Starting phenix.real_space_refine on Mon Jul 6 11:39:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4q_41038/07_2026/8t4q_41038.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4q_41038/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8t4q_41038/07_2026/8t4q_41038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4q_41038/07_2026/8t4q_41038.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t4q_41038/07_2026/8t4q_41038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4q_41038/07_2026/8t4q_41038.map" } 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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 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: 4.10, per 1000 atoms: 0.11 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: 2.56 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: 0.86 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: 6.31 Time building geometry restraints manager: 3.38 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 3.080 nonbonded pdb=" ND1 HIS N 65 " pdb="FE FE N 201 " model vdw 1.928 3.080 nonbonded pdb=" ND1 HIS C 65 " pdb="FE FE C 201 " model vdw 1.928 3.080 nonbonded pdb=" ND1 HIS X 65 " pdb="FE FE X 201 " model vdw 1.928 3.080 nonbonded pdb=" ND1 HIS J 65 " pdb="FE FE J 201 " model vdw 1.928 3.080 ... (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: 0.12 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: 37.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.090 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.580 Find NCS groups from input model: 0.360 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 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/Z covalent geometry : bond 0.01747 / 1.14 (34536) covalent geometry : angle 2.24640 / 1.58 (46464) hydrogen bonds : bond 0.29696 / 19.92 ( 2592) hydrogen bonds : angle 5.53285 / 4.02 ( 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 : 1.502 Fit side-chains outliers start: 48 outliers final: 0 residues processed: 864 average time/residue: 0.9791 time to fit residues: 965.8454 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 : 1.469 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3526 r_free = 0.3526 target = 0.135789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.122198 restraints weight = 21175.836| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 0.62 r_work: 0.3218 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work: 0.2856 rms_B_bonded: 4.74 restraints_weight: 0.1250 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 34536 Z= 0.225 Angle : 0.572 6.237 46464 Z= 0.328 Chirality : 0.037 0.138 4848 Planarity : 0.003 0.027 6120 Dihedral : 5.403 46.028 4536 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 1.02 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: 5.19 (0.12), residues: 4080 helix: 4.05 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.97 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 63 TYR 0.015 0.002 TYR K 32 PHE 0.011 0.002 PHE C 132 TRP 0.002 0.001 TRP L 93 HIS 0.003 0.001 HIS O 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.22 (34536) covalent geometry : angle 0.57247 / 0.33 (46464) hydrogen bonds : bond 0.11091 / 7.44 ( 2592) hydrogen bonds : angle 3.87076 / 2.83 ( 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 624 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 1.333 Fit side-chains REVERT: H 63 ARG cc_start: 0.8712 (tpp80) cc_final: 0.8329 (ttp80) REVERT: L 63 ARG cc_start: 0.8700 (tpp80) cc_final: 0.8330 (ttp80) REVERT: N 63 ARG cc_start: 0.8707 (tpp80) cc_final: 0.8323 (ttp80) REVERT: P 63 ARG cc_start: 0.8715 (tpp80) cc_final: 0.8330 (ttp80) REVERT: Q 63 ARG cc_start: 0.8687 (tpp80) cc_final: 0.8313 (ttp80) REVERT: R 63 ARG cc_start: 0.8686 (tpp80) cc_final: 0.8313 (ttp80) REVERT: S 63 ARG cc_start: 0.8709 (tpp80) cc_final: 0.8316 (ttp80) REVERT: T 63 ARG cc_start: 0.8686 (tpp80) cc_final: 0.8314 (ttp80) REVERT: U 63 ARG cc_start: 0.8723 (tpp80) cc_final: 0.8329 (ttp80) REVERT: V 63 ARG cc_start: 0.8686 (tpp80) cc_final: 0.8322 (ttp80) REVERT: W 63 ARG cc_start: 0.8714 (tpp80) cc_final: 0.8324 (ttp80) REVERT: X 63 ARG cc_start: 0.8705 (tpp80) cc_final: 0.8318 (ttp80) outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 1.0713 time to fit residues: 761.3919 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 : 1.414 ------------------------------------------------------------------------------- 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: 0.8980 chunk 387 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 335 optimal weight: 2.9990 chunk 339 optimal weight: 0.9980 chunk 358 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 = 0.3231 r_free = 0.3231 target = 0.112740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.099699 restraints weight = 20136.035| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 0.59 r_work: 0.2910 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work: 0.2518 rms_B_bonded: 4.37 restraints_weight: 0.1250 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2487 r_free = 0.2487 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.024 34536 Z= 0.366 Angle : 0.749 8.603 46464 Z= 0.425 Chirality : 0.043 0.133 4848 Planarity : 0.004 0.029 6120 Dihedral : 5.035 37.074 4536 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.33 % Allowed : 8.88 % Favored : 90.79 % 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 (0.12), residues: 4080 helix: 3.82 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.36 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG U 63 TYR 0.015 0.002 TYR P 32 PHE 0.016 0.003 PHE K 41 TRP 0.005 0.002 TRP V 93 HIS 0.005 0.001 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.37 (34536) covalent geometry : angle 0.74870 / 0.42 (46464) hydrogen bonds : bond 0.15924 / 10.68 ( 2592) hydrogen bonds : angle 4.26024 / 3.11 ( 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 492 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 480 time to evaluate : 1.803 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 480 average time/residue: 1.1094 time to fit residues: 607.0132 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 : 1.565 ------------------------------------------------------------------------------- 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: 7.9990 chunk 378 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 276 optimal weight: 1.9990 chunk 359 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 394 optimal weight: 3.9990 chunk 287 optimal weight: 5.9990 chunk 356 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 239 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.116248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.103114 