Starting phenix.real_space_refine on Mon Jul 6 11:20:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sjv_54955/07_2026/9sjv_54955_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sjv_54955/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9sjv_54955/07_2026/9sjv_54955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sjv_54955/07_2026/9sjv_54955.map" model { file = "/net/cci-nas-00/data/ceres_data/9sjv_54955/07_2026/9sjv_54955_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sjv_54955/07_2026/9sjv_54955_neut.cif" } 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-6108/lib/python3.11/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, 1 Ad-hoc single atom residues: {' FE': 4} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 4 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 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: 3.96, per 1000 atoms: 0.11 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: 3.10 Conformation dependent library (CDL) restraints added in 1.6 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: 0.59 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: 7.71 Time building geometry restraints manager: 4.19 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 2.960 nonbonded pdb="FE FE D 204 " pdb="FE FE D 205 " model vdw 0.006 2.960 nonbonded pdb="FE FE I 201 " pdb="FE FE I 203 " model vdw 0.006 2.960 nonbonded pdb="FE FE D 201 " pdb="FE FE D 203 " model vdw 0.006 2.960 nonbonded pdb="FE FE F 201 " pdb="FE FE F 205 " model vdw 0.006 2.960 ... (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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'R' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.770 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 29.370 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 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/Z covalent geometry : bond 0.00265 / 0.14 (34704) covalent geometry : angle 0.54769 / 0.31 (46728) hydrogen bonds : bond 0.08472 / 5.79 ( 2688) hydrogen bonds : angle 3.95537 / 2.86 ( 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 : 1.057 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: 0.9408 time to fit residues: 776.3505 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 : 1.413 ------------------------------------------------------------------------------- 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... 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 = 0.132174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.122739 restraints weight = 19787.560| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 0.40 r_work: 0.3150 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work: 0.2737 rms_B_bonded: 3.35 restraints_weight: 0.1250 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 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 = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.0638 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 : 0.612 6.025 46728 Z= 0.342 Chirality : 0.040 0.144 4920 Planarity : 0.005 0.031 6144 Dihedral : 4.504 20.089 4536 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 1.95 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: 4.76 (0.13), residues: 4104 helix: 3.63 (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 O 76 TYR 0.023 0.002 TYR D 36 PHE 0.026 0.003 PHE O 38 TRP 0.008 0.003 TRP O 90 HIS 0.005 0.002 HIS K 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.18 (34704) covalent geometry : angle 0.61208 / 0.34 (46728) hydrogen bonds : bond 0.06290 / 4.30 ( 2688) hydrogen bonds : angle 3.86655 / 2.79 ( 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 : 1.450 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: 0.8440 time to fit residues: 725.9107 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 : 1.107 ------------------------------------------------------------------------------- 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: 5.9990 chunk 292 optimal weight: 20.0000 chunk 250 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 313 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.132535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.122965 restraints weight = 19915.151| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 0.41 r_work: 0.3153 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 1.22 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: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34704 Z= 0.160 Angle : 0.579 5.936 46728 Z= 0.325 Chirality : 0.039 0.149 4920 Planarity : 0.004 0.028 6144 Dihedral : 4.473 20.053 4536 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 1.92 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: 4.80 (0.13), residues: 4104 helix: 3.69 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.97 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 60 TYR 0.021 0.002 TYR K 36 PHE 0.024 0.003 PHE O 38 TRP 0.008 0.002 TRP O 90 HIS 0.005 0.001 HIS K 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (34704) covalent geometry : angle 0.57940 / 0.32 (46728) hydrogen bonds : bond 0.06034 / 4.12 ( 2688) hydrogen bonds : angle 3.80367 / 2.74 ( 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 792 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 744 time to evaluate : 1.401 Fit side-chains REVERT: A 88 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6565 (m-30) REVERT: B 88 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6567 (m-30) REVERT: C 88 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6578 (m-30) REVERT: D 88 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6579 (m-30) REVERT: E 88 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6570 (m-30) REVERT: F 88 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6576 (m-30) REVERT: G 88 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6572 (m-30) REVERT: H 88 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6574 (m-30) REVERT: I 88 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6579 (m-30) REVERT: J 88 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6572 (m-30) REVERT: K 88 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6572 (m-30) REVERT: L 88 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6566 (m-30) REVERT: M 88 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6578 (m-30) REVERT: N 88 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: O 88 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6564 (m-30) REVERT: P 88 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6578 (m-30) REVERT: Q 88 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6563 (m-30) REVERT: R 88 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6577 (m-30) REVERT: S 88 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: T 88 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6569 (m-30) REVERT: V 88 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6576 (m-30) REVERT: W 88 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6569 (m-30) REVERT: X 88 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: Y 88 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6577 (m-30) outliers start: 48 outliers final: 24 residues processed: 792 average time/residue: 0.7972 time to fit residues: 734.7677 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 : 1.451 ------------------------------------------------------------------------------- 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: 10.0000 chunk 122 optimal weight: 5.9990 chunk 272 optimal weight: 0.9990 chunk 352 optimal weight: 5.9990 chunk 89 optimal weight: 30.0000 chunk 385 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS B 57 HIS C 57 HIS D 57 HIS E 57 HIS F 57 HIS G 57 HIS H 57 HIS I 57 HIS J 57 HIS 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 = 0.3380 r_free = 0.3380 target = 0.131832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.122229 restraints weight = 19812.847| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 0.41 r_work: 0.3140 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.2731 rms_B_bonded: 3.36 restraints_weight: 0.1250 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.0824 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= 0.161 Angle : 0.573 5.909 46728 Z= 0.322 Chirality : 0.038 0.149 4920 Planarity : 0.004 0.028 6144 Dihedral : 4.495 20.564 4536 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.65 % Allowed : 8.77 % 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: 4.80 (0.13), residues: 4104 helix: 3.68 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.03 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 60 TYR 0.022 0.002 TYR N 36 PHE 0.024 0.003 PHE I 38 TRP 0.008 0.002 TRP V 90 HIS 0.005 0.001 HIS G 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (34704) covalent geometry : angle 0.57283 / 0.32 (46728) hydrogen bonds : bond 0.06054 / 4.14 ( 2688) hydrogen bonds : angle 3.81344 / 2.75 ( 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 731 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 707 time to evaluate : 1.399 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 731 average time/residue: 0.8705 time to fit residues: 734.1652 Evaluate side-chains 707 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 683 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 200 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 312 optimal weight: 10.0000 chunk 398 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 348 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS B 57 HIS C 57 HIS D 57 HIS E 57 HIS F 57 HIS G 57 HIS H 57 HIS I 57 HIS J 57 HIS 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 = 0.3366 r_free = 0.3366 target = 0.130802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.121132 restraints weight = 19936.386| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 0.41 r_work: 0.3133 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.2724 rms_B_bonded: 3.38 restraints_weight: 0.1250 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.0845 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= 0.185 Angle : 0.608 6.208 46728 Z= 0.344 Chirality : 0.039 0.152 4920 Planarity : 0.005 0.029 6144 Dihedral : 4.567 20.269 4536 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: 4.69 (0.13), residues: 4104 helix: 3.60 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.01 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 60 TYR 0.022 0.003 TYR B 36 PHE 0.027 0.003 PHE Y 38 TRP 0.009 0.003 TRP V 90 HIS 0.006 0.001 HIS N 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (34704) covalent geometry : angle 0.60817 / 0.34 (46728) hydrogen bonds : bond 0.06409 / 4.39 ( 2688) hydrogen bonds : angle 3.90517 / 2.82 ( 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 733 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 685 time to evaluate : 1.411 Fit side-chains REVERT: A 88 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6641 (m-30) REVERT: B 88 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6644 (m-30) REVERT: C 88 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6635 (m-30) REVERT: D 88 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6656 (m-30) REVERT: E 88 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6631 (m-30) REVERT: F 88 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6658 (m-30) REVERT: G 88 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6659 (m-30) REVERT: H 88 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6632 (m-30) REVERT: I 88 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6669 (m-30) REVERT: J 88 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6656 (m-30) REVERT: K 88 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6639 (m-30) REVERT: L 88 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6628 (m-30) REVERT: M 88 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6655 (m-30) REVERT: N 88 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6629 (m-30) REVERT: O 88 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6635 (m-30) REVERT: P 88 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6645 (m-30) REVERT: Q 88 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6624 (m-30) REVERT: R 88 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6654 (m-30) REVERT: S 88 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6653 (m-30) REVERT: T 88 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6639 (m-30) REVERT: V 88 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6648 (m-30) REVERT: W 88 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6629 (m-30) REVERT: X 88 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6648 (m-30) REVERT: Y 88 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6633 (m-30) outliers start: 48 outliers final: 24 residues processed: 733 average time/residue: 0.8574 time to fit residues: 725.3764 Evaluate side-chains 697 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 649 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 355 optimal weight: 4.9990 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: 2.9990 chunk 116 optimal weight: 5.9990 chunk 237 optimal weight: 30.0000 chunk 258 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS B 57 HIS C 57 HIS D 57 HIS E 57 HIS F 57 HIS G 57 HIS H 57 HIS I 57 HIS J 57 HIS 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 = 0.3382 r_free = 0.3382 target = 0.131970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.122360 restraints weight = 19818.206| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 0.41 r_work: 0.3143 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.2735 rms_B_bonded: 3.34 restraints_weight: 0.1250 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34704 Z= 0.157 Angle : 0.572 5.983 46728 Z= 0.322 Chirality : 0.037 0.152 4920 Planarity : 0.004 0.028 6144 Dihedral : 4.491 20.268 4536 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.30 % Allowed : 7.47 % Favored : 91.23 % 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: 4.81 (0.13), residues: 4104 helix: 3.69 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.04 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 60 TYR 0.021 0.002 TYR B 36 PHE 0.024 0.003 PHE A 38 TRP 0.009 0.003 TRP Y 90 HIS 0.005 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (34704) covalent geometry : angle 0.57225 / 0.32 (46728) hydrogen bonds : bond 0.05990 / 4.09 ( 2688) hydrogen bonds : angle 3.80145 / 2.74 ( 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 744 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 696 time to evaluate : 1.477 Fit side-chains REVERT: A 88 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6686 (m-30) REVERT: B 88 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6683 (m-30) REVERT: C 88 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6673 (m-30) REVERT: D 88 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6693 (m-30) REVERT: E 88 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6683 (m-30) REVERT: F 88 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6700 (m-30) REVERT: G 88 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6700 (m-30) REVERT: H 88 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6673 (m-30) REVERT: I 88 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6706 (m-30) REVERT: J 88 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6698 (m-30) REVERT: K 88 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6685 (m-30) REVERT: L 88 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6672 (m-30) REVERT: M 88 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6699 (m-30) REVERT: N 88 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6663 (m-30) REVERT: O 88 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6683 (m-30) REVERT: P 88 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6687 (m-30) REVERT: Q 88 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6663 (m-30) REVERT: R 88 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6695 (m-30) REVERT: S 88 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6698 (m-30) REVERT: T 88 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6683 (m-30) REVERT: V 88 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6693 (m-30) REVERT: W 88 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6673 (m-30) REVERT: X 88 ASP cc_start: 0.7128 (OUTLIER) cc_final: 0.6680 (m-30) REVERT: Y 88 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6684 (m-30) outliers start: 48 outliers final: 24 residues processed: 744 average time/residue: 0.8615 time to fit residues: 741.0914 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 : 1.164 ------------------------------------------------------------------------------- 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: 10.0000 chunk 406 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 