 109 GLN Q 57 HIS Q 102 HIS Q 109 GLN R 57 HIS R 102 HIS R 109 GLN S 57 HIS S 102 HIS S 109 GLN T 57 HIS T 102 HIS T 109 GLN V 57 HIS V 102 HIS V 109 GLN W 57 HIS W 102 HIS W 109 GLN X 57 HIS X 102 HIS X 109 GLN Y 57 HIS Y 102 HIS Y 109 GLN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.136319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.126625 restraints weight = 22313.498| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 0.46 r_work: 0.3195 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work: 0.2783 rms_B_bonded: 4.08 restraints_weight: 0.1250 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34704 Z= 0.176 Angle : 0.575 5.935 46728 Z= 0.319 Chirality : 0.040 0.145 4920 Planarity : 0.004 0.030 6144 Dihedral : 4.398 22.035 4512 Min Nonbonded Distance : 1.022 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.76 % Allowed : 10.15 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.76 (0.13), residues: 4104 helix: 3.69 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.81 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 60 TYR 0.024 0.002 TYR B 36 PHE 0.026 0.004 PHE V 38 TRP 0.011 0.003 TRP S 90 HIS 0.006 0.001 HIS J 125 Details of bonding type rmsd covalent geometry : bond 0.00349 (34704) covalent geometry : angle 0.57466 (46728) hydrogen bonds : bond 0.04778 ( 2688) hydrogen bonds : angle 3.61877 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22679.32 seconds wall clock time: 384 minutes 29.14 seconds (23069.14 seconds total)