restraints weight = 21035.433| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 0.61 r_work: 0.2961 rms_B_bonded: 1.03 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 1.80 restraints_weight: 0.2500 r_work: 0.2583 rms_B_bonded: 4.54 restraints_weight: 0.1250 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2503 r_free = 0.2503 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2501 r_free = 0.2501 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.2787 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= 0.289 Angle : 0.633 7.703 46464 Z= 0.360 Chirality : 0.039 0.137 4848 Planarity : 0.004 0.029 6120 Dihedral : 4.349 18.618 4536 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 0.57 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: 5.02 (0.12), residues: 4080 helix: 3.99 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.54 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 63 TYR 0.011 0.002 TYR S 137 PHE 0.012 0.003 PHE W 51 TRP 0.005 0.001 TRP S 93 HIS 0.003 0.001 HIS S 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.29 (34536) covalent geometry : angle 0.63253 / 0.36 (46464) hydrogen bonds : bond 0.13915 / 9.33 ( 2592) hydrogen bonds : angle 4.11623 / 3.01 ( 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 456 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 432 time to evaluate : 1.656 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 432 average time/residue: 1.0733 time to fit residues: 529.7407 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 : 1.616 ------------------------------------------------------------------------------- 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: 3.9990 chunk 60 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 406 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 237 optimal weight: 0.6980 chunk 387 optimal weight: 10.0000 chunk 355 optimal weight: 6.9990 chunk 303 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.126124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.113211 restraints weight = 22017.422| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 0.62 r_work: 0.3110 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work: 0.2754 rms_B_bonded: 4.78 restraints_weight: 0.1250 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.3307 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= 0.206 Angle : 0.517 6.351 46464 Z= 0.297 Chirality : 0.036 0.136 4848 Planarity : 0.003 0.028 6120 Dihedral : 4.000 18.314 4536 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 0.96 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: 5.54 (0.12), residues: 4080 helix: 4.36 (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 R 63 TYR 0.010 0.001 TYR Q 137 PHE 0.010 0.002 PHE O 51 TRP 0.005 0.001 TRP L 93 HIS 0.002 0.000 HIS K 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.21 (34536) covalent geometry : angle 0.51729 / 0.30 (46464) hydrogen bonds : bond 0.10458 / 7.01 ( 2592) hydrogen bonds : angle 3.68361 / 2.69 ( 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 456 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.538 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 1.0872 time to fit residues: 565.1471 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 : 1.452 ------------------------------------------------------------------------------- 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: 2.9990 chunk 134 optimal weight: 0.1980 chunk 232 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 390 optimal weight: 0.9990 chunk 303 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 346 optimal weight: 2.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.121208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108811 restraints weight = 21494.119| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 0.62 r_work: 0.3047 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 1.82 restraints_weight: 0.2500 r_work: 0.2666 rms_B_bonded: 4.75 restraints_weight: 0.1250 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.3067 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= 0.240 Angle : 0.551 7.029 46464 Z= 0.316 Chirality : 0.037 0.134 4848 Planarity : 0.003 0.027 6120 Dihedral : 3.989 18.485 4536 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 0.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: 5.46 (0.12), residues: 4080 helix: 4.33 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.69 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 63 TYR 0.009 0.001 TYR V 137 PHE 0.010 0.002 PHE J 51 TRP 0.004 0.001 TRP I 93 HIS 0.003 0.001 HIS R 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.24 (34536) covalent geometry : angle 0.55096 / 0.32 (46464) hydrogen bonds : bond 0.12072 / 8.10 ( 2592) hydrogen bonds : angle 3.86712 / 2.83 ( 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 432 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.650 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 1.0768 time to fit residues: 532.2678 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 : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 33 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 chunk 232 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 204 optimal weight: 0.1980 chunk 238 optimal weight: 8.9990 chunk 262 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 156 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.127531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115231 restraints weight = 22198.600| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 0.64 r_work: 0.3136 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work: 0.2767 rms_B_bonded: 4.91 restraints_weight: 0.1250 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.3377 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= 0.200 Angle : 0.500 6.275 46464 Z= 0.288 Chirality : 0.035 0.133 4848 Planarity : 0.003 0.027 6120 Dihedral : 3.896 17.990 4536 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 5.75 (0.12), residues: 4080 helix: 4.55 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.73 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 63 TYR 0.009 0.001 TYR V 137 PHE 0.009 0.002 PHE I 51 TRP 0.004 0.001 TRP Q 93 HIS 0.002 0.000 HIS O 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.20 (34536) covalent geometry : angle 0.50022 / 0.29 (46464) hydrogen bonds : bond 0.10172 / 6.82 ( 2592) hydrogen bonds : angle 3.60824 / 2.64 ( 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 473 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 1.143 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 473 average time/residue: 1.0585 time to fit residues: 570.6163 Evaluate side-chains 451 