Starting phenix.real_space_refine on Tue Aug 26 00:00:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pho_17669/08_2025/8pho_17669.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pho_17669/08_2025/8pho_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 { model { file = "/net/cci-nas-00/data/ceres_data/8pho_17669/08_2025/8pho_17669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pho_17669/08_2025/8pho_17669.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pho_17669/08_2025/8pho_17669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pho_17669/08_2025/8pho_17669.map" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.55, per 1000 atoms: 0.11 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.11 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: 5.30 Time building geometry restraints manager: 3.18 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: 0.09 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 22.450 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 aren 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 covalent geometry : bond 0.00457 (32040) covalent geometry : angle 0.76648 (43128) hydrogen bonds : bond 0.15495 ( 1740) hydrogen bonds : angle 7.01158 ( 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 : 1.110 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: 0.7954 (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: 0.7463 (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: 0.9521 time to fit residues: 745.0487 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 : 1.187 ------------------------------------------------------------------------------- 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: 0.1980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 314 GLN A 368 GLN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 337 GLN B 388 GLN C 76 HIS C 314 GLN C 337 GLN C 388 GLN C 393 ASN D 94 GLN ** D 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN D 368 GLN E 320 ASN F 76 HIS F 314 GLN F 393 ASN G 94 GLN G 187 HIS G 314 GLN G 320 ASN G 368 GLN G 388 GLN ** H 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN H 314 GLN I 76 HIS I 314 GLN I 393 ASN J 76 HIS J 94 GLN J 121 HIS J 314 GLN J 368 GLN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 ASN K 314 GLN K 320 ASN L 312 ASN ** L 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.154153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126216 restraints weight = 32858.629| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.25 r_work: 0.3279 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.143 32040 Z= 0.318 Angle : 1.331 29.735 43128 Z= 0.696 Chirality : 0.068 0.805 4764 Planarity : 0.018 0.439 5448 Dihedral : 6.078 132.360 4200 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.38 % Favored : 97.48 % Rotamer: Outliers : 3.05 % Allowed : 10.06 % Favored : 86.90 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -1.46 (0.12), residues: 3732 helix: -0.73 (0.11), residues: 2004 sheet: -0.95 (0.20), residues: 624 loop : -1.03 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.107 0.004 ARG I 372 TYR 0.265 0.008 TYR J 383 PHE 0.187 0.009 PHE H 119 HIS 0.055 0.005 HIS L 76 Details of bonding type rmsd covalent geometry : bond 0.00676 (32040) covalent geometry : angle 1.33150 (43128) hydrogen bonds : bond 0.07213 ( 1740) hydrogen bonds : angle 6.00046 ( 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 689 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 583 time to evaluate : 1.386 Fit side-chains REVERT: A 55 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7102 (mp) REVERT: A 121 HIS cc_start: 0.7795 (p-80) cc_final: 0.7490 (p90) REVERT: A 326 ARG cc_start: 0.7223 (mmt90) cc_final: 0.6956 (mmt180) REVERT: A 357 LYS cc_start: 0.7577 (tmtt) cc_final: 0.7150 (tttt) REVERT: A 382 LYS cc_start: 0.8093 (mmtt) cc_final: 0.7717 (mmmt) REVERT: B 338 GLU cc_start: 0.8347 (tt0) cc_final: 0.8114 (tt0) REVERT: B 382 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7737 (mmmt) REVERT: C 55 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7259 (mp) REVERT: C 57 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6240 (ttp80) REVERT: C 355 ASP cc_start: 0.6929 (t0) cc_final: 0.6700 (t0) REVERT: C 357 LYS cc_start: 0.7991 (tppt) cc_final: 0.7426 (tttm) REVERT: C 382 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7606 (mmmt) REVERT: D 326 ARG cc_start: 0.7194 (mmt90) cc_final: 0.6893 (mmt180) REVERT: E 120 ASP cc_start: 0.7453 (p0) cc_final: 0.6923 (p0) REVERT: E 121 HIS cc_start: 0.7770 (p-80) cc_final: 0.6867 (m-70) REVERT: E 382 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7794 (mmmt) REVERT: F 111 TYR cc_start: 0.8524 (m-10) cc_final: 0.8184 (m-10) REVERT: F 393 ASN cc_start: 0.5793 (OUTLIER) cc_final: 0.5331 (p0) REVERT: G 110 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: G 144 ARG cc_start: 0.8304 (mtt-85) cc_final: 0.8073 (mtt-85) REVERT: G 326 ARG cc_start: 0.7207 (mmt90) cc_final: 0.6953 (mmt180) REVERT: G 372 ARG cc_start: 0.7789 (mmm-85) cc_final: 0.7561 (mtm180) REVERT: G 382 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7716 (mmmt) REVERT: H 181 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: H 375 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7881 (mmtm) REVERT: H 382 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7679 (mptt) REVERT: I 42 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7775 (mt) REVERT: I 55 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7133 (mp) REVERT: I 357 LYS cc_start: 0.8040 (tppt) cc_final: 0.7421 (tmtt) REVERT: I 363 MET cc_start: 0.7580 (mtp) cc_final: 0.6968 (mmt) REVERT: I 371 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7153 (mt-10) REVERT: I 391 SER cc_start: 0.6413 (OUTLIER) cc_final: 0.5796 (m) REVERT: I 393 ASN cc_start: 0.5858 (OUTLIER) cc_final: 0.5356 (p0) REVERT: J 57 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.6320 (ttp-170) REVERT: J 268 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7694 (ttp) REVERT: J 326 ARG cc_start: 0.7208 (mmt90) cc_final: 0.6908 (mmt180) REVERT: J 372 ARG cc_start: 0.8097 (mmm-85) cc_final: 0.7892 (mmt90) REVERT: K 326 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7207 (mmt180) REVERT: K 357 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7215 (ttpp) REVERT: K 382 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7803 (mmmt) REVERT: K 403 LYS cc_start: 0.7191 (ptpt) cc_final: 0.6915 (ptpt) REVERT: L 55 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7215 (mp) REVERT: L 110 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: L 121 HIS cc_start: 0.7663 (p-80) cc_final: 0.7448 (p-80) outliers start: 106 outliers final: 11 residues processed: 631 average time/residue: 1.0536 time to fit residues: 746.8655 Evaluate side-chains 476 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 448 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain F residue 393 ASN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 375 LYS Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 393 ASN Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 268 MET Chi-restraints excluded: chain K residue 326 ARG Chi-restraints excluded: chain K residue 357 LYS Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 110 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 70 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 360 optimal weight: 0.9980 chunk 259 optimal weight: 8.9990 chunk 313 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 357 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 121 HIS A 314 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN B 121 HIS B 320 ASN B 337 GLN C 61 GLN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 320 ASN C 337 GLN C 393 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 314 GLN ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN F 314 GLN F 339 GLN F 388 GLN F 393 ASN G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 GLN H 121 HIS H 314 GLN ** H 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 385 GLN H 388 GLN I 188 ASN I 314 GLN I 388 GLN I 393 ASN J 94 GLN J 121 HIS J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 368 GLN J 388 GLN K 61 GLN K 121 HIS ** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 388 GLN L 312 ASN L 314 GLN L 320 ASN L 388 GLN L 393 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120854 restraints weight = 32369.812| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.15 r_work: 0.3182 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32040 Z= 0.125 Angle : 0.489 5.098 43128 Z= 0.278 Chirality : 0.040 0.141 4764 Planarity : 0.004 0.066 5448 Dihedral : 5.094 172.175 4200 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.07 % Allowed : 10.92 % Favored : 87.01 % 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 aren not related in a simple way. whole: 0.61 (0.13), residues: 3732 helix: 1.25 (0.12), residues: 2016 sheet: -0.35 (0.21), residues: 600 loop : -0.58 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 74 TYR 0.025 0.002 TYR L 177 PHE 0.019 0.002 PHE E 269 HIS 0.008 0.001 HIS C 121 Details of bonding type rmsd covalent geometry : bond 0.00254 (32040) covalent geometry : angle 0.48877 (43128) hydrogen bonds : bond 0.05607 ( 1740) hydrogen bonds : angle 4.91151 ( 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 583 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 511 time to evaluate : 1.425 Fit side-chains REVERT: A 181 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: A 326 ARG cc_start: 0.7391 (mmt90) cc_final: 0.7080 (mmt180) REVERT: A 372 ARG cc_start: 0.8030 (mmm-85) cc_final: 0.7799 (mtm180) REVERT: B 120 ASP cc_start: 0.7405 (p0) cc_final: 0.7111 (p0) REVERT: B 144 ARG cc_start: 0.8324 (mtt-85) cc_final: 0.8080 (mtt-85) REVERT: B 338 GLU cc_start: 0.8305 (tt0) cc_final: 0.8066 (tt0) REVERT: C 55 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7089 (mp) REVERT: C 181 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7667 (pp20) REVERT: C 341 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8070 (mt-10) REVERT: C 357 LYS cc_start: 0.8115 (tppt) cc_final: 0.7434 (tttm) REVERT: C 388 GLN cc_start: 0.6864 (mt0) cc_final: 0.6651 (mt0) REVERT: D 119 PHE cc_start: 0.7482 (m-80) cc_final: 0.7014 (m-80) REVERT: D 181 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: D 290 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: D 326 ARG cc_start: 0.7369 (mmt90) cc_final: 0.7045 (mmt180) REVERT: D 357 LYS cc_start: 0.8007 (mmmt) cc_final: 0.7515 (tttt) REVERT: E 120 ASP cc_start: 0.7494 (p0) cc_final: 0.7130 (p0) REVERT: E 121 HIS cc_start: 0.7895 (p-80) cc_final: 0.7640 (p-80) REVERT: E 181 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: E 357 LYS cc_start: 0.8072 (tppt) cc_final: 0.7580 (tttp) REVERT: F 185 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: G 185 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: G 326 ARG cc_start: 0.7369 (mmt90) cc_final: 0.7064 (mmt180) REVERT: G 372 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7748 (mtm180) REVERT: H 144 ARG cc_start: 0.8305 (mtt-85) cc_final: 0.8096 (mtt-85) REVERT: H 181 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: H 403 LYS cc_start: 0.7274 (tttp) cc_final: 0.7004 (ttmm) REVERT: I 55 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7134 (mp) REVERT: I 185 