Starting phenix.real_space_refine on Sun Aug 9 01:32:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pho_17669/08_2026/8pho_17669.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pho_17669/08_2026/8pho_17669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pho_17669/08_2026/8pho_17669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pho_17669/08_2026/8pho_17669.map" model { file = "/net/cci-nas-00/data/ceres_data/8pho_17669/08_2026/8pho_17669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pho_17669/08_2026/8pho_17669.cif" } resolution = 2.34 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 20400 2.51 5 N 4992 2.21 5 O 6684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32172 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2621 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 311} Chain breaks: 2 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "F" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "J" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "L" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 3.99, per 1000 atoms: 0.12 Number of scatterers: 32172 At special positions: 0 Unit cell: (170.888, 170.888, 120.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 6684 8.00 N 4992 7.00 C 20400 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: 2.53 Conformation dependent library (CDL) restraints added in 1.3 seconds 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7296 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 60 sheets defined 53.9% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL A 32 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU A 93 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 303 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 389 Processing helix chain 'A' and resid 393 through 404 Processing helix chain 'B' and resid 14 through 22 Processing helix chain 'B' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL B 32 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA B 33 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 77 removed outlier: 3.819A pdb=" N ASN B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU B 93 " --> pdb=" O ILE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 303 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 327 through 353 removed outlier: 4.402A pdb=" N LYS B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 389 Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL C 32 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA C 33 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN C 68 " --> pdb=" O ASN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU C 93 " --> pdb=" O ILE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 303 Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 389 Processing helix chain 'C' and resid 393 through 404 Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL D 32 " --> pdb=" O TYR D 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA D 33 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU D 93 " --> pdb=" O ILE D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR D 177 " --> pdb=" O PHE D 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 303 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS D 347 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'E' and resid 14 through 22 Processing helix chain 'E' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL E 32 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 77 removed outlier: 3.819A pdb=" N ASN E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU E 93 " --> pdb=" O ILE E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR E 177 " --> pdb=" O PHE E 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 178 " --> pdb=" O GLU E 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 303 Processing helix chain 'E' and resid 305 through 310 Processing helix chain 'E' and resid 327 through 353 removed outlier: 4.402A pdb=" N LYS E 347 " --> pdb=" O SER E 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR E 349 " --> pdb=" O ASN E 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS E 350 " --> pdb=" O LEU E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 389 Processing helix chain 'E' and resid 393 through 404 Processing helix chain 'F' and resid 14 through 22 Processing helix chain 'F' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL F 32 " --> pdb=" O TYR F 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU F 93 " --> pdb=" O ILE F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR F 177 " --> pdb=" O PHE F 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 178 " --> pdb=" O GLU F 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 303 Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS F 347 " --> pdb=" O SER F 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR F 349 " --> pdb=" O ASN F 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS F 350 " --> pdb=" O LEU F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 389 Processing helix chain 'F' and resid 393 through 404 Processing helix chain 'G' and resid 14 through 22 Processing helix chain 'G' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL G 32 " --> pdb=" O TYR G 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA G 33 " --> pdb=" O ILE G 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU G 93 " --> pdb=" O ILE G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR G 177 " --> pdb=" O PHE G 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 303 Processing helix chain 'G' and resid 305 through 310 Processing helix chain 'G' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS G 347 " --> pdb=" O SER G 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS G 350 " --> pdb=" O LEU G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 389 Processing helix chain 'G' and resid 393 through 404 Processing helix chain 'H' and resid 14 through 22 Processing helix chain 'H' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL H 32 " --> pdb=" O TYR H 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA H 33 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU H 37 " --> pdb=" O ALA H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 77 removed outlier: 3.819A pdb=" N ASN H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU H 93 " --> pdb=" O ILE H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'H' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR H 177 " --> pdb=" O PHE H 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL H 178 " --> pdb=" O GLU H 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 303 Processing helix chain 'H' and resid 305 through 310 Processing helix chain 'H' and resid 327 through 353 removed outlier: 4.402A pdb=" N LYS H 347 " --> pdb=" O SER H 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR H 349 " --> pdb=" O ASN H 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS H 350 " --> pdb=" O LEU H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 389 Processing helix chain 'H' and resid 393 through 404 Processing helix chain 'I' and resid 14 through 22 Processing helix chain 'I' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL I 32 " --> pdb=" O TYR I 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA I 33 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU I 37 " --> pdb=" O ALA I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN I 68 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU I 93 " --> pdb=" O ILE I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 110 No H-bonds generated for 'chain 'I' and resid 108 through 110' Processing helix chain 'I' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR I 177 " --> pdb=" O PHE I 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL I 178 " --> pdb=" O GLU I 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG I 183 " --> pdb=" O GLU I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 303 Processing helix chain 'I' and resid 305 through 310 Processing helix chain 'I' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS I 347 " --> pdb=" O SER I 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR I 349 " --> pdb=" O ASN I 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS I 350 " --> pdb=" O LEU I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 389 Processing helix chain 'I' and resid 393 through 404 Processing helix chain 'J' and resid 14 through 22 Processing helix chain 'J' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL J 32 " --> pdb=" O TYR J 