Starting phenix.real_space_refine on Fri Mar 6 22:25:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjv_54955/03_2026/9sjv_54955_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjv_54955/03_2026/9sjv_54955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sjv_54955/03_2026/9sjv_54955_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjv_54955/03_2026/9sjv_54955_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sjv_54955/03_2026/9sjv_54955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjv_54955/03_2026/9sjv_54955.map" } resolution = 1.89 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= 0.006 sd= 0.350 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 8184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35664 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Chain: "B" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1417 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' FE': 4, ' MG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "J" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "K" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "L" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "M" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "N" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "O" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "P" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "Q" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "R" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "S" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "T" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "V" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "W" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "X" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "Y" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} 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: 48 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 36 not shown) Time building chain proxies: 3.59, per 1000 atoms: 0.10 Number of scatterers: 35664 At special positions: 0 Unit cell: (133.2, 133.2, 133.2, 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 8184 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: 3.01 Conformation dependent library (CDL) restraints added in 1.3 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: 0.81 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: 5.778A pdb=" N SER A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU A 137 " --> pdb=" O HIS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU B 137 " --> pdb=" O HIS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU C 137 " --> pdb=" O HIS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER D 136 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU D 137 " --> pdb=" O HIS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER E 136 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU E 137 " --> pdb=" O HIS E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER F 136 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU F 137 " --> pdb=" O HIS F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER G 136 " --> pdb=" O THR G 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU G 137 " --> pdb=" O HIS G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER H 136 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU H 137 " --> pdb=" O HIS H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER I 136 " --> pdb=" O THR I 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU I 137 " --> pdb=" O HIS I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER J 136 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU J 137 " --> pdb=" O HIS J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER K 136 " --> pdb=" O THR K 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU K 137 " --> pdb=" O HIS K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER L 136 " --> pdb=" O THR L 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU L 137 " --> pdb=" O HIS L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER M 136 " --> pdb=" O THR M 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU M 137 " --> pdb=" O HIS M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU N 137 " --> pdb=" O HIS N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER O 136 " --> pdb=" O THR O 132 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLU O 137 " --> pdb=" O HIS O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER P 136 " --> pdb=" O THR P 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU P 137 " --> pdb=" O HIS P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER Q 136 " --> pdb=" O THR Q 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU Q 137 " --> pdb=" O HIS Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER R 136 " --> pdb=" O THR R 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU R 137 " --> pdb=" O HIS R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER S 136 " --> pdb=" O THR S 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU S 137 " --> pdb=" O HIS S 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER T 136 " --> pdb=" O THR T 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU T 137 " --> pdb=" O HIS T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER V 136 " --> pdb=" O THR V 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU V 137 " --> pdb=" O HIS V 133 " (cutoff:3.500A) Processing helix chain 'V' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER W 136 " --> pdb=" O THR W 