Starting phenix.real_space_refine on Mon Jul 6 10:41:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjt_54953/07_2026/9sjt_54953_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjt_54953/07_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_54953/07_2026/9sjt_54953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjt_54953/07_2026/9sjt_54953.map" model { file = "/net/cci-nas-00/data/ceres_data/9sjt_54953/07_2026/9sjt_54953_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjt_54953/07_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-6108/lib/python3.11/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, 1 Ad-hoc single atom residues: {' FE': 4} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 3.95, per 1000 atoms: 0.11 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: 3.04 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: 0.66 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: 6.59 Time building geometry restraints manager: 3.95 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 2.960 nonbonded pdb="FE FE F 203 " pdb="FE FE F 204 " model vdw 0.005 2.960 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: 0.14 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.870 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 27.270 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 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/Z covalent geometry : bond 0.00343 / 0.22 (34704) covalent geometry : angle 0.55367 / 0.32 (46728) hydrogen bonds : bond 0.07025 / 4.73 ( 2688) hydrogen bonds : angle 3.81661 / 2.75 ( 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 : 1.545 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: 0.8836 time to fit residues: 828.2463 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 : 1.294 ------------------------------------------------------------------------------- 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... 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 X 122 ASN Y 22 ASN Y 102 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.138921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.129235 restraints weight = 22478.462| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 0.47 r_work: 0.3216 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 1.48 restraints_weight: 0.2500 r_work: 0.2796 rms_B_bonded: 4.15 restraints_weight: 0.1250 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 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 = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 34704 Z= 0.180 Angle : 0.609 5.921 46728 Z= 0.334 Chirality : 0.043 0.345 4920 Planarity : 0.005 0.037 6144 Dihedral : 6.373 45.659 4584 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.65 % Allowed : 10.71 % 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: 4.65 (0.13), residues: 4104 helix: 3.57 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.99 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 60 TYR 0.026 0.003 TYR L 36 PHE 0.029 0.004 PHE A 38 TRP 0.013 0.004 TRP S 90 HIS 0.006 0.002 HIS L 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (34704) covalent geometry : angle 0.60884 / 0.33 (46728) hydrogen bonds : bond 0.04860 / 3.30 ( 2688) hydrogen bonds : angle 3.68885 / 2.66 ( 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 799 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 775 time to evaluate : 1.512 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: 24 outliers final: 24 residues processed: 799 average time/residue: 0.9065 time to fit residues: 838.0355 Evaluate side-chains 758 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 734 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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: 9.9990 chunk 153 optimal weight: 30.0000 chunk 136 optimal weight: 30.0000 chunk 385 optimal weight: 20.0000 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: 3.9990 chunk 155 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS B 72 GLN B 102 HIS B 122 ASN 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 72 GLN K 102 HIS 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 R 122 ASN 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: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.135487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.125693 restraints weight = 22367.539| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 0.46 r_work: 0.3175 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work: 0.2760 rms_B_bonded: 4.01 restraints_weight: 0.1250 r_work (final): 0.2760 ------------------------------------------------------------------------------- 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: 27 | |-----------------------------------------------------------------------------| |-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: 31 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 34704 Z= 0.234 Angle : 0.645 6.041 46728 Z= 0.358 Chirality : 0.044 0.231 4920 Planarity : 0.006 0.042 6144 Dihedral : 4.531 21.343 4512 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.95 % Allowed : 8.50 % Favored : 89.56 % 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: 4.45 (0.13), residues: 4104 helix: 3.40 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.95 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Y 60 TYR 0.028 0.003 TYR N 36 PHE 0.033 0.004 PHE V 38 TRP 0.014 0.004 TRP P 90 HIS 0.007 0.002 HIS F 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.23 (34704) covalent geometry : angle 0.64504 / 0.36 (46728) hydrogen bonds : bond 0.05340 / 3.63 ( 2688) hydrogen bonds : angle 3.77617 / 2.72 ( 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 : 1.369 Fit side-chains outliers start: 72 outliers final: 24 residues processed: 792 average time/residue: 0.8934 time to fit residues: 818.5186 Evaluate side-chains 801 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 777 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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: 6.9990 chunk 369 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 283 optimal weight: 20.0000 chunk 206 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 232 optimal weight: 20.0000 chunk 152 optimal weight: 0.8980 chunk 290 optimal weight: 7.9990 overall best weight: 5.