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA J 33 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU J 93 " --> pdb=" O ILE J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 110 No H-bonds generated for 'chain 'J' and resid 108 through 110' Processing helix chain 'J' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR J 177 " --> pdb=" O PHE J 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL J 178 " --> pdb=" O GLU J 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG J 183 " --> pdb=" O GLU J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 303 Processing helix chain 'J' and resid 305 through 310 Processing helix chain 'J' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS J 347 " --> pdb=" O SER J 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR J 349 " --> pdb=" O ASN J 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS J 350 " --> pdb=" O LEU J 346 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'K' and resid 14 through 22 Processing helix chain 'K' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL K 32 " --> pdb=" O TYR K 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA K 33 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 77 removed outlier: 3.819A pdb=" N ASN K 68 " --> pdb=" O ASN K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU K 93 " --> pdb=" O ILE K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 110 No H-bonds generated for 'chain 'K' and resid 108 through 110' Processing helix chain 'K' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR K 177 " --> pdb=" O PHE K 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL K 178 " --> pdb=" O GLU K 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG K 183 " --> pdb=" O GLU K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 303 Processing helix chain 'K' and resid 305 through 310 Processing helix chain 'K' and resid 327 through 353 removed outlier: 4.402A pdb=" N LYS K 347 " --> pdb=" O SER K 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR K 349 " --> pdb=" O ASN K 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS K 350 " --> pdb=" O LEU K 346 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 389 Processing helix chain 'K' and resid 393 through 404 Processing helix chain 'L' and resid 14 through 22 Processing helix chain 'L' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL L 32 " --> pdb=" O TYR L 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA L 33 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU L 37 " --> pdb=" O ALA L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU L 93 " --> pdb=" O ILE L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 110 No H-bonds generated for 'chain 'L' and resid 108 through 110' Processing helix chain 'L' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR L 177 " --> pdb=" O PHE L 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL L 178 " --> pdb=" O GLU L 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG L 183 " --> pdb=" O GLU L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 303 Processing helix chain 'L' and resid 305 through 310 Processing helix chain 'L' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS L 347 " --> pdb=" O SER L 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR L 349 " --> pdb=" O ASN L 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS L 350 " --> pdb=" O LEU L 346 " (cutoff:3.500A) Processing helix chain 'L' and resid 365 through 389 Processing helix chain 'L' and resid 393 through 404 Processing sheet with id=1, first strand: chain 'A' and resid 41 through 45 Processing sheet with id=2, first strand: chain 'A' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR A 80 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=4, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=5, first strand: chain 'A' and resid 188 through 193 Processing sheet with id=6, first strand: chain 'B' and resid 41 through 45 Processing sheet with id=7, first strand: chain 'B' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR B 80 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 112 through 113 Processing sheet with id=9, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=10, first strand: chain 'B' and resid 188 through 193 Processing sheet with id=11, first strand: chain 'C' and resid 41 through 45 Processing sheet with id=12, first strand: chain 'C' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR C 80 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 112 through 113 Processing sheet with id=14, first strand: chain 'C' and resid 151 through 152 Processing sheet with id=15, first strand: chain 'C' and resid 188 through 193 Processing sheet with id=16, first strand: chain 'D' and resid 41 through 45 Processing sheet with id=17, first strand: chain 'D' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR D 80 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=19, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=20, first strand: chain 'D' and resid 188 through 193 Processing sheet with id=21, first strand: chain 'E' and resid 41 through 45 Processing sheet with id=22, first strand: chain 'E' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR E 80 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 112 through 113 Processing sheet with id=24, first strand: chain 'E' and resid 151 through 152 Processing sheet with id=25, first strand: chain 'E' and resid 188 through 193 Processing sheet with id=26, first strand: chain 'F' and resid 41 through 45 Processing sheet with id=27, first strand: chain 'F' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR F 80 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'F' and resid 112 through 113 Processing sheet with id=29, first strand: chain 'F' and resid 151 through 152 Processing sheet with id=30, first strand: chain 'F' and resid 188 through 193 Processing sheet with id=31, first strand: chain 'G' and resid 41 through 45 Processing sheet with id=32, first strand: chain 'G' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR G 80 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'G' and resid 112 through 113 Processing sheet with id=34, first strand: chain 'G' and resid 151 through 152 Processing sheet with id=35, first strand: chain 'G' and resid 188 through 193 Processing sheet with id=36, first strand: chain 'H' and resid 41 through 45 Processing sheet with id=37, first strand: chain 'H' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR H 80 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'H' and resid 112 through 113 Processing sheet with id=39, first strand: chain 'H' and resid 151 through 152 Processing sheet with id=40, first strand: chain 'H' and resid 188 through 193 Processing sheet with id=41, first strand: chain 'I' and resid 41 through 45 Processing sheet with id=42, first strand: chain 'I' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR I 80 " --> pdb=" O LEU I 107 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'I' and resid 112 through 113 Processing sheet with id=44, first strand: chain 'I' and resid 151 through 152 Processing sheet with id=45, first strand: chain 'I' and resid 188 through 193 Processing sheet with id=46, first strand: chain 'J' and resid 41 through 45 Processing sheet with id=47, first strand: chain 'J' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR J 80 " --> pdb=" O LEU J 107 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'J' and resid 112 through 113 Processing sheet with id=49, first strand: chain 'J' and resid 151 through 152 Processing sheet with id=50, first strand: chain 'J' and resid 188 through 193 Processing sheet with id=51, first strand: chain 'K' and resid 41 through 45 Processing sheet with id=52, first strand: chain 'K' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR K 80 " --> pdb=" O LEU K 107 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'K' and resid 112 through 113 Processing sheet with id=54, first strand: chain 'K' and resid 151 through 152 Processing sheet with id=55, first strand: chain 'K' and resid 188 through 193 Processing sheet with id=56, first strand: chain 'L' and resid 41 through 45 Processing sheet with id=57, first strand: chain 'L' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR L 80 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'L' and resid 112 through 113 Processing sheet with id=59, first strand: chain 'L' and resid 151 through 152 Processing sheet with id=60, first strand: chain 'L' and resid 188 through 193 1740 hydrogen bonds defined for protein. 