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU W 137 " --> pdb=" O HIS W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER X 136 " --> pdb=" O THR X 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU X 137 " --> pdb=" O HIS X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 160 through 171 removed outlier: 3.628A 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: 5.778A pdb=" N SER Y 136 " --> pdb=" O THR Y 132 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU Y 137 " --> pdb=" O HIS Y 133 " (cutoff:3.500A) Processing helix chain 'Y' and resid 160 through 171 removed outlier: 3.628A 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: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11544 1.34 - 1.46: 4995 1.46 - 1.57: 17901 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34704 Sorted by residual: bond pdb=" C ASN L 18 " pdb=" O ASN L 18 " ideal model delta sigma weight residual 1.237 1.244 -0.008 1.17e-02 7.31e+03 4.22e-01 bond pdb=" C ASN W 18 " pdb=" O ASN W 18 " ideal model delta sigma weight residual 1.237 1.244 -0.008 1.17e-02 7.31e+03 4.22e-01 bond pdb=" C ASN E 18 " pdb=" O ASN E 18 " ideal model delta sigma weight residual 1.237 1.244 -0.008 1.17e-02 7.31e+03 4.22e-01 bond pdb=" C ASN S 18 " pdb=" O ASN S 18 " ideal model delta sigma weight residual 1.237 1.244 -0.008 1.17e-02 7.31e+03 4.22e-01 bond pdb=" C ASN J 18 " pdb=" O ASN J 18 " ideal model delta sigma weight residual 1.237 1.244 -0.008 1.17e-02 7.31e+03 4.22e-01 ... (remaining 34699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 44544 1.12 - 2.25: 1848 2.25 - 3.37: 168 3.37 - 4.49: 96 4.49 - 5.61: 72 Bond angle restraints: 46728 Sorted by residual: angle pdb=" C TRP V 90 " pdb=" N GLU V 91 " pdb=" CA GLU V 91 " ideal model delta sigma weight residual 121.54 126.64 -5.10 1.91e+00 2.74e-01 7.13e+00 angle pdb=" C TRP G 90 " pdb=" N GLU G 91 " pdb=" CA GLU G 91 " ideal model delta sigma weight residual 121.54 126.64 -5.10 1.91e+00 2.74e-01 7.13e+00 angle pdb=" C TRP T 90 " pdb=" N GLU T 91 " pdb=" CA GLU T 91 " ideal model delta sigma weight residual 121.54 126.64 -5.10 1.91e+00 2.74e-01 7.13e+00 angle pdb=" C TRP D 90 " pdb=" N GLU D 91 " pdb=" CA GLU D 91 " ideal model delta sigma weight residual 121.54 126.64 -5.10 1.91e+00 2.74e-01 7.13e+00 angle pdb=" C TRP F 90 " pdb=" N GLU F 91 " pdb=" CA GLU F 91 " ideal model delta sigma weight residual 121.54 126.64 -5.10 1.91e+00 2.74e-01 7.13e+00 ... (remaining 46723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 18624 17.73 - 35.47: 1704 35.47 - 53.20: 360 53.20 - 70.94: 240 70.94 - 88.67: 72 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 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TRP I 90 " pdb=" C TRP I 90 " pdb=" N GLU I 91 " pdb=" CA GLU I 91 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+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 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3364 0.032 - 0.065: 1075 0.065 - 0.097: 313 0.097 - 0.129: 120 0.129 - 0.162: 48 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CB THR C 132 " pdb=" CA THR C 132 " pdb=" OG1 THR C 132 " pdb=" CG2 THR C 132 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" CB THR I 132 " pdb=" CA THR I 132 " pdb=" OG1 THR I 132 " pdb=" CG2 THR I 132 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" CB THR J 132 " pdb=" CA THR J 132 " pdb=" OG1 THR J 132 " pdb=" CG2 THR J 132 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 4917 not shown) Planarity restraints: 6144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 131 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" C GLU E 131 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU E 131 " 0.016 2.00e-02 2.50e+03 pdb=" N THR E 132 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 131 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" C GLU R 131 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU R 131 " 0.016 2.00e-02 2.50e+03 pdb=" N THR R 132 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 131 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" C GLU K 131 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU K 131 " 0.016 2.00e-02 2.50e+03 pdb=" N THR K 132 " 0.014 2.00e-02 2.50e+03 ... (remaining 6141 not shown) Histogram of nonbonded interaction distances: 0.01 - 0.98: 84 0.98 - 1.96: 96 1.96 - 2.94: 17388 2.94 - 3.92: 114407 3.92 - 4.90: 206559 Warning: very small nonbonded interaction distances. Nonbonded interactions: 338534 Sorted by model distance: nonbonded pdb="FE FE I 204 " pdb="FE FE I 205 " model vdw 0.005 1.480 nonbonded pdb="FE FE D 204 " pdb="FE FE D 205 " model vdw 0.006 1.480 nonbonded pdb="FE FE I 201 " pdb="FE FE I 203 " model vdw 0.006 1.480 nonbonded pdb="FE FE D 201 " pdb="FE FE D 203 " model vdw 0.006 1.480 nonbonded pdb="FE FE F 201 " pdb="FE FE F 205 " model vdw 0.006 1.480 ... (remaining 338529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 26.070 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 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 0.021 34704 Z= 0.141 Angle : 0.548 5.612 46728 Z= 0.307 Chirality : 0.039 0.162 4920 Planarity : 0.004 0.027 6144 Dihedral : 16.799 88.673 13032 Min Nonbonded Distance : 0.005 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 8.44 % Favored : 90.26 % 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: 5.06 (0.13), residues: 4104 helix: 3.76 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.50 (0.27), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 60 TYR 0.021 0.002 TYR X 36 PHE 0.024 0.003 PHE