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: J 20 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8183 (ttmm) REVERT: J 120 ASP cc_start: 0.7465 (p0) cc_final: 0.7138 (p0) REVERT: J 181 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7959 (pp20) REVERT: J 326 ARG cc_start: 0.7380 (mmt90) cc_final: 0.6995 (mmt180) REVERT: J 399 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.6003 (mpp) REVERT: K 120 ASP cc_start: 0.7601 (p0) cc_final: 0.7247 (p0) REVERT: K 144 ARG cc_start: 0.8364 (mtt-85) cc_final: 0.8149 (mtt-85) REVERT: K 402 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.6160 (mp0) REVERT: K 403 LYS cc_start: 0.7418 (ptpt) cc_final: 0.6986 (ptpt) REVERT: L 121 HIS cc_start: 0.7716 (p-80) cc_final: 0.7471 (p-80) outliers start: 72 outliers final: 15 residues processed: 549 average time/residue: 0.9934 time to fit residues: 612.2267 Evaluate side-chains 482 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 452 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 181 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 399 MET Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 402 GLU Chi-restraints excluded: chain L residue 57 ARG 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: 0.9990 chunk 195 optimal weight: 9.9990 chunk 231 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 332 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 209 optimal weight: 0.6980 chunk 264 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 300 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 121 HIS A 314 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN B 121 HIS B 314 GLN B 320 ASN C 314 GLN C 320 ASN C 393 ASN D 94 GLN D 121 HIS ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN F 314 GLN F 320 ASN F 385 GLN F 388 GLN F 393 ASN G 94 GLN G 187 HIS G 314 GLN G 388 GLN G 393 ASN H 314 GLN H 393 ASN I 314 GLN I 388 GLN I 393 ASN J 94 GLN J 121 HIS J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 HIS L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118484 restraints weight = 32276.437| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.22 r_work: 0.3145 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2283 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= 0.153 Angle : 0.530 4.888 43128 Z= 0.299 Chirality : 0.042 0.141 4764 Planarity : 0.004 0.053 5448 Dihedral : 5.287 178.598 4200 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.18 % Allowed : 11.72 % Favored : 86.09 % 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 aren not related in a simple way. whole: 0.91 (0.14), residues: 3732 helix: 1.50 (0.12), residues: 2028 sheet: -0.23 (0.22), residues: 600 loop : -0.45 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 74 TYR 0.027 0.002 TYR L 177 PHE 0.023 0.002 PHE E 269 HIS 0.004 0.001 HIS L 121 Details of bonding type rmsd covalent geometry : bond 0.00333 (32040) covalent geometry : angle 0.52992 (43128) hydrogen bonds : bond 0.06286 ( 1740) hydrogen bonds : angle 5.00038 ( 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 551 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 475 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: A 326 ARG cc_start: 0.7405 (mmt90) cc_final: 0.7044 (mmt180) REVERT: A 403 LYS cc_start: 0.7313 (ttpt) cc_final: 0.7068 (mtmm) REVERT: B 120 ASP cc_start: 0.7280 (p0) cc_final: 0.6891 (p0) REVERT: C 357 LYS cc_start: 0.8094 (tppt) cc_final: 0.7466 (tttm) REVERT: D 181 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: D 290 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7870 (mm-30) REVERT: D 357 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7562 (tttt) REVERT: E 120 ASP cc_start: 0.7462 (p0) cc_final: 0.7055 (p0) REVERT: E 121 HIS cc_start: 0.8051 (p-80) cc_final: 0.7629 (p90) REVERT: E 144 ARG cc_start: 0.8251 (mtt-85) cc_final: 0.8009 (mtt-85) REVERT: E 181 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: F 64 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7790 (t0) REVERT: F 185 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: G 326 ARG cc_start: 0.7402 (mmt90) cc_final: 0.7039 (mmt180) REVERT: H 105 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7425 (tp30) REVERT: H 120 ASP cc_start: 0.7487 (p0) cc_final: 0.7080 (p0) REVERT: H 144 ARG cc_start: 0.8357 (mtt-85) cc_final: 0.8128 (mtt-85) REVERT: H 181 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: H 357 LYS cc_start: 0.8142 (tppt) cc_final: 0.7497 (tttm) REVERT: H 403 LYS cc_start: 0.7352 (tttp) cc_final: 0.7063 (ttmm) REVERT: I 185 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: J 20 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8206 (ttmm) REVERT: J 181 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7893 (pp20) REVERT: J 326 ARG cc_start: 0.7412 (mmt90) cc_final: 0.7035 (mmt180) REVERT: K 120 ASP cc_start: 0.7493 (p0) cc_final: 0.7116 (p0) REVERT: K 357 LYS cc_start: 0.8111 (tppt) cc_final: 0.7527 (tttp) REVERT: K 403 LYS cc_start: 0.7569 (ptpt) cc_final: 0.7087 (tttt) REVERT: L 357 LYS cc_start: 0.8124 (tppt) cc_final: 0.7526 (tttm) REVERT: L 372 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7838 (mmt90) outliers start: 76 outliers final: 23 residues processed: 518 average time/residue: 0.9333 time to fit residues: 545.4366 Evaluate side-chains 469 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 436 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 123 THR 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 181 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain H residue 105 GLU 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 I residue 185 GLU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 155 optimal