Starting phenix.real_space_refine on Sat Feb 7 16:50:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4q_41038/02_2026/8t4q_41038.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4q_41038/02_2026/8t4q_41038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t4q_41038/02_2026/8t4q_41038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4q_41038/02_2026/8t4q_41038.map" model { file = "/net/cci-nas-00/data/ceres_data/8t4q_41038/02_2026/8t4q_41038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4q_41038/02_2026/8t4q_41038.cif" } resolution = 2.07 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 192 5.16 5 C 21216 2.51 5 N 5928 2.21 5 O 8816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 216 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36176 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1410 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "B" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "E" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "F" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "G" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "H" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "I" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "J" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "K" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Chain: "L" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "M" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "N" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "O" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "P" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "Q" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "R" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "S" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "T" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "U" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "V" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "W" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "X" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Residues with excluded nonbonded symmetry interactions: 456 residue: pdb=" N ARG A 22 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG A 22 " occ=0.50 residue: pdb=" N TYR A 34 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR A 34 " occ=0.50 residue: pdb=" N SER A 38 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER A 38 " occ=0.50 residue: pdb=" N CYS A 39 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS A 39 " occ=0.50 residue: pdb=" N GLU A 64 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU A 64 " occ=0.50 residue: pdb=" N HIS A 65 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HIS A 65 " occ=0.50 residue: pdb=" N SER A 109 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER A 109 " occ=0.50 residue: pdb=" N SER A 113 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER A 113 " occ=0.50 residue: pdb=" N PHE A 132 " occ=0.50 ... (9 atoms not shown) pdb=" CZ PHE A 132 " occ=0.50 residue: pdb=" N ILE A 133 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE A 133 " occ=0.50 residue: pdb=" N SER A 139 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER A 139 " occ=0.50 residue: pdb=" N SER A 144 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER A 144 " occ=0.50 ... (remaining 444 not shown) Time building chain proxies: 3.65, per 1000 atoms: 0.10 Number of scatterers: 36176 At special positions: 0 Unit cell: (137.237, 137.237, 137.237, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 24 26.01 S 192 16.00 O 8816 8.00 N 5928 7.00 C 21216 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: 4.71 Conformation dependent library (CDL) restraints added in 1.4 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN A 25 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 41 " --> pdb=" O MET A 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 77 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN B 25 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 41 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 77 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN C 25 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE C 41 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 77 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN D 25 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE D 41 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 77 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN E 25 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP E 42 " --> pdb=" O SER E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 77 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN F 25 " --> pdb=" O ASN F 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE F 41 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP F 42 " --> pdb=" O SER F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 77 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE G 41 " --> pdb=" O MET G 