O 38 TRP 0.006 0.002 TRP I 90 HIS 0.006 0.001 HIS O 170 Details of bonding type rmsd covalent geometry : bond 0.00265 (34704) covalent geometry : angle 0.54769 (46728) hydrogen bonds : bond 0.08472 ( 2688) hydrogen bonds : angle 3.95537 ( 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 744 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 696 time to evaluate : 1.517 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: 48 outliers final: 24 residues processed: 720 average time/residue: 1.0308 time to fit residues: 844.1114 Evaluate side-chains 696 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 672 time to evaluate : 1.691 ------------------------------------------------------------------------------- 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=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN B 138 GLN C 138 GLN D 138 GLN E 138 GLN F 138 GLN G 138 GLN H 138 GLN I 138 GLN J 138 GLN K 138 GLN L 138 GLN M 138 GLN N 138 GLN O 138 GLN P 138 GLN Q 138 GLN R 138 GLN S 138 GLN T 138 GLN V 138 GLN W 138 GLN X 138 GLN Y 138 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.132324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.122847 restraints weight = 19766.576| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 0.40 r_work: 0.3142 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.2726 rms_B_bonded: 3.39 restraints_weight: 0.1250 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.0620 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= 0.175 Angle : 0.608 6.009 46728 Z= 0.341 Chirality : 0.039 0.144 4920 Planarity : 0.005 0.031 6144 Dihedral : 4.498 20.083 4536 Min Nonbonded Distance : 1.042 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.65 % Allowed : 9.09 % Favored : 90.26 % 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: 4.75 (0.13), residues: 4104 helix: 3.63 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.10 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 76 TYR 0.022 0.002 TYR O 36 PHE 0.026 0.003 PHE A 38 TRP 0.008 0.003 TRP B 90 HIS 0.006 0.002 HIS M 170 Details of bonding type rmsd covalent geometry : bond 0.00340 (34704) covalent geometry : angle 0.60817 (46728) hydrogen bonds : bond 0.06290 ( 2688) hydrogen bonds : angle 3.87291 ( 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 744 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 720 time to evaluate : 1.363 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: 744 average time/residue: 0.9973 time to fit residues: 849.4696 Evaluate side-chains 720 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 696 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 225 optimal weight: 4.9990 chunk 278 optimal weight: 9.9990 chunk 385 optimal weight: 30.0000 chunk 123 optimal weight: 7.9990 chunk 292 optimal weight: 20.0000 chunk 250 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 313 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.132091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.122525 restraints weight = 19904.498| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 0.41 r_work: 0.3142 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work: 0.2728 rms_B_bonded: 3.40 restraints_weight: 0.1250 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34704 Z= 0.167 Angle : 0.589 6.005 46728 Z= 0.331 Chirality : 0.039 0.150 4920 Planarity : 0.004 0.028 6144 Dihedral : 4.493 19.982 4536 Min Nonbonded Distance : 1.057 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 7.79 % Favored : 90.91 % 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: 4.73 (0.13), residues: 4104 helix: 3.64 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.96 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 60 TYR 0.021 0.002 TYR J 36 PHE 0.026 0.003 PHE P 38 TRP 0.008 0.002 TRP O 90 HIS 0.005 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00322 (34704) covalent geometry : angle 0.58872 (46728) hydrogen bonds : bond 0.06152 ( 2688) hydrogen bonds : angle 3.84071 ( 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 768 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 720 time to evaluate : 1.405 Fit side-chains REVERT: A 88 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6561 (m-30) REVERT: B 88 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6566 (m-30) REVERT: C 88 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: D 88 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6571 (m-30) REVERT: E 88 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6566 (m-30) REVERT: F 88 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6575 (m-30) REVERT: G 88 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6571 (m-30) REVERT: H 88 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: I 88 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6569 (m-30) REVERT: J 88 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6567 (m-30) REVERT: K 88 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6566 (m-30) REVERT: L 88 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6562 (m-30) REVERT: M 88 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6577 (m-30) REVERT: N 88 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: O 88 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6562 (m-30) REVERT: P 88 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: Q 88 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6562 (m-30) REVERT: R 88 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6571 (m-30) REVERT: S 88 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6563 (m-30) REVERT: T 88 ASP cc_start: 0.7002 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: V 88 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6576 (m-30) REVERT: W 88 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6565 (m-30) REVERT: X 88 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: Y 88 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6570 (m-30) outliers start: 48 outliers final: 24 residues processed: 768 average time/residue: 0.9273 time to fit residues: 818.5174 Evaluate side-chains 744 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 696 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 88 ASP Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Y residue 2 THR Chi-restraints excluded: chain Y residue 88 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 249 optimal weight: 30.0000 chunk 167 optimal weight: 5.9990 chunk 317 optimal weight: 30.0000 chunk 400 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 272 optimal weight: 20.0000 chunk 352 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 385 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 L 57 HIS M 57 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.131094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.121488 restraints weight = 19845.629| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 0.41 r_work: 0.3131 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work: 0.2720 rms_B_bonded: 3.37 restraints_weight: 0.1250 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 34704 Z= 0.186 Angle : 0.609 6.239 46728 Z= 0.344 Chirality : 0.039 0.152 4920 Planarity : 0.005 0.029 6144 Dihedral : 4.562 20.089 4536 Min Nonbonded Distance : 1.030 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.30 % Allowed : 8.12 % Favored : 90.58 % 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: 4.64 (0.13), residues: 4104 helix: 3.57 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.98 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 60 TYR 0.023 0.003 TYR E 36 PHE 0.027 0.003 PHE C 38 TRP 0.009 0.003 TRP C 90 HIS 0.006 0.001 HIS R 125 Details of bonding type rmsd covalent geometry : bond 0.00366 (34704) covalent geometry : angle 0.60854 (46728) hydrogen bonds : bond 0.06410 ( 2688) hydrogen bonds : angle 3.90171 ( 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 733 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 685 time to evaluate : 1.507 Fit side-chains REVERT: A 88 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6590 (m-30) REVERT: B 88 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6599 (m-30) REVERT: C 88 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6606 (m-30) REVERT: D 88 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6594 (m-30) REVERT: E 88 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6595 (m-30) REVERT: F 88 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6600 (m-30) REVERT: G 88 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6576 (m-30) REVERT: H 88 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6586 (m-30) REVERT: I 88 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6609 (m-30) REVERT: J 88 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6588 (m-30) REVERT: K 88 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6596 (m-30) REVERT: L 88 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6582 (m-30) REVERT: M 88 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6584 (m-30) REVERT: N 88 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6579 (m-30) REVERT: O 88 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6581 (m-30) REVERT: P 88 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6580 (m-30) REVERT: Q 88 ASP cc_start: 0.7056 (OUTLIER) cc_final: 0.6570 (m-30) REVERT: R 88 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6594 (m-30) REVERT: S 88 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6608 (m-30) REVERT: T 88 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6589 (m-30) REVERT: V 88 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6581 (m-30) REVERT: W 88 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6584 (m-30) REVERT: X 88 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6588 (m-30) REVERT: Y 88 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6592 (m-30) outliers start: 48 outliers final: 24 residues processed: 733 average time/residue: 0.9458 time to fit residues: 794.7782 Evaluate side-chains 709 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 661 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 88 ASP Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Y residue 2 THR Chi-restraints excluded: chain Y residue 88 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 200 optimal weight: 5.9990 chunk 255 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 312 optimal weight: 9.9990 chunk 398 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 chunk 348 optimal weight: 0.0270 chunk 76 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 L 57 HIS M 57 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.132685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.123067 restraints weight = 19814.549| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 0.41 r_work: 0.3158 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.2750 rms_B_bonded: 3.38 restraints_weight: 0.1250 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 34704 Z= 0.141 Angle : 0.544 5.670 46728 Z= 0.307 Chirality : 0.036 0.149 4920 Planarity : 0.004 0.027 6144 Dihedral : 