5040 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: 6.66 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9912 1.34 - 1.46: 7388 1.46 - 1.58: 14596 1.58 - 1.70: 0 1.70 - 1.81: 144 Bond restraints: 32040 Sorted by residual: bond pdb=" CB ASN E 394 " pdb=" CG ASN E 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.83e+00 bond pdb=" CB ASN B 394 " pdb=" CG ASN B 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.83e+00 bond pdb=" CB ASN H 394 " pdb=" CG ASN H 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.83e+00 bond pdb=" CB ASN K 394 " pdb=" CG ASN K 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.83e+00 bond pdb=" CB ASN J 394 " pdb=" CG ASN J 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.77e+00 ... (remaining 32035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 39038 1.20 - 2.40: 3300 2.40 - 3.59: 574 3.59 - 4.79: 180 4.79 - 5.99: 36 Bond angle restraints: 43128 Sorted by residual: angle pdb=" CB ARG J 326 " pdb=" CG ARG J 326 " pdb=" CD ARG J 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 angle pdb=" CB ARG A 326 " pdb=" CG ARG A 326 " pdb=" CD ARG A 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 angle pdb=" CB ARG D 326 " pdb=" CG ARG D 326 " pdb=" CD ARG D 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 angle pdb=" CB ARG G 326 " pdb=" CG ARG G 326 " pdb=" CD ARG G 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 angle pdb=" CB ARG F 326 " pdb=" CG ARG F 326 " pdb=" CD ARG F 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 ... (remaining 43123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 17616 16.52 - 33.03: 1296 33.03 - 49.55: 288 49.55 - 66.07: 96 66.07 - 82.58: 60 Dihedral angle restraints: 19356 sinusoidal: 8004 harmonic: 11352 Sorted by residual: dihedral pdb=" CB GLU F 266 " pdb=" CG GLU F 266 " pdb=" CD GLU F 266 " pdb=" OE1 GLU F 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.58 -82.58 1 3.00e+01 1.11e-03 9.29e+00 dihedral pdb=" CB GLU L 266 " pdb=" CG GLU L 266 " pdb=" CD GLU L 266 " pdb=" OE1 GLU L 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.58 -82.58 1 3.00e+01 1.11e-03 9.29e+00 dihedral pdb=" CB GLU I 266 " pdb=" CG GLU I 266 " pdb=" CD GLU I 266 " pdb=" OE1 GLU I 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.58 -82.58 1 3.00e+01 1.11e-03 9.29e+00 ... (remaining 19353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4210 0.085 - 0.171: 482 0.171 - 0.256: 12 0.256 - 0.341: 48 0.341 - 0.427: 12 Chirality restraints: 4764 Sorted by residual: chirality pdb=" CG LEU I 115 " pdb=" CB LEU I 115 " pdb=" CD1 LEU I 115 " pdb=" CD2 LEU I 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CG LEU L 115 " pdb=" CB LEU L 115 " pdb=" CD1 LEU L 115 " pdb=" CD2 LEU L 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CG LEU F 115 " pdb=" CB LEU F 115 " pdb=" CD1 LEU F 115 " pdb=" CD2 LEU F 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 4761 not shown) Planarity restraints: 5448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN L 150 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" CG ASN L 150 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN L 150 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN L 150 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 150 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" CG ASN I 150 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN I 150 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN I 150 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 150 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" CG ASN C 150 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN C 150 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 150 " -0.016 2.00e-02 2.50e+03 ... (remaining 5445 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 396 2.68 - 3.24: 30172 3.24 - 3.79: 50584 3.79 - 4.35: 72748 4.35 - 4.90: 113646 Nonbonded interactions: 267546 Sorted by model distance: nonbonded pdb=" O HOH G 502 " pdb=" O HOH G 533 " model vdw 2.128 3.040 nonbonded pdb=" O HOH D 502 " pdb=" O HOH D 533 " model vdw 2.128 3.040 nonbonded pdb=" O HOH J 502 " pdb=" O HOH J 533 " model vdw 2.128 3.040 nonbonded pdb=" O HOH A 502 " pdb=" O HOH A 533 " model vdw 2.128 3.040 nonbonded pdb=" O HOH I 502 " pdb=" O HOH I 533 " model vdw 2.128 3.040 ... (remaining 267541 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' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 25.090 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 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 : 0.005 0.044 32040 Z= 0.212 Angle : 0.766 5.989 43128 Z= 0.406 Chirality : 0.062 0.427 4764 Planarity : 0.010 0.072 5448 Dihedral : 13.642 82.583 12060 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.13), residues: 3732 helix: 0.55 (0.11), residues: 2004 sheet: -0.38 (0.21), residues: 624 loop : -0.58 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.005 ARG I 157 TYR 0.036 0.008 TYR D 192 PHE 0.034 0.008 PHE I 358 HIS 0.024 0.007 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (32040) covalent geometry : angle 0.76648 / 0.41 (43128) hydrogen bonds : bond 0.15495 / 10.09 ( 1740) hydrogen bonds : angle 7.01158 / 4.88 ( 5040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 696 time to evaluate : 1.275 Fit side-chains REVERT: A 181 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7871 (tm-30) REVERT: A 326 ARG cc_start: 0.7114 (mmt90) cc_final: 0.6818 (mmt180) REVERT: A 382 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7647 (mmmt) REVERT: A 403 LYS cc_start: 0.6967 (ptmt) cc_final: 0.6558 (ptmt) REVERT: B 382 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7689 (mptt) REVERT: C 121 HIS cc_start: 0.7593 (p-80) cc_final: 0.7383 (p-80) REVERT: C 185 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7307 (mp0) REVERT: C 363 MET cc_start: 0.7464 (mtp) cc_final: 0.7080 (mmt) REVERT: C 382 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7606 (mmmt) REVERT: D 181 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7869 (tm-30) REVERT: D 326 ARG cc_start: 0.7114 (mmt90) cc_final: 0.6818 (mmt180) REVERT: D 382 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7646 (mmmt) REVERT: D 403 LYS cc_start: 0.6963 (ptmt) cc_final: 0.6555 (ptmt) REVERT: E 382 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7690 (mptt) REVERT: F 121 HIS cc_start: 0.7593 (p-80) cc_final: 0.7384 (p-80) REVERT: F 185 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7308 (mp0) REVERT: F 363 MET cc_start: 0.7467 (mtp) cc_final: 0.7082 (mmt) REVERT: F 382 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7608 (mmmt) REVERT: G 181 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7868 (tm-30) REVERT: G 326 ARG cc_start: 0.7114 (mmt90) cc_final: 0.6819 (mmt180) REVERT: G 382 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7646 (mmmt) REVERT: G 403 LYS cc_start: 0.6964 (ptmt) cc_final: 0.6556 (ptmt) REVERT: H 382 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7689 (mptt) REVERT: I 121 HIS cc_start: 0.7592 (p-80) cc_final: 0.7382 (p-80) REVERT: I 185 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7308 (mp0) REVERT: I 363 MET cc_start: 0.7466 (mtp) cc_final: 0.7082 (mmt) REVERT: I 382 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7609 (mmmt) REVERT: J 181 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7868 (tm-30) REVERT: J 326 ARG cc_start: 0.7115 (mmt90) cc_final: 0.6820 (mmt180) REVERT: J 382 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7644 (mmmt) REVERT: J 403 LYS cc_start: 0.6964 (ptmt) cc_final: 0.6556 (ptmt) REVERT: K 382 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7689 (mptt) REVERT: L 121 HIS cc_start: 0.7591 (p-80) cc_final: 0.7382 (p-80) REVERT: L 185 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7306 (mp0) REVERT: L 363 MET cc_start: 0.7465 (mtp) cc_final: 0.7081 (mmt) REVERT: L 382 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7610 (mmmt) outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 0.9771 time to fit residues: 769.0156 Evaluate side-chains 492 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN A 121 HIS A 314 GLN A 368 GLN A 388 GLN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 314 GLN B 320 ASN B 388 GLN C 314 GLN C 320 ASN C 393 ASN D 94 GLN D 121 HIS D 314 GLN D 368 GLN D 388 GLN ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 314 GLN E 320 ASN E 388 GLN F 314 GLN F 393 ASN G 94 GLN G 121 HIS G 314 GLN G 368 GLN G 388 GLN ** H 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN H 314 GLN H 320 ASN H 388 