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 77 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN H 25 " --> pdb=" O ASN H 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE H 41 " --> pdb=" O MET H 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 77 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN I 25 " --> pdb=" O ASN I 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE I 41 " --> pdb=" O MET I 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP I 42 " --> pdb=" O SER I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 77 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN J 25 " --> pdb=" O ASN J 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE J 41 " --> pdb=" O MET J 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP J 42 " --> pdb=" O SER J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 77 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN K 25 " --> pdb=" O ASN K 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE K 41 " --> pdb=" O MET K 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP K 42 " --> pdb=" O SER K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 77 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN L 25 " --> pdb=" O ASN L 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE L 41 " --> pdb=" O MET L 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP L 42 " --> pdb=" O SER L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 77 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN M 25 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE M 41 " --> pdb=" O MET M 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 77 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN N 25 " --> pdb=" O ASN N 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE N 41 " --> pdb=" O MET N 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP N 42 " --> pdb=" O SER N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 77 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN O 25 " --> pdb=" O ASN O 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE O 41 " --> pdb=" O MET O 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP O 42 " --> pdb=" O SER O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 77 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN P 25 " --> pdb=" O ASN P 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE P 41 " --> pdb=" O MET P 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP P 42 " --> pdb=" O SER P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 77 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN Q 25 " --> pdb=" O ASN Q 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE Q 41 " --> pdb=" O MET Q 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP Q 42 " --> pdb=" O SER Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 77 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN R 25 " --> pdb=" O ASN R 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE R 41 " --> pdb=" O MET R 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP R 42 " --> pdb=" O SER R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 77 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN S 25 " --> pdb=" O ASN S 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE S 41 " --> pdb=" O MET S 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP S 42 " --> pdb=" O SER S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 77 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN T 25 " --> pdb=" O ASN T 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE T 41 " --> pdb=" O MET T 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP T 42 " --> pdb=" O SER T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 77 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN U 25 " --> pdb=" O ASN U 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE U 41 " --> pdb=" O MET U 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP U 42 " --> pdb=" O SER U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 77 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR U 168 " --> pdb=" O GLY U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN V 25 " --> pdb=" O ASN V 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE V 41 " --> pdb=" O MET V 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP V 42 " --> pdb=" O SER V 38 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 77 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN W 25 " --> pdb=" O ASN W 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE W 41 " --> pdb=" O MET W 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP W 42 " --> pdb=" O SER W 38 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 77 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 removed outlier: 3.534A pdb=" N ASN X 25 " --> pdb=" O ASN X 21 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE X 41 " --> pdb=" O MET X 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP X 42 " --> pdb=" O SER X 38 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 77 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 164 through 174 removed outlier: 4.365A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) 2592 hydrogen bonds defined for protein. 