4.415 20.226 4536 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.65 % Allowed : 8.44 % Favored : 90.91 % 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: 4.89 (0.13), residues: 4104 helix: 3.76 (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 0.001 ARG P 60 TYR 0.021 0.002 TYR F 36 PHE 0.022 0.003 PHE T 38 TRP 0.009 0.003 TRP C 90 HIS 0.004 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00262 (34704) covalent geometry : angle 0.54367 (46728) hydrogen bonds : bond 0.05758 ( 2688) hydrogen bonds : angle 3.73604 ( 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 720 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 696 time to evaluate : 1.363 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 720 average time/residue: 0.9964 time to fit residues: 825.0406 Evaluate side-chains 696 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 672 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 355 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 407 optimal weight: 30.0000 chunk 153 optimal weight: 30.0000 chunk 300 optimal weight: 30.0000 chunk 90 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 258 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 L 57 HIS M 57 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.131137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.121463 restraints weight = 19854.688| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 0.41 r_work: 0.3132 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.2724 rms_B_bonded: 3.37 restraints_weight: 0.1250 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 34704 Z= 0.180 Angle : 0.602 6.163 46728 Z= 0.341 Chirality : 0.038 0.150 4920 Planarity : 0.005 0.028 6144 Dihedral : 4.568 20.514 4536 Min Nonbonded Distance : 1.000 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.30 % Allowed : 7.14 % Favored : 91.56 % 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: 4.66 (0.13), residues: 4104 helix: 3.57 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.00 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 60 TYR 0.022 0.003 TYR H 36 PHE 0.026 0.003 PHE C 38 TRP 0.008 0.003 TRP A 90 HIS 0.006 0.001 HIS H 125 Details of bonding type rmsd covalent geometry : bond 0.00352 (34704) covalent geometry : angle 0.60172 (46728) hydrogen bonds : bond 0.06378 ( 2688) hydrogen bonds : angle 3.90579 ( 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 732 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 684 time to evaluate : 1.385 Fit side-chains REVERT: A 88 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6598 (m-30) REVERT: B 88 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6599 (m-30) REVERT: C 88 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6590 (m-30) REVERT: D 88 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6606 (m-30) REVERT: E 88 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6589 (m-30) REVERT: F 88 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6608 (m-30) REVERT: G 88 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6606 (m-30) REVERT: H 88 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6583 (m-30) REVERT: I 88 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6622 (m-30) REVERT: J 88 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6607 (m-30) REVERT: K 88 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6597 (m-30) REVERT: L 88 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6591 (m-30) REVERT: M 88 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6603 (m-30) REVERT: N 88 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6572 (m-30) REVERT: O 88 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6587 (m-30) REVERT: P 88 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6599 (m-30) REVERT: Q 88 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6587 (m-30) REVERT: R 88 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6599 (m-30) REVERT: S 88 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6605 (m-30) REVERT: T 88 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6596 (m-30) REVERT: V 88 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6603 (m-30) REVERT: W 88 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6577 (m-30) REVERT: X 88 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6592 (m-30) REVERT: Y 88 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6593 (m-30) outliers start: 48 outliers final: 24 residues processed: 732 average time/residue: 1.0016 time to fit residues: 841.2946 Evaluate side-chains 708 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 660 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 88 ASP Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Y residue 2 THR Chi-restraints excluded: chain Y residue 88 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 34 optimal weight: 30.0000 chunk 114 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 260 optimal weight: 9.9990 chunk 406 optimal weight: 0.9980 chunk 268 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 chunk 321 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 L 57 HIS M 57 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.132411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.122740 restraints weight = 19807.965| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 0.41 r_work: 0.3150 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 1.23 restraints_weight: 0.2500 r_work: 0.2740 rms_B_bonded: 3.39 restraints_weight: 0.1250 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 