GLN I 314 GLN I 320 ASN I 393 ASN J 94 GLN J 121 HIS J 314 GLN J 368 GLN J 388 GLN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 ASN K 314 GLN K 320 ASN K 388 GLN L 314 GLN L 320 ASN L 393 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119128 restraints weight = 32351.013| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.20 r_work: 0.3164 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 32040 Z= 0.142 Angle : 0.508 4.505 43128 Z= 0.288 Chirality : 0.041 0.136 4764 Planarity : 0.004 0.030 5448 Dihedral : 4.305 25.612 4200 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 1.95 % Allowed : 8.51 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.14), residues: 3732 helix: 1.63 (0.12), residues: 2028 sheet: -0.07 (0.22), residues: 600 loop : -0.34 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 372 TYR 0.024 0.002 TYR I 177 PHE 0.017 0.002 PHE K 269 HIS 0.006 0.001 HIS L 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (32040) covalent geometry : angle 0.50832 / 0.29 (43128) hydrogen bonds : bond 0.06151 / 4.05 ( 1740) hydrogen bonds : angle 5.12830 / 3.53 ( 5040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 524 time to evaluate : 1.359 Fit side-chains REVERT: A 181 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 185 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7130 (mp0) REVERT: B 120 ASP cc_start: 0.7607 (p0) cc_final: 0.7277 (p0) REVERT: B 121 HIS cc_start: 0.7811 (p-80) cc_final: 0.7590 (p-80) REVERT: B 144 ARG cc_start: 0.8293 (mtt-85) cc_final: 0.8055 (mtt-85) REVERT: B 181 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: B 357 LYS cc_start: 0.8104 (tppt) cc_final: 0.7490 (tttm) REVERT: B 403 LYS cc_start: 0.7433 (ttpt) cc_final: 0.6862 (tttt) REVERT: C 64 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7794 (t0) REVERT: C 121 HIS cc_start: 0.7801 (p-80) cc_final: 0.7571 (p-80) REVERT: C 185 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7037 (mp0) REVERT: D 181 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7912 (tm-30) REVERT: D 185 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7130 (mp0) REVERT: D 403 LYS cc_start: 0.6955 (ptmt) cc_final: 0.6754 (ptmt) REVERT: E 120 ASP cc_start: 0.7603 (p0) cc_final: 0.7275 (p0) REVERT: E 121 HIS cc_start: 0.7803 (p-80) cc_final: 0.7584 (p-80) REVERT: E 144 ARG cc_start: 0.8304 (mtt-85) cc_final: 0.8064 (mtt-85) REVERT: E 181 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: E 357 LYS cc_start: 0.8105 (tppt) cc_final: 0.7499 (tttm) REVERT: E 403 LYS cc_start: 0.7431 (ttpt) cc_final: 0.6859 (tttt) REVERT: F 64 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7789 (t0) REVERT: F 121 HIS cc_start: 0.7802 (p-80) cc_final: 0.7575 (p-80) REVERT: F 185 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7034 (mp0) REVERT: G 181 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7905 (tm-30) REVERT: G 185 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7135 (mp0) REVERT: G 403 LYS cc_start: 0.6954 (ptmt) cc_final: 0.6753 (ptmt) REVERT: H 120 ASP cc_start: 0.7608 (p0) cc_final: 0.7281 (p0) REVERT: H 121 HIS cc_start: 0.7803 (p-80) cc_final: 0.7585 (p-80) REVERT: H 144 ARG cc_start: 0.8303 (mtt-85) cc_final: 0.8062 (mtt-85) REVERT: H 181 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: H 357 LYS cc_start: 0.8106 (tppt) cc_final: 0.7501 (tttm) REVERT: H 403 LYS cc_start: 0.7430 (ttpt) cc_final: 0.6857 (tttt) REVERT: I 64 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7796 (t0) REVERT: I 121 HIS cc_start: 0.7807 (p-80) cc_final: 0.7580 (p-80) REVERT: I 185 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7031 (mp0) REVERT: I 402 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.6163 (mp0) REVERT: J 181 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7916 (tm-30) REVERT: J 185 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7123 (mp0) REVERT: K 120 ASP cc_start: 0.7602 (p0) cc_final: 0.7274 (p0) REVERT: K 121 HIS cc_start: 0.7800 (p-80) cc_final: 0.7580 (p-80) REVERT: K 144 ARG cc_start: 0.8301 (mtt-85) cc_final: 0.8063 (mtt-85) REVERT: K 181 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: K 357 LYS cc_start: 0.8103 (tppt) cc_final: 0.7492 (tttm) REVERT: K 403 LYS cc_start: 0.7432 (ttpt) cc_final: 0.6862 (tttt) REVERT: L 64 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7792 (t0) REVERT: L 121 HIS cc_start: 0.7802 (p-80) cc_final: 0.7572 (p-80) REVERT: L 185 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7037 (mp0) REVERT: L 402 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.6159 (mp0) outliers start: 68 outliers final: 20 residues processed: 564 average time/residue: 0.9834 time to fit residues: 627.0810 Evaluate side-chains 486 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 456 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 57 ARG Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 402 GLU Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain K residue 181 GLU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 64 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 402 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 70 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 360 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 313 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 357 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 280 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS A 314 GLN A 388 GLN B 121 HIS B 314 GLN B 320 ASN C 314 GLN C 320 ASN C 393 ASN D 121 HIS D 314 GLN D 388 GLN E 121 HIS E 314 GLN E 320 ASN F 314 GLN F 320 ASN F 393 ASN G 121 HIS G 314 GLN G 388 GLN H 121 HIS H 314 GLN H 320 ASN I 314 GLN I 320 ASN I 393 ASN J 121 HIS J 314 GLN J 388 GLN K 121 HIS K 314 GLN K 320 ASN L 314 GLN L 320 ASN L 393 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.145136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116207 restraints weight = 32100.829| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.19 r_work: 0.3107 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 32040 Z= 0.198 Angle : 0.592 4.719 43128 Z= 0.332 Chirality : 0.044 0.140 4764 Planarity : 0.004 0.044 5448 Dihedral : 4.741 38.349 4200 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 2.36 % Allowed : 9.08 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.14), residues: 3732 helix: 1.35 (0.12), residues: 2028 sheet: -0.14 (0.22), residues: 600 loop : -0.58 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 182 TYR 0.028 0.002 TYR K 177 PHE 0.023 0.002 PHE K 269 HIS 0.005 0.002 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (32040) covalent geometry : angle 0.59183 / 0.33 (43128) hydrogen bonds : bond 0.07221 / 4.75 ( 1740) hydrogen bonds : angle 5.24757 / 3.59 ( 5040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 486 time to evaluate : 1.234 Fit side-chains REVERT: A 357 LYS cc_start: 0.7996 (tppp) cc_final: 0.7519 (tttm) REVERT: B 120 ASP cc_start: 0.7526 (p0) cc_final: 0.7169 (p0) REVERT: B 144 ARG cc_start: 0.8324 (mtt-85) cc_final: 0.8083 (mtt-85) REVERT: B 170 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8768 (mm) REVERT: B 181 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: B 403 LYS cc_start: 0.7388 (ttpt) cc_final: 0.6786 (tttt) REVERT: C 64 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7937 (t0) REVERT: D 357 LYS cc_start: 0.7994 (tppp) cc_final: 0.7517 (tttm) REVERT: D 403 LYS cc_start: 0.6966 (ptmt) cc_final: 0.6650 (ptmt) REVERT: E 120 ASP cc_start: 0.7528 (p0) cc_final: 0.7168 (p0) REVERT: E 144 ARG cc_start: 0.8328 (mtt-85) cc_final: 0.8084 (mtt-85) REVERT: E 170 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8763 (mm) REVERT: E 181 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: E 403 LYS cc_start: 0.7386 (ttpt) cc_final: 0.6787 (tttt) REVERT: F 64 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7940 (t0) REVERT: G 357 LYS cc_start: 0.7997 (tppp) cc_final: 0.7522 (tttm) REVERT: G 403 LYS cc_start: 0.6965 (ptmt) cc_final: 0.6648 (ptmt) REVERT: H 120 ASP cc_start: 0.7530 (p0) cc_final: 0.7173 (p0) REVERT: H 144 ARG cc_start: 0.8323 (mtt-85) cc_final: 0.8082 (mtt-85) REVERT: H 170 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8762 (mm) REVERT: H 181 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: H 403 LYS cc_start: 0.7388 (ttpt) cc_final: 0.6788 (tttt) REVERT: I 64 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7946 (t0) REVERT: J 357 LYS cc_start: 0.7993 (tppp) cc_final: 0.7518 (tttm) REVERT: K 120 ASP cc_start: 0.7518 (p0) cc_final: 0.7159 (p0) REVERT: K 144 ARG cc_start: 