7776 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7560 1.33 - 1.45: 7728 1.45 - 1.58: 18936 1.58 - 1.71: 0 1.71 - 1.83: 312 Bond restraints: 34536 Sorted by residual: bond pdb=" ND1 HIS M 65 " pdb=" CE1 HIS M 65 " ideal model delta sigma weight residual 1.321 1.367 -0.046 1.00e-02 1.00e+04 2.12e+01 bond pdb=" ND1 HIS F 65 " pdb=" CE1 HIS F 65 " ideal model delta sigma weight residual 1.321 1.367 -0.046 1.00e-02 1.00e+04 2.12e+01 bond pdb=" ND1 HIS G 65 " pdb=" CE1 HIS G 65 " ideal model delta sigma weight residual 1.321 1.367 -0.046 1.00e-02 1.00e+04 2.12e+01 bond pdb=" ND1 HIS U 65 " pdb=" CE1 HIS U 65 " ideal model delta sigma weight residual 1.321 1.367 -0.046 1.00e-02 1.00e+04 2.12e+01 bond pdb=" ND1 HIS V 65 " pdb=" CE1 HIS V 65 " ideal model delta sigma weight residual 1.321 1.367 -0.046 1.00e-02 1.00e+04 2.12e+01 ... (remaining 34531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 42912 3.90 - 7.80: 3432 7.80 - 11.70: 96 11.70 - 15.60: 0 15.60 - 19.50: 24 Bond angle restraints: 46464 Sorted by residual: angle pdb=" OE1 GLU H 62 " pdb=" CD GLU H 62 " pdb=" OE2 GLU H 62 " ideal model delta sigma weight residual 122.90 103.40 19.50 2.40e+00 1.74e-01 6.60e+01 angle pdb=" OE1 GLU X 62 " pdb=" CD GLU X 62 " pdb=" OE2 GLU X 62 " ideal model delta sigma weight residual 122.90 103.40 19.50 2.40e+00 1.74e-01 6.60e+01 angle pdb=" OE1 GLU E 62 " pdb=" CD GLU E 62 " pdb=" OE2 GLU E 62 " ideal model delta sigma weight residual 122.90 103.40 19.50 2.40e+00 1.74e-01 6.60e+01 angle pdb=" OE1 GLU V 62 " pdb=" CD GLU V 62 " pdb=" OE2 GLU V 62 " ideal model delta sigma weight residual 122.90 103.40 19.50 2.40e+00 1.74e-01 6.60e+01 angle pdb=" OE1 GLU G 62 " pdb=" CD GLU G 62 " pdb=" OE2 GLU G 62 " ideal model delta sigma weight residual 122.90 103.40 19.50 2.40e+00 1.74e-01 6.60e+01 ... (remaining 46459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 18936 14.94 - 29.87: 1392 29.87 - 44.81: 360 44.81 - 59.74: 240 59.74 - 74.68: 96 Dihedral angle restraints: 21024 sinusoidal: 8784 harmonic: 12240 Sorted by residual: dihedral pdb=" C ALA S 47 " pdb=" N ALA S 47 " pdb=" CA ALA S 47 " pdb=" CB ALA S 47 " ideal model delta harmonic sigma weight residual -122.60 -131.62 9.02 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" C ALA T 47 " pdb=" N ALA T 47 " pdb=" CA ALA T 47 " pdb=" CB ALA T 47 " ideal model delta harmonic sigma weight residual -122.60 -131.62 9.02 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" C ALA Q 47 " pdb=" N ALA Q 47 " pdb=" CA ALA Q 47 " pdb=" CB ALA Q 47 " ideal model delta harmonic sigma weight residual -122.60 -131.62 9.02 0 2.50e+00 1.60e-01 1.30e+01 ... (remaining 21021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2400 0.068 - 0.136: 1656 0.136 - 0.204: 480 0.204 - 0.272: 264 0.272 - 0.340: 48 Chirality restraints: 4848 Sorted by residual: chirality pdb=" CA GLU O 94 " pdb=" N GLU O 94 " pdb=" C GLU O 94 " pdb=" CB GLU O 94 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA GLU D 94 " pdb=" N GLU D 94 " pdb=" C GLU D 94 " pdb=" CB GLU D 94 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA GLU Q 94 " pdb=" N GLU Q 94 " pdb=" C GLU Q 94 " pdb=" CB GLU Q 94 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 4845 not shown) Planarity restraints: 6120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR U 137 " 0.104 2.00e-02 2.50e+03 6.11e-02 7.47e+01 pdb=" CG TYR U 137 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR U 137 " -0.078 2.00e-02 2.50e+03 pdb=" CD2 TYR U 137 " -0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR U 137 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR U 137 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR U 137 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR U 137 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 137 " 0.104 2.00e-02 2.50e+03 6.11e-02 7.47e+01 pdb=" CG TYR F 137 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR F 137 " -0.078 2.00e-02 2.50e+03 pdb=" CD2 TYR F 137 " -0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR F 137 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR F 137 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR F 137 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR F 137 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 137 " 0.104 2.00e-02 2.50e+03 6.11e-02 7.47e+01 pdb=" CG TYR V 137 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR V 137 " -0.078 2.00e-02 2.50e+03 pdb=" CD2 TYR V 137 " -0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR V 137 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR V 137 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR V 137 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR V 137 " 0.084 2.00e-02 2.50e+03 ... (remaining 6117 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 72 2.52 - 3.12: 24408 3.12 - 3.71: 56340 3.71 - 4.31: 85888 4.31 - 4.90: 135448 Nonbonded interactions: 302156 Sorted by model distance: nonbonded pdb=" ND1 HIS W 65 " pdb="FE FE W 201 " model vdw 1.928 2.340 nonbonded pdb=" ND1 HIS N 65 " pdb="FE FE N 201 " model vdw 1.928 2.340 nonbonded pdb=" ND1 HIS C 65 " pdb="FE FE C 201 " model vdw 1.928 2.340 nonbonded pdb=" ND1 HIS X 65 " pdb="FE FE X 201 " model vdw 1.928 2.340 nonbonded pdb=" ND1 HIS J 65 " pdb="FE FE J 201 " model vdw 1.928 2.340 ... (remaining 302151 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.95 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: 35.