34704 Z= 0.144 Angle : 0.549 5.789 46728 Z= 0.309 Chirality : 0.036 0.148 4920 Planarity : 0.004 0.026 6144 Dihedral : 4.448 20.579 4536 Min Nonbonded Distance : 1.079 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 7.14 % Favored : 91.56 % 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: 4.88 (0.13), residues: 4104 helix: 3.74 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.06 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG T 60 TYR 0.021 0.002 TYR T 36 PHE 0.022 0.003 PHE S 38 TRP 0.009 0.002 TRP M 90 HIS 0.004 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00269 (34704) covalent geometry : angle 0.54944 (46728) hydrogen bonds : bond 0.05789 ( 2688) hydrogen bonds : angle 3.74812 ( 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 744 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 696 time to evaluate : 1.533 Fit side-chains REVERT: A 88 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: B 88 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6571 (m-30) REVERT: C 88 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6561 (m-30) REVERT: D 88 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6583 (m-30) REVERT: E 88 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6566 (m-30) REVERT: F 88 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6582 (m-30) REVERT: G 88 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6576 (m-30) REVERT: H 88 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6562 (m-30) REVERT: I 88 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6585 (m-30) REVERT: J 88 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6582 (m-30) REVERT: K 88 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: L 88 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6567 (m-30) REVERT: M 88 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6572 (m-30) REVERT: N 88 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6555 (m-30) REVERT: O 88 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6558 (m-30) REVERT: P 88 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6570 (m-30) REVERT: Q 88 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6555 (m-30) REVERT: R 88 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6581 (m-30) REVERT: S 88 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6575 (m-30) REVERT: T 88 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6567 (m-30) REVERT: V 88 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6571 (m-30) REVERT: W 88 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6550 (m-30) REVERT: X 88 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6574 (m-30) REVERT: Y 88 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6563 (m-30) outliers start: 48 outliers final: 24 residues processed: 744 average time/residue: 0.9540 time to fit residues: 818.6759 Evaluate side-chains 720 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 672 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 88 ASP Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Y residue 2 THR Chi-restraints excluded: chain Y residue 88 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 332 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 240 optimal weight: 7.9990 chunk 338 optimal weight: 4.9990 chunk 384 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 chunk 391 optimal weight: 0.3980 chunk 192 optimal weight: 6.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 L 57 HIS M 57 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.131308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.121656 restraints weight = 19807.581| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.41 r_work: 0.3131 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work: 0.2723 rms_B_bonded: 3.35 restraints_weight: 0.1250 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34704 Z= 0.169 Angle : 0.589 6.056 46728 Z= 0.333 Chirality : 0.038 0.150 4920 Planarity : 0.004 0.027 6144 Dihedral : 4.544 20.583 4536 Min Nonbonded Distance : 1.032 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.30 % Allowed : 7.14 % Favored : 91.56 % 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: 4.72 (0.13), residues: 4104 helix: 3.62 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.02 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 60 TYR 0.021 0.002 TYR F 36 PHE 0.025 0.003 PHE C 38 TRP 0.008 0.003 TRP N 90 HIS 0.005 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00328 (34704) covalent geometry : angle 0.58931 (46728) hydrogen bonds : bond 0.06213 ( 2688) hydrogen bonds : angle 3.86179 ( 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 740 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 692 time to evaluate : 1.618 Fit side-chains REVERT: A 88 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6641 (m-30) REVERT: B 88 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6643 (m-30) REVERT: C 88 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6630 (m-30) REVERT: D 88 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6654 (m-30) REVERT: E 88 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6631 (m-30) REVERT: F 88 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6652 (m-30) REVERT: G 88 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6647 (m-30) REVERT: H 88 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6629 (m-30) REVERT: I 88 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6650 (m-30) REVERT: J 88 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6648 (m-30) REVERT: K 88 