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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: 4.9990 chunk 221 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 394 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 399 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.117897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.105419 restraints weight = 21330.854| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 0.62 r_work: 0.2986 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 1.80 restraints_weight: 0.2500 r_work: 0.2596 rms_B_bonded: 4.66 restraints_weight: 0.1250 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 34536 Z= 0.272 Angle : 0.590 7.561 46464 Z= 0.338 Chirality : 0.038 0.133 4848 Planarity : 0.003 0.028 6120 Dihedral : 4.097 18.316 4536 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 5.35 (0.12), residues: 4080 helix: 4.23 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.77 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 63 TYR 0.010 0.001 TYR D 137 PHE 0.012 0.002 PHE O 51 TRP 0.004 0.001 TRP O 93 HIS 0.003 0.001 HIS H 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.27 (34536) covalent geometry : angle 0.59034 / 0.34 (46464) hydrogen bonds : bond 0.13315 / 8.93 ( 2592) hydrogen bonds : angle 3.99843 / 2.92 ( 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 408 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.524 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 1.0820 time to fit residues: 502.1402 Evaluate side-chains 410 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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: 0.8980 chunk 238 optimal weight: 0.0020 chunk 132 optimal weight: 4.9990 chunk 395 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 340 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 397 optimal weight: 0.6980 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.128737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.116453 restraints weight = 22338.926| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 0.64 r_work: 0.3153 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.2785 rms_B_bonded: 4.95 restraints_weight: 0.1250 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.3424 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= 0.194 Angle : 0.494 6.205 46464 Z= 0.285 Chirality : 0.035 0.133 4848 Planarity : 0.003 0.028 6120 Dihedral : 3.915 17.789 4536 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 5.79 (0.12), residues: 4080 helix: 4.58 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.75 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 63 TYR 0.010 0.001 TYR N 137 PHE 0.009 0.002 PHE F 132 TRP 0.004 0.001 TRP B 93 HIS 0.002 0.000 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.19 (34536) covalent geometry : angle 0.49359 / 0.28 (46464) hydrogen bonds : bond 0.09890 / 6.63 ( 2592) hydrogen bonds : angle 3.57145 / 2.61 ( 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 472 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 1.428 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 472 average time/residue: 1.0383 time to fit residues: 558.6475 Evaluate side-chains 459 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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: 1.9990 chunk 299 optimal weight: 10.0000 chunk 230 optimal weight: 0.9980 chunk 237 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 241 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 336 optimal weight: 0.8980 chunk 233 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.123550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.111228 restraints weight = 21872.511| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 0.62 r_work: 0.3086 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work: 0.2708 rms_B_bonded: 4.82 restraints_weight: 0.1250 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 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 = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.3193 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= 0.223 Angle : 0.525 6.749 46464 Z= 0.302 Chirality : 0.036 0.132 4848 Planarity : 0.003 0.028 6120 Dihedral : 3.991 18.132 4536 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 5.63 (0.12), residues: 4080 helix: 4.44 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.80 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 63 TYR 0.009 0.001 TYR W 137 PHE 0.010 0.002 PHE O 51 TRP 0.004 0.001 TRP Q 93 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.22 (34536) covalent geometry : angle 0.52484 / 0.30 (46464) hydrogen bonds : bond 0.11299 / 7.58 ( 2592) hydrogen bonds : angle 3.75877 / 2.75 ( 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 456 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.902 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 1.0573 time to fit residues: 548.8022 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 : 1.575 ------------------------------------------------------------------------------- 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: 0.8980 chunk 295 optimal weight: 0.8980 chunk 247 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 233 optimal weight: 0.8980 chunk 212 optimal weight: 0.7980 chunk 398 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.126465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.114222 restraints weight = 22025.852| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 0.63 r_work: 0.3132 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work: 0.2760 rms_B_bonded: 4.88 restraints_weight: 0.1250 r_work (final): 0.2760 ------------------------------------------------------------------------------- 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 = 0.45 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 = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.3337 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= 0.205 Angle : 0.503 6.397 46464 Z= 0.290 Chirality : 0.035 0.131 4848 Planarity : 0.003 0.028 6120 Dihedral : 3.944 17.856 4536 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 5.74 (0.12), residues: 4080 helix: 4.53 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.80 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 63 TYR 0.009 0.001 TYR B 137 PHE 0.009 0.002 PHE D 51 TRP 0.004 0.001 TRP R 93 HIS 0.002 0.000 HIS Q 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.20 (34536) covalent geometry : angle 0.50330 / 0.29 (46464) hydrogen bonds : bond 0.10442 / 7.00 ( 2592) hydrogen bonds : angle 3.63697 / 2.66 ( 7776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19932.98 seconds wall clock time: 338 minutes 46.96 seconds (20326.96 seconds total)