weight: 7.9990 chunk 353 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 172 optimal weight: 8.9990 chunk 195 optimal weight: 10.0000 chunk 369 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 314 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 320 ASN C 121 HIS C 314 GLN C 320 ASN C 388 GLN C 393 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN E 121 HIS E 314 GLN E 320 ASN E 388 GLN E 393 ASN F 121 HIS F 314 GLN F 320 ASN F 393 ASN G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 GLN H 314 GLN H 393 ASN I 314 GLN I 388 GLN I 393 ASN J 121 HIS J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.116909 restraints weight = 32180.973| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.19 r_work: 0.3129 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 32040 Z= 0.199 Angle : 0.593 5.291 43128 Z= 0.333 Chirality : 0.044 0.144 4764 Planarity : 0.004 0.051 5448 Dihedral : 5.563 176.761 4200 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.56 % Allowed : 11.01 % Favored : 86.44 % 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 aren not related in a simple way. whole: 0.68 (0.14), residues: 3732 helix: 1.26 (0.12), residues: 2028 sheet: -0.15 (0.22), residues: 600 loop : -0.57 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 74 TYR 0.027 0.002 TYR L 177 PHE 0.025 0.002 PHE I 269 HIS 0.005 0.001 HIS H 48 Details of bonding type rmsd covalent geometry : bond 0.00453 (32040) covalent geometry : angle 0.59335 (43128) hydrogen bonds : bond 0.07126 ( 1740) hydrogen bonds : angle 5.18798 ( 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 546 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 457 time to evaluate : 1.346 Fit side-chains REVERT: A 357 LYS cc_start: 0.7664 (tttm) cc_final: 0.7329 (tttt) REVERT: B 120 ASP cc_start: 0.7284 (p0) cc_final: 0.6899 (p0) REVERT: B 144 ARG cc_start: 0.8297 (mtt-85) cc_final: 0.8041 (mtt-85) REVERT: B 357 LYS cc_start: 0.8159 (tppt) cc_final: 0.7521 (tttm) REVERT: C 64 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7831 (t0) REVERT: D 181 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: D 290 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7938 (mm-30) REVERT: D 341 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8075 (mt-10) REVERT: D 357 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7673 (tttp) REVERT: E 20 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8372 (mtmm) REVERT: E 120 ASP cc_start: 0.7471 (p0) cc_final: 0.7051 (p0) REVERT: E 121 HIS cc_start: 0.8005 (p90) cc_final: 0.7606 (p90) REVERT: E 144 ARG cc_start: 0.8299 (mtt-85) cc_final: 0.8066 (mtt-85) REVERT: E 181 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: E 388 GLN cc_start: 0.7175 (mt0) cc_final: 0.6914 (mt0) REVERT: F 64 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7798 (t0) REVERT: F 185 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: G 357 LYS cc_start: 0.8136 (tppt) cc_final: 0.7574 (tttm) REVERT: H 105 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7457 (tp30) REVERT: H 120 ASP cc_start: 0.7477 (p0) cc_final: 0.7030 (p0) REVERT: H 144 ARG cc_start: 0.8335 (mtt-85) cc_final: 0.8110 (mtt-85) REVERT: H 181 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: I 185 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: J 20 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8184 (ttmm) REVERT: J 181 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8066 (pp20) REVERT: J 313 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: J 357 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7374 (mtmm) REVERT: K 120 ASP cc_start: 0.7486 (p0) cc_final: 0.7091 (p0) REVERT: K 144 ARG cc_start: 0.8359 (mtt-85) cc_final: 0.8110 (mtt-85) REVERT: K 157 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7935 (ptp90) REVERT: K 403 LYS cc_start: 0.7540 (ptpt) cc_final: 0.7081 (tttt) REVERT: L 64 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7821 (t0) REVERT: L 372 ARG cc_start: 0.8139 (mmm-85) cc_final: 0.7899 (mmt90) outliers start: 89 outliers final: 30 residues processed: 510 average time/residue: 1.0285 time to fit residues: 590.0507 Evaluate side-chains 471 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 426 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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 89 LEU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain H residue 105 GLU 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 I residue 185 GLU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain J residue 313 GLU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 157 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 244 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 292 optimal weight: 0.0030 chunk 217 optimal weight: 10.0000 chunk 225 optimal weight: 0.0370 chunk 240 optimal weight: 0.8980 chunk 269 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 268 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.4668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 388 GLN B 314 GLN B 388 GLN C 121 HIS C 314 GLN C 388 GLN C 393 ASN D 388 GLN E 314 GLN E 388 GLN E 393 ASN F 121 HIS F 314 GLN F 388 GLN F 393 ASN G 314 GLN G 393 ASN H 314 GLN H 393 ASN I 314 GLN I 388 GLN I 393 ASN J 314 GLN J 320 ASN L 121 HIS L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.123704 restraints weight = 32508.179| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.15 r_work: 0.3200 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 32040 Z= 0.093 Angle : 0.414 4.385 43128 Z= 0.238 Chirality : 0.038 0.139 4764 Planarity : 0.003 0.040 5448 Dihedral : 5.023 179.917 4200 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.86 % Allowed : 12.59 % Favored : 86.55 % 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 aren not related in a simple way. whole: 1.50 (0.14), residues: 3732 helix: 2.01 (0.12), residues: 2028 sheet: 0.01 (0.22), residues: 600 loop : -0.25 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 144 TYR 0.018 0.001 TYR H 177 PHE 0.014 0.001 PHE E 189 HIS 0.003 0.001 HIS K 121 Details of bonding type rmsd covalent geometry : bond 0.00178 (32040) covalent geometry : angle 0.41376 (43128) hydrogen bonds : bond 0.04209 ( 1740) hydrogen bonds : angle 4.42597 ( 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 486 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 456 time to evaluate : 1.221 Fit side-chains REVERT: A 326 ARG cc_start: 0.7369 (mmt90) cc_final: 0.7002 (mmt180) REVERT: A 357 LYS cc_start: 0.7659 (tttm) cc_final: 0.7359 (tttt) REVERT: A 403 LYS cc_start: 0.7703 (mtmm) cc_final: 0.7489 (mtmm) REVERT: B 120 ASP cc_start: 0.7429 (p0) cc_final: 0.7039 (p0) REVERT: C 268 MET cc_start: 0.8304 (ttp) cc_final: 0.8074 (ttp) REVERT: C 269 PHE cc_start: 0.8496 (t80) cc_final: 0.8258 (t80) REVERT: C 375 LYS cc_start: 0.8609 (mmtp) cc_final: 0.8347 (tptt) REVERT: C 399 MET cc_start: 0.6589 (ttp) cc_final: 0.6290 (tpt) REVERT: D 326 ARG cc_start: 0.7374 (mmt90) cc_final: 0.7000 (mmt180) REVERT: D 357 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7667 (tttt) REVERT: E 120 ASP cc_start: 0.7507 (p0) cc_final: 0.7091 (p0) REVERT: E 121 HIS cc_start: 0.8033 (p90) cc_final: 0.7594 (p90) REVERT: E 144 ARG cc_start: 0.8249 (mtt-85) cc_final: 0.8028 (mtt-85) REVERT: E 181 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: E 357 LYS cc_start: 0.8136 (tppt) cc_final: 0.7528 (tttp) REVERT: F 269 PHE cc_start: 0.8488 (t80) cc_final: 0.8251 (t80) REVERT: F 290 GLU cc_start: 0.8090 (mp0) cc_final: 0.7745 (mm-30) REVERT: F 403 LYS cc_start: 0.7527 (ttpt) cc_final: 0.7283 (mtmm) REVERT: G 326 ARG cc_start: 0.7370 (mmt90) cc_final: 0.7008 (mmt180) REVERT: G 341 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8037 (tt0) REVERT: G 357 LYS cc_start: 0.8150 (tppt) cc_final: 0.7454 (tttt) REVERT: G 372 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7787 (mmt90) REVERT: G 403 LYS cc_start: 0.7707 (mtmm) cc_final: 0.7485 (mtmm) REVERT: H 105 GLU cc_start: 0.7841 (pt0) cc_final: 0.7536 (tp30) REVERT: H 121 HIS cc_start: 0.7994 (p-80) cc_final: 0.7592 (p90) REVERT: H 144 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.8061 (mtt-85) REVERT: H 181 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: H 357 LYS cc_start: 0.8134 (tppt) cc_final: 0.7536 (tttp) REVERT: J 181 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7936 (pp20) REVERT: J 326 ARG cc_start: 0.7386 (mmt90) cc_final: 0.7008 (mmt180) REVERT: J 399 MET cc_start: 0.6481 (ttp) cc_final: 0.6110 (tpt) REVERT: K 120 ASP cc_start: 0.7571 (p0) cc_final: 0.7181 (p0) REVERT: K 144 ARG cc_start: 0.8333 (mtt-85) cc_final: 0.8103 (mtt-85) REVERT: K 282 LYS cc_start: 0.8720 (mttm) cc_final: 0.8482 (mtmm) REVERT: K 357 LYS cc_start: 0.8114 (tppt) cc_final: 0.7508 (tttp) REVERT: K 403 LYS cc_start: 0.7401 (ptpt) cc_final: 0.7031 (tttt) REVERT: L 290 GLU cc_start: 0.8055 (mp0) cc_final: 0.7715 (mm-30) REVERT: L 403 LYS cc_start: 0.7387 (ttpt) cc_final: 0.7158 (mtmm) outliers start: 30 outliers final: 4 residues processed: 476 average time/residue: 0.9416 time to fit residues: 505.1290 Evaluate side-chains 420 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 413 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain J residue 181 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 1 optimal weight: 6.9990 chunk 269 optimal weight: 1.9990 chunk 21 optimal weight: 0.0060 chunk 207 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 352 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 overall best weight: 2.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN C 121 HIS C 314 GLN C 320 ASN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 ASN F 121 HIS F 314 GLN F 393 ASN G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 ASN H 314 GLN H 393 ASN I 121 HIS I 314 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 HIS L 314 GLN L 393 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117476 restraints weight = 32211.529| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.17 r_work: 0.3131 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32040 Z= 0.169 Angle : 0.544 4.929 43128 Z= 0.307 Chirality : 0.042 0.141 4764 Planarity : 0.004 0.048 5448 Dihedral : 5.406 178.029 4200 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.78 % Allowed : 12.27 % Favored : 85.95 % 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 aren not related in a simple way. whole: 1.07 (0.14), residues: 3732 helix: 1.60 (0.12), residues: 2028 sheet: -0.04 (0.22), residues: 600 loop : -0.42 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 74 TYR 0.026 0.002 TYR L 177 PHE 0.026 0.002 PHE E 269 HIS 0.004 0.001 HIS L 76 Details of bonding type rmsd covalent geometry : bond 0.00376 (32040) covalent geometry : angle 0.54429 (43128) hydrogen bonds : bond 0.06509 ( 1740) hydrogen bonds : angle 4.96457 ( 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 500 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 438 time to evaluate : 1.150 Fit side-chains REVERT: A 326 ARG cc_start: 0.7446 (mmt90) cc_final: 0.7050 (mmt180) REVERT: B 120 ASP cc_start: 0.7379 (p0) cc_final: 0.6980 (p0) REVERT: B 144 ARG cc_start: 0.8271 (mtt-85) cc_final: 0.8015 (mtt-85) REVERT: B 185 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: C 144 ARG cc_start: 0.8316 (mtt-85) cc_final: 0.8083 (mtt-85) REVERT: D 290 