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3425 r_free = 0.3425 target = 0.135860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.126186 restraints weight = 22297.725| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 0.46 r_work: 0.3203 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work: 0.2793 rms_B_bonded: 4.02 restraints_weight: 0.1250 r_work (final): 0.2793 ------------------------------------------------------------------------------- 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: 31 | |-----------------------------------------------------------------------------| |-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: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34704 Z= 0.183 Angle : 0.575 5.862 46728 Z= 0.320 Chirality : 0.041 0.193 4920 Planarity : 0.005 0.034 6144 Dihedral : 4.425 20.729 4512 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.24 % Allowed : 9.79 % Favored : 88.96 % 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: 4.57 (0.13), residues: 4104 helix: 3.50 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.94 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 76 TYR 0.025 0.002 TYR I 36 PHE 0.028 0.004 PHE K 38 TRP 0.013 0.004 TRP X 90 HIS 0.006 0.001 HIS G 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (34704) covalent geometry : angle 0.57478 / 0.32 (46728) hydrogen bonds : bond 0.04921 / 3.34 ( 2688) hydrogen bonds : angle 3.68848 / 2.65 ( 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 847 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 801 time to evaluate : 1.406 Fit side-chains outliers start: 46 outliers final: 22 residues processed: 823 average time/residue: 0.8782 time to fit residues: 838.3613 Evaluate side-chains 790 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 768 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 363 optimal weight: 6.9990 chunk 119 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 chunk 296 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 338 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 291 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3439 r_free = 0.3439 target = 0.136810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.127154 restraints weight = 22459.546| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 0.46 r_work: 0.3209 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work: 0.2800 rms_B_bonded: 4.04 restraints_weight: 0.1250 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.0934 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= 0.166 Angle : 0.554 5.877 46728 Z= 0.309 Chirality : 0.040 0.169 4920 Planarity : 0.004 0.031 6144 Dihedral : 4.414 21.558 4512 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.43 % Allowed : 10.61 % Favored : 88.96 % 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: 4.71 (0.13), residues: 4104 helix: 3.65 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.85 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 60 TYR 0.025 0.002 TYR I 36 PHE 0.026 0.003 PHE J 38 TRP 0.012 0.004 TRP X 90 HIS 0.006 0.001 HIS V 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (34704) covalent geometry : angle 0.55427 / 0.31 (46728) hydrogen bonds : bond 0.04745 / 3.22 ( 2688) hydrogen bonds : angle 3.64016 / 2.62 ( 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 807 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 791 time to evaluate : 1.573 Fit side-chains REVERT: M 91 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7784 (pp20) REVERT: R 91 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7786 (pp20) outliers start: 16 outliers final: 14 residues processed: 805 average time/residue: 0.8726 time to fit residues: 813.5593 Evaluate side-chains 774 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 758 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain H 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 M residue 91 GLU 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 91 GLU Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain W residue 2 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 404 optimal weight: 10.0000 chunk 359 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 4 optimal weight: 30.0000 chunk 162 optimal weight: 6.9990 chunk 335 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 304 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 11 GLN 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: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.135076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.125430 restraints weight = 22347.404| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 0.46 r_work: 0.3178 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work: 0.2766 rms_B_bonded: 4.00 restraints_weight: 0.1250 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 34704 Z= 0.210 Angle : 0.608 6.009 46728 Z= 0.338 Chirality : 0.042 0.174 4920 Planarity : 0.005 0.037 6144 Dihedral : 4.489 21.308 4512 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.68 % Allowed : 10.36 % Favored : 88.96 % 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: 4.53 (0.13), residues: 4104 helix: 3.47 (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 0.001 ARG G 60 TYR 0.027 0.003 TYR D 36 PHE 0.030 0.004 PHE J 38 TRP 0.014 0.004 TRP X 90 HIS 0.007 0.002 HIS R 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.21 (34704) covalent geometry : angle 0.60764 / 0.34 (46728) hydrogen bonds : bond 0.05174 / 3.51 ( 2688) hydrogen bonds : angle 3.73749 / 2.69 ( 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 808 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 783 time to evaluate : 1.315 Fit side-chains REVERT: M 91 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7806 (pp20) REVERT: R 91 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7812 (pp20) outliers start: 25 outliers final: 23 residues processed: 806 average time/residue: 0.8638 time to fit residues: 808.3196 Evaluate side-chains 785 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 760 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 M residue 91 GLU 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 91 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 126 optimal weight: 1.9990 chunk 308 optimal weight: 0.9990 chunk 348 optimal weight: 20.0000 chunk 211 optimal weight: 20.0000 chunk 396 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 325 optimal weight: 0.9990 chunk 361 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 340 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3448 r_free = 0.3448 target = 0.137640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.128020 restraints weight = 22494.408| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 0.46 r_work: 0.3217 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 1.47 restraints_weight: 0.2500 r_work: 0.2803 rms_B_bonded: 4.13 restraints_weight: 0.1250 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.0998 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= 0.134 Angle : 0.519 5.647 46728 Z= 0.286 Chirality : 0.039 0.152 4920 Planarity : 0.004 0.023 6144 Dihedral : 4.305 21.675 4512 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.05 % Allowed : 10.98 % Favored : 88.96 % 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: 4.95 (0.13), residues: 4104 helix: 3.84 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.84 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 60 TYR 0.022 0.002 TYR L 36 PHE 0.021 0.003 PHE M 38 TRP 0.012 0.003 TRP C 90 HIS 0.005 0.001 HIS R 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (34704) covalent geometry : angle 0.51862 / 0.29 (46728) hydrogen bonds : bond 0.04296 / 2.91 ( 2688) hydrogen bonds : angle 3.53286 / 2.54 ( 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 835 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 833 time to evaluate : 1.474 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 833 average time/residue: 0.8464 time to fit residues: 820.7953 Evaluate side-chains 759 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 759 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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: 10.0000 chunk 183 optimal weight: 0.9980 chunk 294 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 349 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 396 optimal weight: 0.9980 chunk 218 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 320 optimal weight: 9.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS A 95 ASN A 102 HIS B 57 HIS B 95 ASN B 102 HIS C 57 HIS C 95 ASN C 102 HIS D 57 HIS D 95 ASN D 102 HIS E 57 HIS E 95 ASN E 102 HIS F 57 HIS F 95 ASN F 102 HIS G 57 HIS G 95 ASN G 102 HIS H 57 HIS H 95 ASN H 102 HIS I 57 HIS I 95 ASN I 102 HIS J 57 HIS J 95 ASN J 102 HIS K 57 HIS K 95 ASN K 102 HIS L 57 HIS L 95 ASN L 102 HIS M 57 HIS M 95 ASN M 102 HIS N 57 HIS N 95 ASN N 102 HIS O 57 HIS O 95 ASN O 102 HIS P 57 HIS P 95 ASN P 102 HIS Q 57 HIS Q 95 ASN Q 102 HIS R 57 HIS R 95 ASN R 102 HIS S 57 HIS S 95 ASN S 102 HIS T 57 HIS T 95 ASN T 102 HIS V 57 HIS V 95 ASN V 102 HIS W 57 HIS W 95 ASN W 102 HIS X 57 HIS X 95 ASN X 102 HIS Y 57 HIS Y 95 ASN Y 102 HIS Y 122 ASN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.137563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.127906 restraints weight = 22446.699| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 0.46 r_work: 0.3213 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 1.47 restraints_weight: 0.2500 r_work: 0.2801 rms_B_bonded: 4.10 restraints_weight: 0.1250 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1009 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= 0.139 Angle : 0.527 5.676 46728 Z= 0.290 Chirality : 0.039 0.173 4920 Planarity : 0.004 0.024 6144 Dihedral : 4.308 21.774 4512 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.70 % Allowed : 9.69 % 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: 4.90 (0.13), residues: 4104 helix: 3.81 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.79 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 60 TYR 0.022 0.002 TYR D 36 PHE 0.022 0.003 PHE N 38 TRP 0.012 0.003 TRP W 90 HIS 0.005 0.001 HIS R 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (34704) covalent geometry : angle 0.52695 / 0.29 (46728) hydrogen bonds : bond 0.04365 / 2.96 ( 2688) hydrogen bonds : angle 3.54302 / 2.55 ( 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 811 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 785 time to evaluate : 1.182 Fit side-chains REVERT: G 88 ASP cc_start: 0.7318 (m-30) cc_final: 0.7115 (m-30) outliers start: 26 outliers final: 0 residues processed: 809 average time/residue: 0.8527 time to fit