0.8324 (mtt-85) cc_final: 0.8082 (mtt-85) REVERT: K 170 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8764 (mm) REVERT: K 181 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: K 403 LYS cc_start: 0.7387 (ttpt) cc_final: 0.6785 (tttt) REVERT: L 64 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7945 (t0) outliers start: 82 outliers final: 32 residues processed: 516 average time/residue: 0.9321 time to fit residues: 547.3766 Evaluate side-chains 510 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 466 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 57 ARG Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 181 GLU Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 64 ASN Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 89 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 332 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 300 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 388 GLN B 314 GLN B 320 ASN C 314 GLN C 320 ASN C 388 GLN C 393 ASN D 314 GLN D 388 GLN E 314 GLN E 320 ASN F 314 GLN F 320 ASN F 388 GLN F 393 ASN G 314 GLN G 388 GLN H 314 GLN H 320 ASN I 314 GLN I 388 GLN I 393 ASN J 314 GLN J 388 GLN K 314 GLN K 320 ASN L 314 GLN L 320 ASN L 388 GLN L 393 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116730 restraints weight = 31959.558| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.16 r_work: 0.3127 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 32040 Z= 0.170 Angle : 0.543 4.553 43128 Z= 0.308 Chirality : 0.042 0.139 4764 Planarity : 0.004 0.038 5448 Dihedral : 4.708 40.520 4200 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.16 % Allowed : 9.34 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.14), residues: 3732 helix: 1.36 (0.12), residues: 2028 sheet: -0.07 (0.22), residues: 600 loop : -0.60 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 309 TYR 0.026 0.002 TYR B 177 PHE 0.021 0.002 PHE E 269 HIS 0.004 0.001 HIS H 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (32040) covalent geometry : angle 0.54333 / 0.31 (43128) hydrogen bonds : bond 0.06690 / 4.40 ( 1740) hydrogen bonds : angle 5.08031 / 3.47 ( 5040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 484 time to evaluate : 1.303 Fit side-chains REVERT: B 120 ASP cc_start: 0.7517 (p0) cc_final: 0.7124 (p0) REVERT: B 144 ARG cc_start: 0.8295 (mtt-85) cc_final: 0.8052 (mtt-85) REVERT: B 170 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8750 (mm) REVERT: B 181 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7959 (tt0) REVERT: B 403 LYS cc_start: 0.7397 (ttpt) cc_final: 0.6751 (tttt) REVERT: D 403 LYS cc_start: 0.7044 (ptmt) cc_final: 0.6791 (ptmt) REVERT: E 120 ASP cc_start: 0.7516 (p0) cc_final: 0.7125 (p0) REVERT: E 144 ARG cc_start: 0.8295 (mtt-85) cc_final: 0.8051 (mtt-85) REVERT: E 170 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8745 (mm) REVERT: E 181 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: E 403 LYS cc_start: 0.7395 (ttpt) cc_final: 0.6751 (tttt) REVERT: G 403 LYS cc_start: 0.7047 (ptmt) cc_final: 0.6793 (ptmt) REVERT: H 120 ASP cc_start: 0.7520 (p0) cc_final: 0.7126 (p0) REVERT: H 144 ARG cc_start: 0.8291 (mtt-85) cc_final: 0.8048 (mtt-85) REVERT: H 170 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8744 (mm) REVERT: H 181 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: H 403 LYS cc_start: 0.7397 (ttpt) cc_final: 0.6750 (tttt) REVERT: I 403 LYS cc_start: 0.7483 (ttpt) cc_final: 0.7184 (mtmm) REVERT: K 120 ASP cc_start: 0.7513 (p0) cc_final: 0.7120 (p0) REVERT: K 144 ARG cc_start: 0.8294 (mtt-85) cc_final: 0.8052 (mtt-85) REVERT: K 170 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8746 (mm) REVERT: K 181 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: K 403 LYS cc_start: 0.7398 (ttpt) cc_final: 0.6752 (tttt) REVERT: L 372 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7593 (mmm-85) REVERT: L 403 LYS cc_start: 0.7484 (ttpt) cc_final: 0.7186 (mtmm) outliers start: 75 outliers final: 36 residues processed: 523 average time/residue: 0.9655 time to fit residues: 572.2798 Evaluate side-chains 501 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 456 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 57 ARG Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 181 GLU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 372 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 155 optimal weight: 10.0000 chunk 353 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 172 optimal weight: 0.0870 chunk 195 optimal weight: 7.9990 chunk 369 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN B 314 GLN B 320 ASN C 314 GLN C 320 ASN C 388 GLN C 393 ASN D 314 GLN E 314 GLN E 320 ASN F 314 GLN F 388 GLN F 393 ASN G 314 GLN G 388 GLN H 314 GLN H 320 ASN I 314 GLN I 388 GLN I 393 ASN J 314 GLN K 314 GLN K 320 ASN L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.145967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116634 restraints weight = 31948.980| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.18 r_work: 0.3127 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 32040 Z= 0.155 Angle : 0.519 4.426 43128 Z= 0.295 Chirality : 0.042 0.140 4764 Planarity : 0.003 0.034 5448 Dihedral : 4.653 40.238 4200 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.04 % Allowed : 10.09 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.14), residues: 3732 helix: 1.46 (0.12), residues: 2028 sheet: -0.05 (0.22), residues: 600 loop : -0.55 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 309 TYR 0.025 0.002 TYR K 177 PHE 0.020 0.002 PHE H 269 HIS 0.003 0.001 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (32040) covalent geometry : angle 0.51933 / 0.29 (43128) hydrogen bonds : bond 0.06381 / 4.20 ( 1740) hydrogen bonds : angle 4.97981 / 3.40 ( 5040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 468 time to evaluate : 1.312 Fit side-chains REVERT: B 120 ASP cc_start: 0.7432 (p0) cc_final: 0.7027 (p0) REVERT: B 121 HIS cc_start: 0.7996 (p-80) cc_final: 0.7450 (p90) REVERT: B 139 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7274 (tttm) REVERT: B 144 ARG cc_start: 0.8286 (mtt-85) cc_final: 0.8045 (mtt-85) REVERT: B 181 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: B 403 LYS cc_start: 0.7374 (ttpt) cc_final: 0.6785 (tttt) REVERT: C 185 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7177 (mp0) REVERT: C 372 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7547 (mmm-85) REVERT: C 402 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6296 (mp0) REVERT: D 403 LYS cc_start: 0.6989 (ptmt) cc_final: 0.6770 (ptmt) REVERT: E 120 ASP cc_start: 0.7426 (p0) cc_final: 0.7018 (p0) REVERT: E 121 HIS cc_start: 0.8002 (p-80) cc_final: 0.7454 (p90) REVERT: E 139 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7276 (tttm) REVERT: E 144 ARG cc_start: 0.8289 (mtt-85) cc_final: 0.8048 (mtt-85) REVERT: E 181 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: E 403 LYS cc_start: 0.7373 (ttpt) cc_final: 0.6785 (tttt) REVERT: F 185 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7173 (mp0) REVERT: F 372 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7547 (mmm-85) REVERT: F 402 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6290 (mp0) REVERT: G 403 LYS cc_start: 0.6995 (ptmt) cc_final: 0.6776 (ptmt) REVERT: H 120 ASP cc_start: 0.7429 (p0) cc_final: 0.7022 (p0) REVERT: H 121 HIS cc_start: 0.8002 (p-80) cc_final: 0.7454 (p90) REVERT: H 139 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7274 (tttm) REVERT: H 144 ARG cc_start: 0.8284 (mtt-85) cc_final: 0.8044 (mtt-85) REVERT: H 181 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: H 403 LYS cc_start: 0.7377 (ttpt) cc_final: 0.6787 (tttt) REVERT: I 185 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7173 (mp0) REVERT: I 372 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7547 (mmm-85) REVERT: I 403 LYS cc_start: 0.7507 (ttpt) cc_final: 0.7178 (mtmm) REVERT: K 120 ASP cc_start: 0.7420 (p0) cc_final: 0.7013 (p0) REVERT: K 121 HIS cc_start: 0.7991 (p-80) cc_final: 0.7436 (p90) REVERT: K 139 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7278 (tttm) REVERT: K 144 ARG cc_start: 0.8284 (mtt-85) cc_final: 0.8046 (mtt-85) REVERT: K 181 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: K 403 LYS cc_start: 0.7374 (ttpt) cc_final: 0.6784 (tttt) REVERT: L 185 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7177 (mp0) REVERT: L 403 LYS cc_start: 0.7505 (ttpt) cc_final: 0.7177 (mtmm) outliers start: 71 outliers final: 26 residues processed: 517 