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: D 326 ARG cc_start: 0.7434 (mmt90) cc_final: 0.7014 (mmt-90) REVERT: D 341 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8079 (mt-10) REVERT: D 357 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7692 (tttp) REVERT: E 120 ASP cc_start: 0.7488 (p0) cc_final: 0.7083 (p0) REVERT: E 121 HIS cc_start: 0.7993 (p90) cc_final: 0.7555 (p90) REVERT: E 144 ARG cc_start: 0.8293 (mtt-85) cc_final: 0.8067 (mtt-85) REVERT: E 181 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: E 282 LYS cc_start: 0.8717 (mttm) cc_final: 0.8485 (mtmm) REVERT: E 357 LYS cc_start: 0.8144 (tppt) cc_final: 0.7519 (tttm) REVERT: F 185 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: G 185 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: G 326 ARG cc_start: 0.7445 (mmt90) cc_final: 0.7053 (mmt180) REVERT: G 341 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8006 (mt-10) REVERT: H 105 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7537 (tp30) REVERT: H 120 ASP cc_start: 0.7524 (p0) cc_final: 0.7059 (p0) REVERT: H 121 HIS cc_start: 0.8014 (p-80) cc_final: 0.7622 (p90) REVERT: H 144 ARG cc_start: 0.8330 (mtt-85) cc_final: 0.8083 (mtt-85) REVERT: H 181 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: H 357 LYS cc_start: 0.8146 (tppt) cc_final: 0.7505 (tttm) REVERT: I 185 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: J 326 ARG cc_start: 0.7440 (mmt90) cc_final: 0.7017 (mmt-90) REVERT: K 120 ASP cc_start: 0.7536 (p0) cc_final: 0.7156 (p0) REVERT: K 185 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: K 357 LYS cc_start: 0.8128 (tppt) cc_final: 0.7500 (tttm) REVERT: K 403 LYS cc_start: 0.7433 (ptpt) cc_final: 0.7078 (tttt) REVERT: L 144 ARG cc_start: 0.8299 (mtt-85) cc_final: 0.7950 (mtt-85) REVERT: L 403 LYS cc_start: 0.7473 (ttpt) cc_final: 0.7224 (mtmm) outliers start: 62 outliers final: 14 residues processed: 477 average time/residue: 1.0237 time to fit residues: 550.0526 Evaluate side-chains 451 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 428 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H 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 185 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain L residue 57 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 72 optimal weight: 7.9990 chunk 17 optimal weight: 0.1980 chunk 287 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 367 optimal weight: 9.9990 chunk 366 optimal weight: 0.8980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN C 121 HIS C 314 GLN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 ASN F 121 HIS F 314 GLN F 393 ASN G 314 GLN G 393 ASN H 393 ASN I 121 HIS I 314 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 HIS L 314 GLN L 388 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 = 0.3669 r_free = 0.3669 target = 0.147092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.118716 restraints weight = 32226.432| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.17 r_work: 0.3155 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32040 Z= 0.132 Angle : 0.492 5.535 43128 Z= 0.279 Chirality : 0.040 0.139 4764 Planarity : 0.003 0.040 5448 Dihedral : 5.299 178.809 4200 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.41 % Allowed : 12.64 % Favored : 85.95 % 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 aren not related in a simple way. whole: 1.19 (0.14), residues: 3732 helix: 1.70 (0.12), residues: 2028 sheet: -0.02 (0.22), residues: 600 loop : -0.35 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 144 TYR 0.023 0.002 TYR H 177 PHE 0.020 0.002 PHE B 269 HIS 0.003 0.001 HIS L 76 Details of bonding type rmsd covalent geometry : bond 0.00279 (32040) covalent geometry : angle 0.49187 (43128) hydrogen bonds : bond 0.05700 ( 1740) hydrogen bonds : angle 4.79092 ( 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 489 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 440 time to evaluate : 1.324 Fit side-chains REVERT: A 326 ARG cc_start: 0.7425 (mmt90) cc_final: 0.7007 (mmt180) REVERT: B 120 ASP cc_start: 0.7378 (p0) cc_final: 0.6935 (p0) REVERT: B 121 HIS cc_start: 0.8027 (p-80) cc_final: 0.7724 (p-80) REVERT: B 144 ARG cc_start: 0.8261 (mtt-85) cc_final: 0.8037 (mtt-85) REVERT: B 185 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: D 290 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: D 326 ARG cc_start: 0.7422 (mmt90) cc_final: 0.7023 (mmt180) REVERT: D 341 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8029 (mt-10) REVERT: D 357 LYS cc_start: 0.8068 (mmmt) cc_final: 0.7672 (tttt) REVERT: E 120 ASP cc_start: 0.7476 (p0) cc_final: 0.7045 (p0) REVERT: E 121 HIS cc_start: 0.8033 (p90) cc_final: 0.7570 (p90) REVERT: E 144 ARG cc_start: 0.8264 (mtt-85) cc_final: 0.8013 (mtt-85) REVERT: E 181 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: E 357 LYS cc_start: 0.8114 (tppt) cc_final: 0.7486 (tttm) REVERT: F 403 LYS cc_start: 0.7566 (ttpt) cc_final: 0.7355 (mtmm) REVERT: G 326 ARG cc_start: 0.7421 (mmt90) cc_final: 0.7003 (mmt180) REVERT: G 341 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7959 (tt0) REVERT: H 105 GLU cc_start: 0.7821 (pt0) cc_final: 0.7512 (tp30) REVERT: H 120 ASP cc_start: 0.7509 (p0) cc_final: 0.7050 (p0) REVERT: H 121 HIS cc_start: 0.8081 (p-80) cc_final: 0.7676 (p90) REVERT: H 144 ARG cc_start: 0.8304 (mtt-85) cc_final: 0.8052 (mtt-85) REVERT: H 181 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: H 357 LYS cc_start: 0.8125 (tppt) cc_final: 0.7486 (tttm) REVERT: I 185 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: J 181 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7826 (pp20) REVERT: J 326 ARG cc_start: 0.7423 (mmt90) cc_final: 