residues: 796.2951 Evaluate side-chains 771 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 771 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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: 0.8980 chunk 370 optimal weight: 5.9990 chunk 305 optimal weight: 0.9990 chunk 228 optimal weight: 0.5980 chunk 298 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 325 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS B 57 HIS C 57 HIS D 57 HIS E 57 HIS F 57 HIS G 57 HIS H 57 HIS I 57 HIS J 57 HIS K 57 HIS L 57 HIS M 57 HIS N 57 HIS O 57 HIS P 57 HIS Q 57 HIS R 57 HIS S 57 HIS T 57 HIS V 57 HIS W 57 HIS X 57 HIS Y 57 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.143821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.134592 restraints weight = 22355.637| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 0.45 r_work: 0.3314 rms_B_bonded: 0.77 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work: 0.2914 rms_B_bonded: 4.11 restraints_weight: 0.1250 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 34704 Z= 0.095 Angle : 0.464 4.969 46728 Z= 0.248 Chirality : 0.036 0.154 4920 Planarity : 0.003 0.020 6144 Dihedral : 4.038 22.197 4512 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 11.36 % 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: 5.31 (0.13), residues: 4104 helix: 4.19 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.65 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 60 TYR 0.016 0.002 TYR M 36 PHE 0.011 0.002 PHE N 38 TRP 0.010 0.002 TRP X 90 HIS 0.003 0.001 HIS E 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.10 (34704) covalent geometry : angle 0.46439 / 0.25 (46728) hydrogen bonds : bond 0.03290 / 2.23 ( 2688) hydrogen bonds : angle 3.24795 / 2.34 ( 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 826 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 826 time to evaluate : 1.342 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 826 average time/residue: 0.7826 time to fit residues: 751.7375 Evaluate side-chains 858 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 858 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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: 10.0000 chunk 226 optimal weight: 10.0000 chunk 339 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 355 optimal weight: 2.9990 chunk 167 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 336 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 350 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 55 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 55 GLN X 57 HIS X 102 HIS X 109 GLN Y 57 HIS Y 109 GLN Y 122 ASN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.136868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.127319 restraints weight = 22356.051| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 0.46 r_work: 0.3218 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work: 0.2810 rms_B_bonded: 4.07 restraints_weight: 0.1250 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 34704 Z= 0.150 Angle : 0.556 5.778 46728 Z= 0.303 Chirality : 0.039 0.179 4920 Planarity : 0.004 0.026 6144 Dihedral : 4.292 22.122 4512 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % 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: 3.85 (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 0.004 0.001 ARG D 60 TYR 0.022 0.002 TYR M 36 PHE 0.025 0.003 PHE F 38 TRP 0.011 0.003 TRP I 90 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (34704) covalent geometry : angle 0.55638 / 0.30 (46728) hydrogen bonds : bond 0.04491 / 3.05 ( 2688) hydrogen bonds : angle 3.53024 / 2.54 ( 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 848 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 848 time to evaluate : 1.445 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 848 average time/residue: 0.8194 time to fit residues: 802.4784 Evaluate side-chains 800 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 800 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 292 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 30.0000 chunk 102 optimal weight: 30.0000 chunk 78 optimal weight: 8.9990 chunk 131 optimal weight: 0.7980 chunk 281 optimal weight: 6.9990 chunk 367 optimal weight: 6.9990 chunk 242 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS A 102 HIS B 57 HIS B 102 HIS C 57 HIS C 102 HIS D 57 HIS D 72 GLN 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 72 GLN 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 72 GLN X 102 HIS Y 57 HIS Y 102 HIS Y 122 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.136796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.127271 restraints weight = 22245.122| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 0.46 r_work: 0.3212 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work: 0.2803 rms_B_bonded: 4.04 restraints_weight: 0.1250 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 34704 Z= 0.147 Angle : 0.552 5.741 46728 Z= 0.301 Chirality : 0.039 0.182 4920 Planarity : 0.004 0.025 6144 Dihedral : 4.313 22.328 4512 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % 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: 4.85 (0.13), residues: 4104 helix: 3.76 (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 D 60 TYR 0.022 0.002 TYR F 36 PHE 0.024 0.003 PHE M 38 TRP 0.010 0.003 TRP I 90 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (34704) covalent geometry : angle 0.55182 / 0.30 (46728) hydrogen bonds : bond 0.04453 / 3.02 ( 2688) hydrogen bonds : angle 3.54167 / 2.55 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22693.59 seconds wall clock time: 385 minutes 42.79 seconds (23142.79 seconds total)