321 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS B 57 HIS C 57 HIS D 57 HIS E 57 HIS F 57 HIS G 57 HIS H 57 HIS I 57 HIS J 57 HIS 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 = 0.3374 r_free = 0.3374 target = 0.131409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.121785 restraints weight = 19872.278| |-----------------------------------------------------------------------------| r_work (start): 0.3236 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: 1.22 restraints_weight: 0.2500 r_work: 0.2720 rms_B_bonded: 3.39 restraints_weight: 0.1250 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.0854 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= 0.171 Angle : 0.594 6.167 46728 Z= 0.335 Chirality : 0.038 0.151 4920 Planarity : 0.004 0.028 6144 Dihedral : 4.550 20.256 4536 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 1.30 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: 4.70 (0.13), residues: 4104 helix: 3.60 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.03 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG S 60 TYR 0.022 0.003 TYR A 36 PHE 0.025 0.003 PHE P 38 TRP 0.009 0.003 TRP V 90 HIS 0.005 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (34704) covalent geometry : angle 0.59403 / 0.34 (46728) hydrogen bonds : bond 0.06258 / 4.28 ( 2688) hydrogen bonds : angle 3.87436 / 2.79 ( 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 732 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 684 time to evaluate : 1.481 Fit side-chains REVERT: A 88 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6651 (m-30) REVERT: B 88 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6654 (m-30) REVERT: C 88 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6646 (m-30) REVERT: D 88 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6665 (m-30) REVERT: E 88 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6647 (m-30) REVERT: F 88 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6670 (m-30) REVERT: G 88 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6670 (m-30) REVERT: H 88 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6646 (m-30) REVERT: I 88 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6678 (m-30) REVERT: J 88 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6672 (m-30) REVERT: K 88 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6656 (m-30) REVERT: L 88 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6647 (m-30) REVERT: M 88 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6669 (m-30) REVERT: N 88 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6633 (m-30) REVERT: O 88 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6647 (m-30) REVERT: P 88 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6659 (m-30) REVERT: Q 88 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6635 (m-30) REVERT: R 88 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6671 (m-30) REVERT: S 88 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6670 (m-30) REVERT: T 88 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6653 (m-30) REVERT: V 88 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6662 (m-30) REVERT: W 88 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6640 (m-30) REVERT: X 88 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6659 (m-30) REVERT: Y 88 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6653 (m-30) outliers start: 48 outliers final: 24 residues processed: 732 average time/residue: 0.8481 time to fit residues: 716.6221 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 : 1.161 ------------------------------------------------------------------------------- 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: 6.9990 chunk 60 optimal weight: 6.9990 chunk 169 optimal weight: 30.0000 chunk 240 optimal weight: 6.9990 chunk 338 optimal weight: 1.9990 chunk 384 optimal weight: 20.0000 chunk 186 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 391 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS B 57 HIS C 57 HIS D 57 HIS E 57 HIS F 57 HIS G 57 HIS H 57 HIS I 57 HIS J 57 HIS 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 = 0.3392 r_free = 0.3392 target = 0.132728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.123128 restraints weight = 19741.294| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 0.41 r_work: 0.3154 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.2748 rms_B_bonded: 3.34 restraints_weight: 0.1250 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 34704 Z= 0.141 Angle : 0.550 5.743 46728 Z= 0.309 Chirality : 0.037 0.148 4920 Planarity : 0.004 0.026 6144 Dihedral : 4.436 20.290 4536 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 1.33 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: 4.91 (0.13), residues: 4104 helix: 3.76 (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 W 60 TYR 0.021 0.002 TYR V 36 PHE 0.022 0.003 PHE A 38 TRP 0.010 0.003 TRP Q 90 HIS 0.004 0.001 HIS Y 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (34704) covalent geometry : angle 0.54984 / 0.31 (46728) hydrogen bonds : bond 0.05741 / 3.92 ( 2688) hydrogen bonds : angle 3.73752 / 2.70 ( 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 768 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 720 time to evaluate : 1.499 Fit side-chains REVERT: A 88 ASP cc_start: 0.7128 (OUTLIER) cc_final: 0.6656 (m-30) REVERT: B 88 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6655 (m-30) REVERT: C 88 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6644 (m-30) REVERT: D 88 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6668 (m-30) REVERT: E 88 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6643 (m-30) REVERT: F 88 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6658 (m-30) REVERT: G 88 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6665 (m-30) REVERT: H 88 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6644 (m-30) REVERT: I 88 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6667 (m-30) REVERT: J 88 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6669 (m-30) REVERT: K 88 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6645 (m-30) REVERT: L 88 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6637 (m-30) REVERT: M 88 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6661 (m-30) REVERT: N 88 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6643 (m-30) REVERT: O 88 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6642 (m-30) REVERT: P 88 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6661 (m-30) REVERT: Q 88 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6639 (m-30) REVERT: R 88 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6666 (m-30) REVERT: S 88 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6659 (m-30) REVERT: T 88 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6644 (m-30) REVERT: V 88 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6648 (m-30) REVERT: W 88 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6647 (m-30) REVERT: X 88 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6658 (m-30) REVERT: Y 88 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6646 (m-30) outliers start: 48 outliers final: 24 residues processed: 768 average time/residue: 0.8818 time to fit residues: 787.8275 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 : 1.440 ------------------------------------------------------------------------------- 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: 8.9990 chunk 247 optimal weight: 20.0000 chunk 188 optimal weight: 6.9990 chunk 271 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 311 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS B 57 HIS C 57 HIS D 57 HIS E 57 HIS F 57 HIS G 57 HIS H 57 HIS I 57 HIS J 57 HIS 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 = 0.3377 r_free = 0.3377 target = 0.131572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.121923 restraints weight = 19790.627| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 0.41 r_work: 0.3139 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 1.22 restraints_weight: 0.2500 r_work: 0.2729 rms_B_bonded: 3.36 restraints_weight: 0.1250 r_work (final): 0.2729 ------------------------------------------------------------------------------- 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 = 0.00 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 = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.0854 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 : 0.591 6.057 46728 Z= 0.333 Chirality : 0.038 0.149 4920 Planarity : 0.004 0.027 6144 Dihedral : 4.541 20.792 4536 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 1.65 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: 4.75 (0.13), residues: 4104 helix: 3.63 (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 S 60 TYR 0.022 0.003 TYR B 36 PHE 0.024 0.003 PHE H 38 TRP 0.009 0.003 TRP K 90 HIS 0.005 0.001 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (34704) covalent geometry : angle 0.59071 / 0.33 (46728) hydrogen bonds : bond 0.06147 / 4.20 ( 2688) hydrogen bonds : angle 3.84119 / 2.77 ( 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 732 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 684 time to evaluate : 1.548 Fit side-chains REVERT: A 88 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: B 88 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6737 (m-30) REVERT: C 88 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6734 (m-30) REVERT: D 88 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6756 (m-30) REVERT: E 88 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6731 (m-30) REVERT: F 88 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6757 (m-30) REVERT: G 88 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6757 (m-30) REVERT: H 88 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6737 (m-30) REVERT: I 88 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6751 (m-30) REVERT: J 88 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6759 (m-30) REVERT: K 88 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6736 (m-30) REVERT: L 88 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6731 (m-30) REVERT: M 88 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6752 (m-30) REVERT: N 88 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6724 (m-30) REVERT: O 88 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6730 (m-30) REVERT: P 88 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6743 (m-30) REVERT: Q 88 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6723 (m-30) REVERT: R 88 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6752 (m-30) REVERT: S 88 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6748 (m-30) REVERT: T 88 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: V 88 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6742 (m-30) REVERT: W 88 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6727 (m-30) REVERT: X 88 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6747 (m-30) REVERT: Y 88 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6728 (m-30) outliers start: 48 outliers final: 24 residues processed: 732 average time/residue: 0.8739 time to fit residues: 740.0399 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 : 1.519 ------------------------------------------------------------------------------- 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: 5.9990 chunk 3 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 297 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 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: 6.9990 chunk 104 optimal weight: 20.