0.7023 (mmt180) REVERT: J 357 LYS cc_start: 0.7907 (mmmm) cc_final: 0.7382 (tttm) REVERT: J 399 MET cc_start: 0.6537 (ttp) cc_final: 0.6201 (tpt) REVERT: K 120 ASP cc_start: 0.7535 (p0) cc_final: 0.7135 (p0) REVERT: K 144 ARG cc_start: 0.8334 (mtt-85) cc_final: 0.8082 (mtt-85) REVERT: K 357 LYS cc_start: 0.8115 (tppt) cc_final: 0.7484 (tttm) REVERT: K 403 LYS cc_start: 0.7369 (ptpt) cc_final: 0.7054 (tttt) REVERT: L 357 LYS cc_start: 0.8122 (tppt) cc_final: 0.7486 (tttm) REVERT: L 403 LYS cc_start: 0.7494 (ttpt) cc_final: 0.7249 (mtmm) outliers start: 49 outliers final: 9 residues processed: 470 average time/residue: 1.0254 time to fit residues: 542.3537 Evaluate side-chains 445 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 430 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 355 ASP Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 57 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 178 optimal weight: 10.0000 chunk 351 optimal weight: 1.9990 chunk 288 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 320 ASN C 121 HIS C 314 GLN C 320 ASN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN E 393 ASN F 121 HIS F 314 GLN F 393 ASN G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 ASN H 393 ASN I 121 HIS I 314 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 HIS L 314 GLN L 393 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116784 restraints weight = 32000.702| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.19 r_work: 0.3126 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32040 Z= 0.189 Angle : 0.581 6.628 43128 Z= 0.326 Chirality : 0.043 0.143 4764 Planarity : 0.004 0.047 5448 Dihedral : 5.549 177.406 4200 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.44 % Allowed : 12.76 % Favored : 85.80 % 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 aren not related in a simple way. whole: 0.80 (0.14), residues: 3732 helix: 1.36 (0.12), residues: 2028 sheet: -0.09 (0.22), residues: 600 loop : -0.53 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 74 TYR 0.026 0.002 TYR C 177 PHE 0.025 0.002 PHE E 269 HIS 0.004 0.001 HIS H 48 Details of bonding type rmsd covalent geometry : bond 0.00428 (32040) covalent geometry : angle 0.58077 (43128) hydrogen bonds : bond 0.06923 ( 1740) hydrogen bonds : angle 5.07734 ( 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 492 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 442 time to evaluate : 1.232 Fit side-chains REVERT: B 120 ASP cc_start: 0.7376 (p0) cc_final: 0.6934 (p0) REVERT: B 121 HIS cc_start: 0.8038 (p-80) cc_final: 0.7604 (p-80) REVERT: B 144 ARG cc_start: 0.8286 (mtt-85) cc_final: 0.8043 (mtt-85) REVERT: C 64 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7799 (t0) REVERT: C 144 ARG cc_start: 0.8308 (mtt-85) cc_final: 0.8086 (mtt-85) REVERT: D 290 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7932 (mm-30) REVERT: D 341 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8101 (mt-10) REVERT: D 357 LYS cc_start: 0.8044 (mmmt) cc_final: 0.7689 (tttp) REVERT: E 120 ASP cc_start: 0.7391 (p0) cc_final: 0.6965 (p0) REVERT: E 121 HIS cc_start: 0.8064 (p90) cc_final: 0.7550 (p90) REVERT: E 144 ARG cc_start: 0.8289 (mtt-85) cc_final: 0.8046 (mtt-85) REVERT: E 181 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: F 185 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: G 185 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: H 55 LEU cc_start: 0.7618 (tp) cc_final: 0.7399 (tp) REVERT: H 105 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7501 (tp30) REVERT: H 120 ASP cc_start: 0.7479 (p0) cc_final: 0.6980 (p0) REVERT: H 121 HIS cc_start: 0.8072 (p-80) cc_final: 0.7619 (p90) REVERT: H 144 ARG cc_start: 0.8326 (mtt-85) cc_final: 0.8068 (mtt-85) REVERT: H 181 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: I 64 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7821 (t0) REVERT: I 185 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: J 20 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8267 (ttmm) REVERT: J 181 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8123 (pp20) REVERT: J 357 LYS cc_start: 0.7973 (mmmm) cc_final: 0.7465 (tttm) REVERT: J 401 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.5942 (mmtp) REVERT: K 120 ASP cc_start: 0.7432 (p0) cc_final: 0.7026 (p0) REVERT: K 121 HIS cc_start: 0.8025 (p-80) cc_final: 0.7564 (p90) REVERT: K 144 ARG cc_start: 0.8337 (mtt-85) cc_final: 0.8075 (mtt-85) REVERT: L 144 ARG cc_start: 0.8327 (mtt-85) cc_final: 0.8083 (mtt-85) REVERT: L 372 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7931 (mmt90) REVERT: L 403 LYS cc_start: 0.7526 (ttpt) cc_final: 0.7296 (mtmm) outliers start: 50 outliers final: 17 residues processed: 469 average time/residue: 0.9195 time to fit residues: 487.8680 Evaluate side-chains 463 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 434 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 363 MET 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 C residue 181 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain H residue 105 GLU 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 185 GLU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 401 LYS Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 102 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 316 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 193 optimal weight: 0.1980 chunk 363 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 225 optimal weight: 0.0870 chunk 146 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 393 ASN F 121 HIS F 314 GLN F 393 ASN G 314 GLN G 393 ASN H 393 ASN I 121 HIS I 314 GLN I 393 ASN J 314 GLN J 320 ASN L 121 HIS