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.020 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 28.850 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.100 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:9.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.051 34536 Z= 1.140 Angle : 2.246 19.497 46464 Z= 1.576 Chirality : 0.102 0.340 4848 Planarity : 0.019 0.124 6120 Dihedral : 14.264 74.681 13104 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 0.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.32 % Allowed : 1.97 % Favored : 96.71 % 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: 2.64 (0.13), residues: 4080 helix: 2.04 (0.08), residues: 3144 sheet: None (None), residues: 0 loop : 0.91 (0.24), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.004 ARG O 76 TYR 0.104 0.027 TYR A 137 PHE 0.063 0.016 PHE A 41 TRP 0.023 0.013 TRP T 93 HIS 0.020 0.008 HIS R 128 Details of bonding type rmsd covalent geometry : bond 0.01747 (34536) covalent geometry : angle 2.24640 (46464) hydrogen bonds : bond 0.29696 ( 2592) hydrogen bonds : angle 5.53285 ( 7776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 864 time to evaluate : 1.575 Fit side-chains outliers start: 48 outliers final: 0 residues processed: 864 average time/residue: 1.0557 time to fit residues: 1036.4318 Evaluate side-chains 600 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 141 GLN B 14 GLN B 141 GLN C 14 GLN C 141 GLN D 14 GLN D 141 GLN E 14 GLN E 141 GLN F 14 GLN F 141 GLN G 14 GLN G 141 GLN H 14 GLN H 141 GLN I 14 GLN I 141 GLN J 14 GLN J 141 GLN K 14 GLN K 141 GLN L 14 GLN L 141 GLN M 14 GLN M 141 GLN N 14 GLN N 141 GLN O 14 GLN O 141 GLN P 14 GLN P 141 GLN Q 14 GLN Q 141 GLN R 14 GLN R 141 GLN S 14 GLN S 141 GLN T 14 GLN T 141 GLN U 14 GLN U 141 GLN V 14 GLN V 141 GLN W 14 GLN W 141 GLN X 14 GLN X 141 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115821 restraints weight = 21979.915| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 0.65 r_work: 0.3124 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.2759 rms_B_bonded: 4.75 restraints_weight: 0.1250 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 34536 Z= 0.263 Angle : 0.621 6.922 46464 Z= 0.356 Chirality : 0.039 0.137 4848 Planarity : 0.004 0.028 6120 Dihedral : 5.480 47.466 4536 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % 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: 4.96 (0.12), residues: 4080 helix: 3.89 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.90 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 63 TYR 0.017 0.002 TYR N 32 PHE 0.012 0.002 PHE T 132 TRP 0.002 0.001 TRP R 93 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00378 (34536) covalent geometry : angle 0.62105 (46464) hydrogen bonds : bond 0.12710 ( 2592) hydrogen bonds : angle 4.05523 ( 7776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 1.519 Fit side-chains REVERT: A 143 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8376 (tptp) REVERT: B 143 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8380 (tptp) REVERT: C 143 LYS cc_start: 0.8949 (ttmm) cc_final: 0.8381 (tptp) REVERT: D 143 LYS cc_start: 0.8950 (ttmm) cc_final: 0.8373 (tptp) REVERT: E 143 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8390 (tptp) REVERT: F 143 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8390 (tptp) REVERT: G 143 LYS cc_start: 0.8950 (ttmm) cc_final: 0.8388 (tptp) REVERT: H 143 LYS cc_start: 0.8949 (ttmm) cc_final: 0.8375 (tptp) REVERT: I 143 LYS cc_start: 0.8962 (ttmm) cc_final: 0.8393 (tptp) REVERT: J 143 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8383 (tptp) REVERT: K 143 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8382 (tptp) REVERT: L 143 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8385 (tptp) REVERT: M 143 LYS cc_start: 0.8961 (ttmm) cc_final: 0.8389 (tptp) REVERT: N 143 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8375 (tptp) REVERT: O 143 LYS cc_start: 0.8953 (ttmm) cc_final: 0.8380 (tptp) REVERT: P 143 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8371 (tptp) REVERT: Q 143 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8381 (tptp) REVERT: R 143 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8377 (tptp) REVERT: S 143 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8381 (tptp) REVERT: T 143 