average time/residue: 0.9706 time to fit residues: 568.8072 Evaluate side-chains 488 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 449 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 372 ARG Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 139 LYS Chi-restraints excluded: chain K residue 181 GLU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 64 ASN Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 244 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 269 optimal weight: 0.7980 chunk 192 optimal weight: 7.9990 chunk 268 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN B 314 GLN B 320 ASN C 121 HIS C 314 GLN C 320 ASN C 388 GLN C 393 ASN D 314 GLN E 314 GLN E 320 ASN F 121 HIS F 314 GLN F 320 ASN F 393 ASN G 314 GLN H 314 GLN H 320 ASN I 121 HIS I 314 GLN I 388 GLN I 393 ASN J 314 GLN J 388 GLN K 314 GLN K 320 ASN L 121 HIS L 314 GLN L 320 ASN L 388 GLN L 393 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.145870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.116936 restraints weight = 31810.562| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.17 r_work: 0.3122 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 32040 Z= 0.160 Angle : 0.531 4.480 43128 Z= 0.301 Chirality : 0.042 0.141 4764 Planarity : 0.003 0.033 5448 Dihedral : 4.678 40.279 4200 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.95 % Allowed : 10.29 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.14), residues: 3732 helix: 1.43 (0.12), residues: 2028 sheet: -0.06 (0.22), residues: 600 loop : -0.56 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 182 TYR 0.025 0.002 TYR K 177 PHE 0.020 0.002 PHE H 269 HIS 0.004 0.001 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (32040) covalent geometry : angle 0.53129 / 0.30 (43128) hydrogen bonds : bond 0.06499 / 4.28 ( 1740) hydrogen bonds : angle 4.98296 / 3.39 ( 5040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 462 time to evaluate : 1.291 Fit side-chains REVERT: A 185 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7308 (mp0) REVERT: A 357 LYS cc_start: 0.8013 (tppp) cc_final: 0.7508 (tttm) REVERT: B 120 ASP cc_start: 0.7423 (p0) cc_final: 0.7021 (p0) REVERT: B 121 HIS cc_start: 0.8040 (p-80) cc_final: 0.7475 (p90) REVERT: B 139 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7316 (tttm) REVERT: B 181 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: B 403 LYS cc_start: 0.7413 (ttpt) cc_final: 0.6805 (tttt) REVERT: C 185 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7299 (mp0) REVERT: C 403 LYS cc_start: 0.7528 (ttpt) cc_final: 0.7287 (mtmm) REVERT: D 185 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7312 (mp0) REVERT: D 357 LYS cc_start: 0.8008 (tppp) cc_final: 0.7503 (tttm) REVERT: D 403 LYS cc_start: 0.7044 (ptmt) cc_final: 0.6829 (ptmt) REVERT: E 120 ASP cc_start: 0.7421 (p0) cc_final: 0.7020 (p0) REVERT: E 121 HIS cc_start: 0.8041 (p-80) cc_final: 0.7484 (p90) REVERT: E 139 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7318 (tttm) REVERT: E 181 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: E 403 LYS cc_start: 0.7414 (ttpt) cc_final: 0.6808 (tttt) REVERT: F 185 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7293 (mp0) REVERT: F 403 LYS cc_start: 0.7528 (ttpt) cc_final: 0.7288 (mtmm) REVERT: G 185 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7310 (mp0) REVERT: G 357 LYS cc_start: 0.8012 (tppp) cc_final: 0.7509 (tttm) REVERT: G 403 LYS cc_start: 0.7049 (ptmt) cc_final: 0.6837 (ptmt) REVERT: H 120 ASP cc_start: 0.7424 (p0) cc_final: 0.7021 (p0) REVERT: H 121 HIS cc_start: 0.8043 (p-80) cc_final: 0.7476 (p90) REVERT: H 139 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7315 (tttm) REVERT: H 181 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: H 403 LYS cc_start: 0.7416 (ttpt) cc_final: 0.6808 (tttt) REVERT: I 185 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7298 (mp0) REVERT: I 403 LYS cc_start: 0.7519 (ttpt) cc_final: 0.7282 (mtmm) REVERT: J 185 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7298 (mp0) REVERT: J 357 LYS cc_start: 0.8014 (tppp) cc_final: 0.7513 (tttm) REVERT: K 120 ASP cc_start: 0.7415 (p0) cc_final: 0.7012 (p0) REVERT: K 121 HIS cc_start: 0.8039 (p-80) cc_final: 0.7468 (p90) REVERT: K 139 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7315 (tttm) REVERT: K 181 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: K 403 LYS cc_start: 0.7413 (ttpt) cc_final: 0.6806 (tttt) REVERT: L 185 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7298 (mp0) REVERT: L 403 LYS cc_start: 0.7521 (ttpt) cc_final: 0.7284 (mtmm) outliers start: 68 outliers final: 33 residues processed: 502 average time/residue: 0.9447 time to fit residues: 537.4845 Evaluate side-chains 509 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 468 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 139 LYS Chi-restraints excluded: chain K residue 181 GLU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 64 ASN Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 1 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 352 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN B 314 GLN B 320 ASN C 121 HIS C 314 GLN C 320 ASN C 393 ASN D 314 GLN E 314 GLN E 320 ASN F 121 HIS F 314 GLN F 320 ASN F 393 ASN G 314 GLN H 314 GLN H 320 ASN I 121 HIS I 314 GLN I 393 ASN J 314 GLN K 314 GLN K 320 ASN L 121 HIS L 314 GLN L 320 ASN L 393 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.145867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116824 restraints weight = 32023.121| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.17 r_work: 0.3120 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 32040 Z= 0.163 Angle : 0.538 4.613 43128 Z= 0.305 Chirality : 0.042 0.141 4764 Planarity : 0.004 0.033 5448 Dihedral : 4.690 40.322 4200 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.84 % Allowed : 10.69 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.85 (0.14), residues: 3732 helix: 1.41 (0.12), residues: 2028 sheet: -0.06 (0.22), residues: 600 loop : -0.54 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 309 TYR 0.025 0.002 TYR B 177 PHE 0.020 0.002 PHE H 269 HIS 0.004 0.001 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (32040) covalent geometry : angle 0.53799 / 0.30 (43128) hydrogen bonds : bond 0.06517 / 4.29 ( 1740) hydrogen bonds : angle 4.97887 / 3.39 ( 5040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 464 time to evaluate : 1.245 Fit side-chains REVERT: A 185 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7291 (mp0) REVERT: B 120 ASP cc_start: 0.7420 (p0) cc_final: 0.7018 (p0) REVERT: B 121 HIS cc_start: 0.8076 (p-80) cc_final: 0.7513 (p90) REVERT: B 139 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7294 (tttm) REVERT: B 144 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.8008 (mtt-85) REVERT: B 181 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: B 403 LYS cc_start: 0.7443 (ttpt) cc_final: 0.6847 (tttt) REVERT: C 185 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7295 (mp0) REVERT: C 403 LYS cc_start: 0.7528 (ttpt) cc_final: 0.7259 (mtmm) REVERT: D 185 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7294 (mp0) REVERT: D 403 LYS cc_start: 0.7043 (ptmt) cc_final: 0.6832 (ptmt) REVERT: E 120 ASP cc_start: 0.7422 (p0) cc_final: 0.7021 (p0) REVERT: E 121 HIS cc_start: 0.8082 (p-80) cc_final: 0.7518 (p90) REVERT: E 139 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7298 (tttm) REVERT: E 144 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.8009 (mtt-85) REVERT: E 181 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: E 403 LYS cc_start: 0.7446 (ttpt) cc_final: 0.6851 (tttt) REVERT: F 185 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7292 (mp0) REVERT: F 403 LYS cc_start: 0.7527 (ttpt) cc_final: 0.7260 (mtmm) REVERT: G 185 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7295 (mp0) REVERT: G 403 LYS cc_start: 0.7048 (ptmt) cc_final: 0.6839 (ptmt) REVERT: H 120 ASP cc_start: 0.7422 (p0) cc_final: 0.7021 (p0) REVERT: H 121 HIS cc_start: 0.8078 (p-80) cc_final: 0.7512 (p90) REVERT: H 139 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7296 (tttm) REVERT: H 144 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.8011 (mtt-85) REVERT: H 181 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: H 403 LYS cc_start: 0.7447 (ttpt) cc_final: 0.6852 (tttt) REVERT: I 185 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7293 (mp0) REVERT: I 403 LYS cc_start: 0.7532 (ttpt) cc_final: 0.7248 (mtmm) REVERT: J 185 