L 314 GLN L 388 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 = 0.3703 r_free = 0.3703 target = 0.150066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121602 restraints weight = 32450.619| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.18 r_work: 0.3197 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 32040 Z= 0.102 Angle : 0.444 6.639 43128 Z= 0.253 Chirality : 0.038 0.136 4764 Planarity : 0.003 0.037 5448 Dihedral : 5.110 179.594 4200 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.63 % Allowed : 13.85 % Favored : 85.52 % 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 aren not related in a simple way. whole: 1.46 (0.14), residues: 3732 helix: 1.95 (0.12), residues: 2028 sheet: 0.04 (0.23), residues: 600 loop : -0.26 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 144 TYR 0.018 0.001 TYR K 177 PHE 0.016 0.001 PHE D 269 HIS 0.002 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00203 (32040) covalent geometry : angle 0.44391 (43128) hydrogen bonds : bond 0.04507 ( 1740) hydrogen bonds : angle 4.46069 ( 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 463 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 441 time to evaluate : 1.292 Fit side-chains REVERT: A 326 ARG cc_start: 0.7376 (mmt90) cc_final: 0.6982 (mmt180) REVERT: B 120 ASP cc_start: 0.7380 (p0) cc_final: 0.6934 (p0) REVERT: B 121 HIS cc_start: 0.8020 (p-80) cc_final: 0.7703 (p-80) REVERT: B 144 ARG cc_start: 0.8248 (mtt-85) cc_final: 0.8019 (mtt-85) REVERT: B 357 LYS cc_start: 0.8078 (tppt) cc_final: 0.7464 (tttm) REVERT: C 144 ARG cc_start: 0.8294 (mtt-85) cc_final: 0.8065 (mtt-85) REVERT: C 399 MET cc_start: 0.6746 (ttp) cc_final: 0.6244 (tpt) REVERT: D 326 ARG cc_start: 0.7395 (mmt90) cc_final: 0.7000 (mmt180) REVERT: D 357 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7596 (tttt) REVERT: E 120 ASP cc_start: 0.7424 (p0) cc_final: 0.7008 (p0) REVERT: E 121 HIS cc_start: 0.8015 (p90) cc_final: 0.7527 (p90) REVERT: E 144 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.7980 (mtt-85) REVERT: E 181 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: E 403 LYS cc_start: 0.7809 (mtmm) cc_final: 0.7510 (mtpt) REVERT: F 268 MET cc_start: 0.8205 (ttp) cc_final: 0.7977 (ttp) REVERT: F 269 PHE cc_start: 0.8547 (t80) cc_final: 0.8290 (t80) REVERT: F 403 LYS cc_start: 0.7553 (ttpt) cc_final: 0.7339 (mtmm) REVERT: G 326 ARG cc_start: 0.7374 (mmt90) cc_final: 0.6986 (mmt180) REVERT: G 341 GLU cc_start: 0.8130 (tt0) cc_final: 0.7909 (tt0) REVERT: G 357 LYS cc_start: 0.8180 (tppt) cc_final: 0.7564 (tttm) REVERT: H 105 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7515 (tp30) REVERT: H 121 HIS cc_start: 0.8040 (p-80) cc_final: 0.7599 (p90) REVERT: H 181 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: I 144 ARG cc_start: 0.8214 (mtt-85) cc_final: 0.8003 (mtt-85) REVERT: J 181 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7836 (pp20) REVERT: J 326 ARG cc_start: 0.7403 (mmt90) cc_final: 0.7006 (mmt180) REVERT: J 357 LYS cc_start: 0.7919 (mmmm) cc_final: 0.7442 (tttm) REVERT: J 399 MET cc_start: 0.6555 (ttp) cc_final: 0.6224 (tpt) REVERT: J 401 LYS cc_start: 0.6548 (OUTLIER) cc_final: 0.5929 (mmtp) REVERT: K 120 ASP cc_start: 0.7453 (p0) cc_final: 0.7064 (p0) REVERT: K 144 ARG cc_start: 0.8286 (mtt-85) cc_final: 0.8035 (mtt-85) REVERT: K 341 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8046 (mt-10) REVERT: L 290 GLU cc_start: 0.8059 (mp0) cc_final: 0.7802 (mm-30) REVERT: L 357 LYS cc_start: 0.8092 (tppt) cc_final: 0.7459 (tttm) REVERT: L 372 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7815 (mmt90) REVERT: L 403 LYS cc_start: 0.7474 (ttpt) cc_final: 0.7224 (mtmm) outliers start: 22 outliers final: 3 residues processed: 452 average time/residue: 0.9209 time to fit residues: 468.6293 Evaluate side-chains 434 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 426 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 401 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 336 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 280 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 208 optimal weight: 0.0670 chunk 180 optimal weight: 4.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 320 ASN C 121 HIS C 314 GLN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN E 320 ASN E 393 ASN F 121 HIS F 314 GLN F 393 ASN G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 ASN H 314 GLN H 393 ASN I 121 HIS I 314 GLN I 393 ASN J 314 GLN 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 = 0.3649 r_free = 0.3649 target = 0.145484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.116914 restraints weight = 32046.069| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.15 r_work: 0.3119 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32040 Z= 0.191 Angle : 0.591 8.614 43128 Z= 0.329 Chirality : 0.044 0.144 4764 Planarity : 0.004 0.050 5448 Dihedral : 5.539 177.300 4200 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.80 % Allowed : 13.99 % Favored : 85.20 % 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 aren not related in a simple way. whole: 0.92 (0.14), residues: 3732 helix: 1.47 (0.12), residues: 2028 sheet: -0.08 (0.22), residues: 600 loop : -0.46 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 144 TYR 0.027 0.002 TYR C 177 PHE 0.025 0.002 PHE E 269 HIS 0.004 0.001 HIS E 48 Details of bonding type rmsd covalent geometry : bond 0.00434 (32040) covalent geometry : angle 0.59076 (43128) hydrogen bonds : bond 0.06871 ( 1740) hydrogen bonds : angle 5.04123 ( 5040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14886.14 seconds wall clock time: 253 minutes 28.66 seconds (15208.66 seconds total)