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8383 (tptp) REVERT: U 143 LYS cc_start: 0.8955 (ttmm) cc_final: 0.8383 (tptp) REVERT: V 143 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8391 (tptp) REVERT: W 143 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8377 (tptp) REVERT: X 143 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8370 (tptp) outliers start: 0 outliers final: 0 residues processed: 552 average time/residue: 1.0595 time to fit residues: 660.4328 Evaluate side-chains 496 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 402 optimal weight: 4.9990 chunk 379 optimal weight: 5.9990 chunk 387 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 335 optimal weight: 0.7980 chunk 339 optimal weight: 0.9990 chunk 358 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.102017 restraints weight = 21860.368| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 0.64 r_work: 0.2939 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work: 0.2557 rms_B_bonded: 4.62 restraints_weight: 0.1250 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2505 r_free = 0.2505 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2495 r_free = 0.2495 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 34536 Z= 0.315 Angle : 0.669 7.967 46464 Z= 0.381 Chirality : 0.040 0.134 4848 Planarity : 0.004 0.029 6120 Dihedral : 4.975 36.600 4536 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.66 % Allowed : 8.22 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.83 (0.12), residues: 4080 helix: 3.88 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.37 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 156 TYR 0.013 0.002 TYR W 32 PHE 0.013 0.003 PHE M 51 TRP 0.005 0.001 TRP V 93 HIS 0.004 0.001 HIS R 105 Details of bonding type rmsd covalent geometry : bond 0.00466 (34536) covalent geometry : angle 0.66874 (46464) hydrogen bonds : bond 0.14667 ( 2592) hydrogen bonds : angle 4.19366 ( 7776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 528 time to evaluate : 1.276 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 552 average time/residue: 1.0676 time to fit residues: 666.6068 Evaluate side-chains 456 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 327 optimal weight: 0.8980 chunk 378 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 276 optimal weight: 0.8980 chunk 359 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 394 optimal weight: 4.9990 chunk 287 optimal weight: 5.9990 chunk 356 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 239 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.111558 restraints weight = 22850.747| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 0.65 r_work: 0.3085 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.2729 rms_B_bonded: 4.83 restraints_weight: 0.1250 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 34536 Z= 0.214 Angle : 0.529 6.481 46464 Z= 0.303 Chirality : 0.036 0.137 4848 Planarity : 0.003 0.028 6120 Dihedral : 4.288 21.525 4536 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % 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: 5.46 (0.13), residues: 4080 helix: 4.30 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.69 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 63 TYR 0.010 0.001 TYR N 137 PHE 0.010 0.002 PHE E 51 TRP 0.004 0.001 TRP J 93 HIS 0.002 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00301 (34536) covalent geometry : angle 0.52872 (46464) hydrogen bonds : bond 0.10833 ( 2592) hydrogen bonds : angle 3.74316 ( 7776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 475 time to evaluate : 1.480 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 475 average time/residue: 1.1090 time to fit residues: 596.7883 Evaluate side-chains 432 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 258 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 194 optimal weight: 9.9990 chunk 406 optimal weight: 7.9990 chunk 187 optimal weight: 0.4980 chunk 129 optimal weight: 9.9990 chunk 237 optimal weight: 0.6980 chunk 387 optimal weight: 4.9990 chunk 355 optimal weight: 7.9990 chunk 303 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.118934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.106008 restraints weight = 22568.010| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 0.64 r_work: 0.3001 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work: 0.2632 rms_B_bonded: 4.75 restraints_weight: 0.1250 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.013 34536 Z= 0.252 Angle : 0.567 7.153 46464 Z= 0.325 Chirality : 0.037 0.136 4848 Planarity : 0.003 0.028 6120 Dihedral : 4.038 18.729 4536 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % 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: 5.40 (0.12), residues: 4080 helix: 4.27 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.74 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG W 63 TYR 0.009 0.001 TYR J 137 PHE 0.011 0.002 PHE A 51 TRP 0.004 0.001 TRP K 93 HIS 0.003 0.001 HIS P 105 Details of bonding type rmsd