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7281 (mp0) REVERT: K 120 ASP cc_start: 0.7411 (p0) cc_final: 0.7011 (p0) REVERT: K 121 HIS cc_start: 0.8074 (p-80) cc_final: 0.7505 (p90) REVERT: K 139 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7294 (tttm) REVERT: K 144 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.8009 (mtt-85) REVERT: K 181 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: K 403 LYS cc_start: 0.7443 (ttpt) cc_final: 0.6847 (tttt) REVERT: L 185 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7293 (mp0) REVERT: L 403 LYS cc_start: 0.7530 (ttpt) cc_final: 0.7250 (mtmm) outliers start: 64 outliers final: 30 residues processed: 506 average time/residue: 0.8915 time to fit residues: 511.4200 Evaluate side-chains 502 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 464 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 139 LYS Chi-restraints excluded: chain K residue 181 GLU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 64 ASN Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 72 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 287 optimal weight: 0.6980 chunk 259 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 367 optimal weight: 7.9990 chunk 366 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN B 314 GLN C 121 HIS C 314 GLN C 388 GLN C 393 ASN D 314 GLN E 314 GLN E 320 ASN F 121 HIS F 314 GLN F 388 GLN F 393 ASN G 314 GLN H 314 GLN I 121 HIS I 314 GLN I 388 GLN I 393 ASN J 314 GLN K 314 GLN L 121 HIS L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119136 restraints weight = 32113.158| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.16 r_work: 0.3166 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32040 Z= 0.113 Angle : 0.463 5.621 43128 Z= 0.264 Chirality : 0.039 0.137 4764 Planarity : 0.003 0.023 5448 Dihedral : 4.389 39.213 4200 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 1.18 % Allowed : 11.35 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.14), residues: 3732 helix: 1.80 (0.12), residues: 2028 sheet: -0.02 (0.23), residues: 600 loop : -0.37 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 144 TYR 0.021 0.001 TYR B 177 PHE 0.015 0.001 PHE H 269 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (32040) covalent geometry : angle 0.46316 / 0.26 (43128) hydrogen bonds : bond 0.05167 / 3.40 ( 1740) hydrogen bonds : angle 4.61935 / 3.14 ( 5040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 486 time to evaluate : 1.317 Fit side-chains REVERT: A 185 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7271 (mp0) REVERT: A 326 ARG cc_start: 0.7407 (mmt90) cc_final: 0.7035 (mmt180) REVERT: A 357 LYS cc_start: 0.8007 (tppp) cc_final: 0.7485 (tttt) REVERT: B 120 ASP cc_start: 0.7412 (p0) cc_final: 0.7015 (p0) REVERT: B 121 HIS cc_start: 0.8047 (p-80) cc_final: 0.7548 (p90) REVERT: B 139 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7319 (tttm) REVERT: B 144 ARG cc_start: 0.8237 (mtt-85) cc_final: 0.7993 (mtt-85) REVERT: B 181 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: B 403 LYS cc_start: 0.7388 (ttpt) cc_final: 0.7104 (mtpp) REVERT: C 185 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7144 (mp0) REVERT: C 290 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7879 (mm-30) REVERT: C 403 LYS cc_start: 0.7507 (ttpt) cc_final: 0.7215 (mtmm) REVERT: D 185 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7278 (mp0) REVERT: D 326 ARG cc_start: 0.7407 (mmt90) cc_final: 0.7038 (mmt180) REVERT: D 357 LYS cc_start: 0.8008 (tppp) cc_final: 0.7483 (tttt) REVERT: E 120 ASP cc_start: 0.7412 (p0) cc_final: 0.7015 (p0) REVERT: E 121 HIS cc_start: 0.8040 (p-80) cc_final: 0.7592 (p90) REVERT: E 144 ARG cc_start: 0.8235 (mtt-85) cc_final: 0.7992 (mtt-85) REVERT: E 181 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: E 403 LYS cc_start: 0.7394 (ttpt) cc_final: 0.7109 (mtpp) REVERT: F 185 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7134 (mp0) REVERT: F 290 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7883 (mm-30) REVERT: F 403 LYS cc_start: 0.7508 (ttpt) cc_final: 0.7215 (mtmm) REVERT: G 185 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7285 (mp0) REVERT: G 326 ARG cc_start: 0.7406 (mmt90) cc_final: 0.7035 (mmt180) REVERT: G 357 LYS cc_start: 0.8009 (tppp) cc_final: 0.7492 (tttt) REVERT: H 120 ASP cc_start: 0.7421 (p0) cc_final: 0.7025 (p0) REVERT: H 121 HIS cc_start: 0.8042 (p-80) cc_final: 0.7537 (p90) REVERT: H 139 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7321 (tttm) REVERT: H 144 ARG cc_start: 0.8237 (mtt-85) cc_final: 0.7991 (mtt-85) REVERT: H 181 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: H 403 LYS cc_start: 0.7392 (ttpt) cc_final: 0.7109 (mtpp) REVERT: I 185 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7142 (mp0) REVERT: I 290 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7882 (mm-30) REVERT: I 403 LYS cc_start: 0.7500 (ttpt) cc_final: 0.7206 (mtmm) REVERT: J 185 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7272 (mp0) REVERT: J 326 ARG cc_start: 0.7407 (mmt90) cc_final: 0.7034 (mmt180) REVERT: J 357 LYS cc_start: 0.8010 (tppp) cc_final: 0.7485 (tttt) REVERT: K 120 ASP cc_start: 0.7412 (p0) cc_final: 0.7014 (p0) REVERT: K 121 HIS cc_start: 0.8044 (p-80) cc_final: 0.7537 (p90) REVERT: K 139 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7323 (tttm) REVERT: K 144 ARG cc_start: 0.8235 (mtt-85) cc_final: 0.7992 (mtt-85) REVERT: K 181 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: K 403 LYS cc_start: 0.7391 (ttpt) cc_final: 0.7109 (mtpp) REVERT: L 185 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7148 (mp0) REVERT: L 290 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: L 403 LYS cc_start: 0.7502 (ttpt) cc_final: 0.7211 (mtmm) outliers start: 41 outliers final: 10 residues processed: 513 average time/residue: 0.9836 time to fit residues: 570.1402 Evaluate side-chains 485 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 464 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain K residue 139 LYS Chi-restraints excluded: chain K residue 181 GLU Chi-restraints excluded: chain L residue 290 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 178 optimal weight: 8.9990 chunk 351 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN B 314 GLN B 320 ASN C 121 HIS C 314 GLN C 393 ASN D 314 GLN E 314 GLN E 320 ASN F 121 HIS F 314 GLN F 393 ASN G 314 GLN H 314 GLN H 320 ASN I 121 HIS I 314 GLN I 393 ASN J 314 GLN K 314 GLN K 320 ASN L 121 HIS L 314 GLN L 393 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.146110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117574 restraints weight = 31806.626| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.11 r_work: 0.3130 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32040 Z= 0.154 Angle : 0.532 5.777 43128 Z= 0.300 Chirality : 0.041 0.137 4764 Planarity : 0.003 0.031 5448 Dihedral : 4.591 40.266 4200 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.09 % Allowed : 12.13 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.14), residues: 3732 helix: 1.59 (0.12), residues: 2028 sheet: -0.05 (0.22), residues: 600 loop : -0.44 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 144 TYR 0.024 0.002 TYR E 177 PHE 0.019 0.002 PHE H 269 HIS 0.003 0.001 HIS D 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (32040) covalent geometry : angle 0.53219 / 0.30 (43128) hydrogen bonds : bond 0.06273 / 4.13 ( 1740) hydrogen bonds : angle 4.85910 / 3.30 ( 5040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 482 time to evaluate : 1.339 Fit side-chains REVERT: A 185 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7335 (mp0) REVERT: A 326 ARG cc_start: 0.7462 (mmt90) cc_final: 0.7067 (mmt180) REVERT: A 402 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5932 (mp0) REVERT: B 120 ASP cc_start: 0.7409 (p0) cc_final: 0.7026 (p0) REVERT: B 121 HIS cc_start: 0.8048 (p-80) cc_final: 0.7495 (p90) REVERT: B 139 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7299 (tttm) REVERT: B 144 ARG cc_start: 0.8269 (mtt-85) cc_final: 0.8019 (mtt-85) REVERT: B 181 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: B 403 LYS cc_start: 0.7408 (ttpt) cc_final: 0.7098 (mtpp) REVERT: C 185 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7317 (mp0) REVERT: C 403 LYS cc_start: 0.7553 (ttpt) cc_final: 0.7277 (mtmm) REVERT: D 185 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7331 (mp0) REVERT: D 326 ARG cc_start: 0.7464 (mmt90) cc_final: 0.7070 (mmt180) REVERT: E 120 ASP cc_start: 0.7413 (p0) cc_final: 0.7034 (p0) REVERT: E 121 