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6639 (m-30) REVERT: L 88 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6630 (m-30) REVERT: M 88 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6648 (m-30) REVERT: N 88 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6620 (m-30) REVERT: O 88 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6626 (m-30) REVERT: P 88 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6638 (m-30) REVERT: Q 88 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6630 (m-30) REVERT: R 88 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6638 (m-30) REVERT: S 88 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6641 (m-30) REVERT: T 88 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6637 (m-30) REVERT: V 88 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6644 (m-30) REVERT: W 88 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6623 (m-30) REVERT: X 88 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6639 (m-30) REVERT: Y 88 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6636 (m-30) outliers start: 48 outliers final: 24 residues processed: 740 average time/residue: 0.9998 time to fit residues: 850.4374 Evaluate side-chains 708 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 660 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 88 ASP Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Y residue 2 THR Chi-restraints excluded: chain Y residue 88 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 56 optimal weight: 6.9990 chunk 288 optimal weight: 5.9990 chunk 214 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 chunk 271 optimal weight: 7.9990 chunk 217 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 chunk 221 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 L 57 HIS M 57 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.131658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.122016 restraints weight = 19751.483| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 0.41 r_work: 0.3137 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.2727 rms_B_bonded: 3.36 restraints_weight: 0.1250 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34704 Z= 0.165 Angle : 0.588 6.086 46728 Z= 0.331 Chirality : 0.038 0.152 4920 Planarity : 0.004 0.027 6144 Dihedral : 4.534 20.382 4536 Min Nonbonded Distance : 1.045 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 7.14 % Favored : 91.56 % 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: 4.73 (0.13), residues: 4104 helix: 3.62 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.06 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 60 TYR 0.021 0.002 TYR L 36 PHE 0.024 0.003 PHE T 38 TRP 0.010 0.003 TRP J 90 HIS 0.005 0.001 HIS I 125 Details of bonding type rmsd covalent geometry : bond 0.00319 (34704) covalent geometry : angle 0.58762 (46728) hydrogen bonds : bond 0.06110 ( 2688) hydrogen bonds : angle 3.83685 ( 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 712 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 664 time to evaluate : 1.448 Fit side-chains REVERT: A 88 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6616 (m-30) REVERT: B 88 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6623 (m-30) REVERT: C 88 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6602 (m-30) REVERT: D 88 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6635 (m-30) REVERT: E 88 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6614 (m-30) REVERT: F 88 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6637 (m-30) REVERT: G 88 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6635 (m-30) REVERT: H 88 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6615 (m-30) REVERT: I 88 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6630 (m-30) REVERT: J 88 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6633 (m-30) REVERT: K 88 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6627 (m-30) REVERT: L 88 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6617 (m-30) REVERT: M 88 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6628 (m-30) REVERT: N 88 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6596 (m-30) REVERT: O 88 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6606 (m-30) REVERT: P 88 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6614 (m-30) REVERT: Q 88 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6607 (m-30) REVERT: R 88 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6617 (m-30) REVERT: S 88 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6623 (m-30) REVERT: T 88 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6624 (m-30) REVERT: V 88 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6617 (m-30) REVERT: W 88 ASP cc_start: 0.7079 (OUTLIER) cc_final: 0.6595 (m-30) REVERT: X 88 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6617 (m-30) REVERT: Y 88 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6615 (m-30) outliers start: 48 outliers final: 24 residues processed: 712 average time/residue: 0.9914 time to fit residues: 809.7889 Evaluate side-chains 708 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 660 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 88 ASP Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Y residue 2 THR Chi-restraints excluded: chain Y residue 88 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 259 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 297 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 394 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 208 optimal weight: 0.9980 chunk 275 optimal weight: 5.9990 chunk 376 optimal weight: 7.9990 chunk 104 optimal weight: 20.