covalent geometry : bond 0.00360 (34536) covalent geometry : angle 0.56721 (46464) hydrogen bonds : bond 0.12557 ( 2592) hydrogen bonds : angle 3.93437 ( 7776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.637 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 1.1333 time to fit residues: 555.0529 Evaluate side-chains 432 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 47 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 390 optimal weight: 3.9990 chunk 303 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 346 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.110679 restraints weight = 22886.993| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 0.64 r_work: 0.3072 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.2714 rms_B_bonded: 4.82 restraints_weight: 0.1250 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 34536 Z= 0.217 Angle : 0.520 6.570 46464 Z= 0.300 Chirality : 0.036 0.134 4848 Planarity : 0.003 0.027 6120 Dihedral : 3.928 18.382 4536 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.66 % Allowed : 8.88 % Favored : 90.46 % 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: 5.58 (0.12), residues: 4080 helix: 4.37 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.79 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 79 TYR 0.010 0.001 TYR R 137 PHE 0.010 0.002 PHE F 51 TRP 0.004 0.001 TRP N 93 HIS 0.002 0.000 HIS P 105 Details of bonding type rmsd covalent geometry : bond 0.00303 (34536) covalent geometry : angle 0.52029 (46464) hydrogen bonds : bond 0.11029 ( 2592) hydrogen bonds : angle 3.73816 ( 7776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 432 time to evaluate : 1.313 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 432 average time/residue: 1.0693 time to fit residues: 524.7970 Evaluate side-chains 456 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 432 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain U residue 165 MET Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 165 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 33 optimal weight: 0.9980 chunk 288 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 238 optimal weight: 0.0970 chunk 262 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.114034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.101736 restraints weight = 20952.029| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 0.60 r_work: 0.2931 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 1.77 restraints_weight: 0.2500 r_work: 0.2534 rms_B_bonded: 4.53 restraints_weight: 0.1250 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2456 r_free = 0.2456 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2456 r_free = 0.2456 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 34536 Z= 0.322 Angle : 0.665 8.252 46464 Z= 0.378 Chirality : 0.041 0.143 4848 Planarity : 0.004 0.028 6120 Dihedral : 4.182 18.021 4536 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % 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: 5.11 (0.12), residues: 4080 helix: 4.02 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.70 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 22 TYR 0.012 0.002 TYR P 137 PHE 0.013 0.003 PHE B 51 TRP 0.004 0.001 TRP A 93 HIS 0.004 0.001 HIS X 105 Details of bonding type rmsd covalent geometry : bond 0.00485 (34536) covalent geometry : angle 0.66483 (46464) hydrogen bonds : bond 0.14860 ( 2592) hydrogen bonds : angle 4.14952 ( 7776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.302 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 1.1160 time to fit residues: 575.6795 Evaluate side-chains 456 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 339 optimal weight: 2.9990 chunk 221 optimal weight: 0.1980 chunk 242 optimal weight: 0.5980 chunk 219 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 394 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 399 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.118684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.106463 restraints weight = 21419.532| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 0.62 r_work: 0.3031 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 1.82 restraints_weight: 0.2500 r_work: 0.2649 rms_B_bonded: 4.70 restraints_weight: 0.1250 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2563 r_free = 0.2563 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2563 r_free = 0.2563 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.013 34536 Z= 0.249 Angle : 0.560 7.197 46464 Z= 0.323 Chirality : 0.037 0.136 4848 Planarity : 0.003 0.027 6120 Dihedral : 4.094 18.459 4536 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % 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: 5.27 (0.12), residues: 4080 helix: 4.16 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.64 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 63 TYR 0.010 0.001 TYR R 137 PHE 0.011 0.002 PHE D 51 TRP 0.005 0.001 TRP M 93 HIS 0.002 0.001 HIS F 105 Details of bonding type rmsd covalent geometry : bond 0.00353 (34536) covalent geometry : angle 0.56024 (46464) hydrogen bonds : bond 0.12439 ( 2592) hydrogen bonds : angle 3.92908 ( 7776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.649 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.9935 time to fit residues: 515.6797 Evaluate side-chains 456 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 29 optimal weight: 0.3980 chunk 238 optimal weight: 0.0670 chunk 132 optimal weight: 0.6980 chunk 395 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 340 optimal weight: 0.9980 chunk 260 optimal weight: 9.9990 chunk 200 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 221 optimal weight: 0.9990 chunk 397 optimal weight: 6.