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS B 57 HIS C 57 HIS D 57 HIS E 57 HIS F 57 HIS G 57 HIS H 57 HIS I 57 HIS J 57 HIS 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 = 0.132696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.123027 restraints weight = 19805.622| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 0.41 r_work: 0.3151 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 1.22 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: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 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 = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34704 Z= 0.148 Angle : 0.567 5.840 46728 Z= 0.318 Chirality : 0.037 0.149 4920 Planarity : 0.004 0.026 6144 Dihedral : 4.492 20.827 4536 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 1.83 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: 4.87 (0.13), residues: 4104 helix: 3.72 (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 K 60 TYR 0.022 0.002 TYR K 36 PHE 0.023 0.003 PHE O 38 TRP 0.011 0.003 TRP T 90 HIS 0.004 0.001 HIS W 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (34704) covalent geometry : angle 0.56672 / 0.32 (46728) hydrogen bonds : bond 0.05837 / 3.99 ( 2688) hydrogen bonds : angle 3.76990 / 2.72 ( 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 732 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 684 time to evaluate : 1.602 Fit side-chains REVERT: A 88 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6637 (m-30) REVERT: B 88 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6638 (m-30) REVERT: C 88 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6623 (m-30) REVERT: D 88 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6651 (m-30) REVERT: E 88 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6622 (m-30) REVERT: F 88 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6653 (m-30) REVERT: G 88 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6651 (m-30) REVERT: H 88 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6627 (m-30) REVERT: I 88 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6655 (m-30) REVERT: J 88 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6654 (m-30) REVERT: K 88 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6630 (m-30) REVERT: L 88 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6628 (m-30) REVERT: M 88 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6645 (m-30) REVERT: N 88 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6617 (m-30) REVERT: O 88 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6635 (m-30) REVERT: P 88 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6645 (m-30) REVERT: Q 88 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6619 (m-30) REVERT: R 88 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6653 (m-30) REVERT: S 88 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6646 (m-30) REVERT: T 88 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6637 (m-30) REVERT: V 88 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6643 (m-30) REVERT: W 88 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6622 (m-30) REVERT: X 88 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6648 (m-30) REVERT: Y 88 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6625 (m-30) outliers start: 48 outliers final: 24 residues processed: 732 average time/residue: 0.9332 time to fit residues: 789.0297 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 : 1.476 ------------------------------------------------------------------------------- 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: 6.9990 chunk 0 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 chunk 216 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 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: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS B 57 HIS C 57 HIS D 57 HIS E 57 HIS F 57 HIS G 57 HIS H 57 HIS I 57 HIS J 57 HIS 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 = 0.131085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.121467 restraints weight = 19735.613| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 0.41 r_work: 0.3132 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 1.22 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: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34704 Z= 0.190 Angle : 0.625 6.307 46728 Z= 0.352 Chirality : 0.039 0.149 4920 Planarity : 0.005 0.028 6144 Dihedral : 4.611 20.774 4536 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 1.59 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: 4.62 (0.13), residues: 4104 helix: 3.54 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.05 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 60 TYR 0.024 0.003 TYR E 36 PHE 0.026 0.003 PHE W 38 TRP 0.009 0.003 TRP S 90 HIS 0.006 0.001 HIS H 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (34704) covalent geometry : angle 0.62506 / 0.35 (46728) hydrogen bonds : bond 0.06455 / 4.42 ( 2688) hydrogen bonds : angle 3.93353 / 2.84 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20724.86 seconds wall clock time: 352 minutes 6.56 seconds (21126.56 seconds total)