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 L 57 HIS M 57 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.132433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.122758 restraints weight = 19827.268| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 0.41 r_work: 0.3150 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.2741 rms_B_bonded: 3.37 restraints_weight: 0.1250 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.0840 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= 0.148 Angle : 0.562 5.826 46728 Z= 0.316 Chirality : 0.037 0.150 4920 Planarity : 0.004 0.026 6144 Dihedral : 4.478 20.336 4536 Min Nonbonded Distance : 1.078 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 7.14 % Favored : 91.56 % 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: 4.83 (0.13), residues: 4104 helix: 3.69 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.09 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 60 TYR 0.021 0.002 TYR C 36 PHE 0.023 0.003 PHE S 38 TRP 0.011 0.003 TRP B 90 HIS 0.004 0.001 HIS P 125 Details of bonding type rmsd covalent geometry : bond 0.00280 (34704) covalent geometry : angle 0.56211 (46728) hydrogen bonds : bond 0.05835 ( 2688) hydrogen bonds : angle 3.77116 ( 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 720 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 672 time to evaluate : 1.322 Fit side-chains REVERT: A 88 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6614 (m-30) REVERT: B 88 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6616 (m-30) REVERT: C 88 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6599 (m-30) REVERT: D 88 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6620 (m-30) REVERT: E 88 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6610 (m-30) REVERT: F 88 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6622 (m-30) REVERT: G 88 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6629 (m-30) REVERT: H 88 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6602 (m-30) REVERT: I 88 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6629 (m-30) REVERT: J 88 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6626 (m-30) REVERT: K 88 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6615 (m-30) REVERT: L 88 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6607 (m-30) REVERT: M 88 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6615 (m-30) REVERT: N 88 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6595 (m-30) REVERT: O 88 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6606 (m-30) REVERT: P 88 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6614 (m-30) REVERT: Q 88 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6602 (m-30) REVERT: R 88 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6623 (m-30) REVERT: S 88 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6618 (m-30) REVERT: T 88 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6613 (m-30) REVERT: V 88 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6610 (m-30) REVERT: W 88 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6593 (m-30) REVERT: X 88 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6620 (m-30) REVERT: Y 88 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6611 (m-30) outliers start: 48 outliers final: 24 residues processed: 720 average time/residue: 0.9804 time to fit residues: 809.3889 Evaluate side-chains 720 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 672 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 88 ASP Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 2 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain Q residue 2 THR Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 2 THR Chi-restraints excluded: chain R residue 88 ASP Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 2 THR Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 88 ASP Chi-restraints excluded: chain Y residue 2 THR Chi-restraints excluded: chain Y residue 88 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 266 optimal weight: 30.0000 chunk 148 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 L 57 HIS M 57 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.131112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.121484 restraints weight = 19726.755| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 0.41 r_work: 0.3128 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work: 0.2717 rms_B_bonded: 3.37 restraints_weight: 0.1250 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 34704 Z= 0.186 Angle : 0.617 6.274 46728 Z= 0.348 Chirality : 0.038 0.149 4920 Planarity : 0.005 0.028 6144 Dihedral : 4.592 20.405 4536 Min Nonbonded Distance : 1.004 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.30 % Allowed : 7.09 % Favored : 91.61 % 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: 4.62 (0.13), residues: 4104 helix: 3.53 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.06 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 60 TYR 0.023 0.003 TYR Q 36 PHE 0.026 0.003 PHE L 38 TRP 0.010 0.003 TRP L 90 HIS 0.006 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00365 (34704) covalent geometry : angle 0.61663 (46728) hydrogen bonds : bond 0.06421 ( 2688) hydrogen bonds : angle 3.92364 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22711.11 seconds wall clock time: 385 minutes 37.96 seconds (23137.96 seconds total)