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121046 restraints weight = 22449.973| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 0.64 r_work: 0.3223 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.2871 rms_B_bonded: 4.99 restraints_weight: 0.1250 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 34536 Z= 0.174 Angle : 0.474 5.785 46464 Z= 0.273 Chirality : 0.035 0.132 4848 Planarity : 0.003 0.027 6120 Dihedral : 3.868 17.494 4536 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 0.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % 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: 5.89 (0.12), residues: 4080 helix: 4.67 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.71 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 90 TYR 0.011 0.001 TYR H 137 PHE 0.008 0.002 PHE I 132 TRP 0.005 0.001 TRP S 93 HIS 0.002 0.000 HIS Q 105 Details of bonding type rmsd covalent geometry : bond 0.00241 (34536) covalent geometry : angle 0.47386 (46464) hydrogen bonds : bond 0.08825 ( 2592) hydrogen bonds : angle 3.42353 ( 7776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.335 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.9576 time to fit residues: 553.5000 Evaluate side-chains 432 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 225 optimal weight: 0.5980 chunk 299 optimal weight: 9.9990 chunk 230 optimal weight: 0.9990 chunk 237 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 241 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 336 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.127615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115358 restraints weight = 21865.776| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 0.63 r_work: 0.3129 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work: 0.2759 rms_B_bonded: 4.84 restraints_weight: 0.1250 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 34536 Z= 0.202 Angle : 0.502 6.330 46464 Z= 0.289 Chirality : 0.036 0.129 4848 Planarity : 0.003 0.028 6120 Dihedral : 3.907 17.848 4536 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % 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: 5.78 (0.12), residues: 4080 helix: 4.56 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.79 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 90 TYR 0.011 0.001 TYR O 137 PHE 0.010 0.002 PHE J 51 TRP 0.005 0.001 TRP M 93 HIS 0.002 0.000 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00284 (34536) covalent geometry : angle 0.50235 (46464) hydrogen bonds : bond 0.10233 ( 2592) hydrogen bonds : angle 3.61031 ( 7776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 1.449 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.9450 time to fit residues: 456.4183 Evaluate side-chains 420 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 336 optimal weight: 8.9990 chunk 295 optimal weight: 5.9990 chunk 247 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 274 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 233 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 398 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.121733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.109463 restraints weight = 21229.049| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 0.61 r_work: 0.3057 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 1.82 restraints_weight: 0.2500 r_work: 0.2675 rms_B_bonded: 4.74 restraints_weight: 0.1250 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34536 Z= 0.238 Angle : 0.544 7.003 46464 Z= 0.313 Chirality : 0.037 0.130 4848 Planarity : 0.003 0.027 6120 Dihedral : 4.031 18.184 4536 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % 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: 5.55 (0.12), residues: 4080 helix: 4.37 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.82 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 79 TYR 0.009 0.001 TYR V 137 PHE 0.010 0.002 PHE E 51 TRP 0.004 0.001 TRP U 93 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00339 (34536) covalent geometry : angle 0.54371 (46464) hydrogen bonds : bond 0.11923 ( 2592) hydrogen bonds : angle 3.84246 ( 7776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19864.30 seconds wall clock time: 337 minutes 17.04 seconds (20237.04 seconds total)