HIS cc_start: 0.8054 (p-80) cc_final: 0.7501 (p90) REVERT: E 139 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7305 (tttm) REVERT: E 144 ARG cc_start: 0.8269 (mtt-85) cc_final: 0.8020 (mtt-85) REVERT: E 181 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: E 403 LYS cc_start: 0.7414 (ttpt) cc_final: 0.7104 (mtpp) REVERT: F 185 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7313 (mp0) REVERT: F 403 LYS cc_start: 0.7551 (ttpt) cc_final: 0.7278 (mtmm) REVERT: G 185 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7332 (mp0) REVERT: G 326 ARG cc_start: 0.7465 (mmt90) cc_final: 0.7070 (mmt180) REVERT: H 120 ASP cc_start: 0.7411 (p0) cc_final: 0.7031 (p0) REVERT: H 121 HIS cc_start: 0.8049 (p-80) cc_final: 0.7495 (p90) REVERT: H 139 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7301 (tttm) REVERT: H 144 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.8017 (mtt-85) REVERT: H 181 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: H 403 LYS cc_start: 0.7414 (ttpt) cc_final: 0.7104 (mtpp) REVERT: I 185 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7314 (mp0) REVERT: I 403 LYS cc_start: 0.7557 (ttpt) cc_final: 0.7271 (mtmm) REVERT: J 185 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7320 (mp0) REVERT: J 326 ARG cc_start: 0.7464 (mmt90) cc_final: 0.7069 (mmt180) REVERT: J 402 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5929 (mp0) REVERT: K 120 ASP cc_start: 0.7403 (p0) cc_final: 0.7021 (p0) REVERT: K 121 HIS cc_start: 0.8048 (p-80) cc_final: 0.7492 (p90) REVERT: K 139 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7298 (tttm) REVERT: K 144 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.8021 (mtt-85) REVERT: K 181 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: K 403 LYS cc_start: 0.7413 (ttpt) cc_final: 0.7103 (mtpp) REVERT: L 185 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7317 (mp0) REVERT: L 403 LYS cc_start: 0.7557 (ttpt) cc_final: 0.7274 (mtmm) outliers start: 38 outliers final: 13 residues processed: 506 average time/residue: 0.9329 time to fit residues: 534.4349 Evaluate side-chains 490 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 467 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 402 GLU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 139 LYS Chi-restraints excluded: chain K residue 181 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 316 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 193 optimal weight: 0.0370 chunk 363 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN B 314 GLN C 121 HIS C 314 GLN C 393 ASN D 314 GLN E 314 GLN E 320 ASN F 121 HIS F 314 GLN F 393 ASN G 314 GLN H 314 GLN H 320 ASN I 121 HIS I 314 GLN I 393 ASN J 314 GLN K 314 GLN L 121 HIS L 314 GLN L 393 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.147339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.118459 restraints weight = 32021.952| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.18 r_work: 0.3146 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32040 Z= 0.126 Angle : 0.495 6.274 43128 Z= 0.280 Chirality : 0.040 0.137 4764 Planarity : 0.003 0.026 5448 Dihedral : 4.450 39.636 4200 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.69 % Allowed : 12.64 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.14), residues: 3732 helix: 1.74 (0.12), residues: 2028 sheet: -0.01 (0.22), residues: 600 loop : -0.37 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 144 TYR 0.022 0.001 TYR B 177 PHE 0.018 0.001 PHE E 269 HIS 0.002 0.001 HIS J 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (32040) covalent geometry : angle 0.49471 / 0.28 (43128) hydrogen bonds : bond 0.05504 / 3.62 ( 1740) hydrogen bonds : angle 4.67775 / 3.18 ( 5040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 462 time to evaluate : 1.228 Fit side-chains REVERT: A 185 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7288 (mp0) REVERT: A 282 LYS cc_start: 0.8610 (mttm) cc_final: 0.8343 (mttm) REVERT: A 326 ARG cc_start: 0.7444 (mmt90) cc_final: 0.7045 (mmt180) REVERT: A 357 LYS cc_start: 0.7971 (tppp) cc_final: 0.7455 (tttt) REVERT: B 120 ASP cc_start: 0.7413 (p0) cc_final: 0.7032 (p0) REVERT: B 121 HIS cc_start: 0.8033 (p-80) cc_final: 0.7508 (p90) REVERT: B 144 ARG cc_start: 0.8246 (mtt-85) cc_final: 0.8013 (mtt-85) REVERT: B 181 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8035 (tt0) REVERT: B 403 LYS cc_start: 0.7405 (ttpt) cc_final: 0.7130 (mtpp) REVERT: C 185 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7268 (mp0) REVERT: C 403 LYS cc_start: 0.7506 (ttpt) cc_final: 0.7233 (mtmm) REVERT: D 185 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7291 (mp0) REVERT: D 282 LYS cc_start: 0.8604 (mttm) cc_final: 0.8337 (mttm) REVERT: D 326 ARG cc_start: 0.7443 (mmt90) cc_final: 0.7044 (mmt180) REVERT: D 357 LYS cc_start: 0.7970 (tppp) cc_final: 0.7453 (tttt) REVERT: E 120 ASP cc_start: 0.7418 (p0) cc_final: 0.7034 (p0) REVERT: E 121 HIS cc_start: 0.8035 (p-80) cc_final: 0.7511 (p90) REVERT: E 144 ARG cc_start: 0.8245 (mtt-85) cc_final: 0.8012 (mtt-85) REVERT: E 181 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: E 403 LYS cc_start: 0.7408 (ttpt) cc_final: 0.7134 (mtpp) REVERT: F 185 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7259 (mp0) REVERT: F 403 LYS cc_start: 0.7506 (ttpt) cc_final: 0.7234 (mtmm) REVERT: G 185 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7297 (mp0) REVERT: G 282 LYS cc_start: 0.8609 (mttm) cc_final: 0.8342 (mttm) REVERT: G 326 ARG cc_start: 0.7444 (mmt90) cc_final: 0.7043 (mmt180) REVERT: G 357 LYS cc_start: 0.7973 (tppp) cc_final: 0.7459 (tttt) REVERT: H 120 ASP cc_start: 0.7415 (p0) cc_final: 0.7035 (p0) REVERT: H 121 HIS cc_start: 0.8035 (p-80) cc_final: 0.7513 (p90) REVERT: H 144 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.8012 (mtt-85) REVERT: H 181 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: H 403 LYS cc_start: 0.7406 (ttpt) cc_final: 0.7134 (mtpp) REVERT: I 185 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7275 (mp0) REVERT: I 403 LYS cc_start: 0.7498 (ttpt) cc_final: 0.7222 (mtmm) REVERT: J 185 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7284 (mp0) REVERT: J 282 LYS cc_start: 0.8619 (mttm) cc_final: 0.8350 (mttm) REVERT: J 326 ARG cc_start: 0.7446 (mmt90) cc_final: 0.7047 (mmt180) REVERT: J 357 LYS cc_start: 0.7973 (tppp) cc_final: 0.7459 (tttt) REVERT: K 120 ASP cc_start: 0.7409 (p0) cc_final: 0.7030 (p0) REVERT: K 121 HIS cc_start: 0.8034 (p-80) cc_final: 0.7507 (p90) REVERT: K 144 ARG cc_start: 0.8245 (mtt-85) cc_final: 0.8013 (mtt-85) REVERT: K 181 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: K 403 LYS cc_start: 0.7406 (ttpt) cc_final: 0.7134 (mtpp) REVERT: L 185 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7270 (mp0) REVERT: L 403 LYS cc_start: 0.7501 (ttpt) cc_final: 0.7233 (mtmm) outliers start: 24 outliers final: 12 residues processed: 474 average time/residue: 0.9266 time to fit residues: 498.6553 Evaluate side-chains 477 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 461 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 181 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 336 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN B 314 GLN B 320 ASN C 121 HIS C 314 GLN C 393 ASN D 314 GLN E 314 GLN E 320 ASN F 121 HIS F 314 GLN F 393 ASN G 314 GLN H 314 GLN H 320 ASN I 121 HIS I 314 GLN I 393 ASN J 314 GLN K 314 GLN K 320 ASN L 121 HIS L 314 GLN L 393 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.146862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118395 restraints weight = 31893.135| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.11 r_work: 0.3145 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32040 Z= 0.131 Angle : 0.499 6.502 43128 Z= 0.283 Chirality : 0.040 0.136 4764 Planarity : 0.003 0.029 5448 Dihedral : 4.484 39.404 4200 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.89 % Allowed : 12.33 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.14), residues: 3732 helix: 1.71 (0.12), residues: 2028 sheet: 0.00 (0.23), residues: 600 loop : -0.39 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 144 TYR 0.023 0.001 TYR K 177 PHE 0.018 0.002 PHE K 269 HIS 0.002 0.001 HIS G 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (32040) covalent geometry : angle 0.49949 / 0.28 (43128) hydrogen bonds : bond 0.05727 / 3.77 ( 1740) hydrogen bonds : angle 4.71590 / 3.20 ( 5040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15330.11 seconds wall clock time: 261 minutes 7.85 seconds (15667.85 seconds total)