Starting phenix.real_space_refine on Thu May 29 06:51:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pho_17669/05_2025/8pho_17669.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pho_17669/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pho_17669/05_2025/8pho_17669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pho_17669/05_2025/8pho_17669.map" model { file = "/net/cci-nas-00/data/ceres_data/8pho_17669/05_2025/8pho_17669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pho_17669/05_2025/8pho_17669.cif" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 9.19, per 1000 atoms: 0.29 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: 7.52 Conformation dependent library (CDL) restraints added in 3.7 seconds 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7296 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 60 sheets defined 53.9% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 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: 11.08 Time building geometry restraints manager: 8.72 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: 0.26 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.320 Check model and map are aligned: 0.230 Set scattering table: 0.320 Process input model: 56.680 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.210 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.024 0.007 HIS E 48 PHE 0.034 0.008 PHE I 358 TYR 0.036 0.008 TYR D 192 ARG 0.023 0.005 ARG I 157 Details of bonding type rmsd hydrogen bonds : bond 0.15495 ( 1740) hydrogen bonds : angle 7.01158 ( 5040) covalent geometry : bond 0.00457 (32040) covalent geometry : angle 0.76648 (43128) *********************** 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 : 4.019 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: 1.9671 time to fit residues: 1546.6815 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 : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.5980 chunk 281 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 190 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 chunk 291 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 217 optimal weight: 7.9990 chunk 337 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 368 GLN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 314 GLN C 76 HIS C 314 GLN C 388 GLN C 393 ASN D 94 GLN ** D 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 121 HIS ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 ASN F 76 HIS F 314 GLN ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 ASN G 94 GLN ** G 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124447 restraints weight = 32604.543| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.21 r_work: 0.3219 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 32040 Z= 0.327 Angle : 1.310 31.796 43128 Z= 0.682 Chirality : 0.069 0.842 4764 Planarity : 0.018 0.439 5448 Dihedral : 6.023 137.226 4200 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.09 % Favored : 97.78 % Rotamer: Outliers : 3.25 % Allowed : 9.77 % Favored : 86.98 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.12), residues: 3732 helix: -0.60 (0.11), residues: 2004 sheet: -0.86 (0.20), residues: 624 loop : -1.02 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.054 0.005 HIS L 76 PHE 0.190 0.009 PHE H 119 TYR 0.275 0.008 TYR J 383 ARG 0.109 0.004 ARG I 372 Details of bonding type rmsd hydrogen bonds : bond 0.07652 ( 1740) hydrogen bonds : angle 5.97249 ( 5040) covalent geometry : bond 0.00703 (32040) covalent geometry : angle 1.31027 (43128) *********************** 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 687 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 574 time to evaluate : 3.840 Fit side-chains REVERT: A 55 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7148 (mp) REVERT: A 119 PHE cc_start: 0.7413 (m-80) cc_final: 0.6942 (m-80) REVERT: A 121 HIS cc_start: 0.7693 (p90) cc_final: 0.7454 (p90) REVERT: A 181 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7932 (tm-30) REVERT: A 185 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7067 (mp0) REVERT: A 326 ARG cc_start: 0.7327 (mmt90) cc_final: 0.7008 (mmt180) REVERT: A 357 LYS cc_start: 0.7604 (tmtt) cc_final: 0.7174 (tttt) REVERT: A 372 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7781 (mtm180) REVERT: B 338 GLU cc_start: 0.8364 (tt0) cc_final: 0.8116 (tt0) REVERT: B 382 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7769 (mmmt) REVERT: C 55 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7264 (mp) REVERT: C 57 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6387 (ttp80) REVERT: C 357 LYS cc_start: 0.8016 (tppt) cc_final: 0.7466 (tttm) REVERT: C 403 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6886 (pttm) REVERT: D 326 ARG cc_start: 0.7275 (mmt90) cc_final: 0.6925 (mmt180) REVERT: E 120 ASP cc_start: 0.7475 (p0) cc_final: 0.6945 (p0) REVERT: E 121 HIS cc_start: 0.7627 (p90) cc_final: 0.6877 (m-70) REVERT: E 338 GLU cc_start: 0.8127 (tt0) cc_final: 0.7895 (tt0) REVERT: E 382 LYS cc_start: 0.8274 (mmtt) cc_final: 0.7820 (mptt) REVERT: F 121 HIS cc_start: 0.7746 (p-80) cc_final: 0.7540 (p-80) REVERT: F 144 ARG cc_start: 0.8242 (mtt-85) cc_final: 0.8026 (mtt-85) REVERT: F 185 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7187 (mp0) REVERT: F 393 ASN cc_start: 0.5798 (OUTLIER) cc_final: 0.5322 (p0) REVERT: G 110 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: G 121 HIS cc_start: 0.7678 (p-80) cc_final: 0.7398 (p90) REVERT: G 326 ARG cc_start: 0.7306 (mmt90) cc_final: 0.7008 (mmt180) REVERT: G 382 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7721 (mmmt) REVERT: H 181 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: H 375 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7911 (mmtm) REVERT: H 382 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7701 (mptt) REVERT: I 55 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7150 (mp) REVERT: I 185 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7016 (mp0) REVERT: I 357 LYS cc_start: 0.8079 (tppt) cc_final: 0.7441 (tmtt) REVERT: I 363 MET cc_start: 0.7602 (mtp) cc_final: 0.7007 (mmt) REVERT: I 391 SER cc_start: 0.6487 (OUTLIER) cc_final: 0.5839 (m) REVERT: J 57 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6333 (ttp-170) REVERT: J 268 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7742 (ttp) REVERT: J 313 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: J 326 ARG cc_start: 0.7292 (mmt90) cc_final: 0.6958 (mmt180) REVERT: K 326 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7251 (mmt180) REVERT: K 357 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7287 (tmtt) REVERT: K 382 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7793 (mmmt) REVERT: K 401 LYS cc_start: 0.6582 (mmmm) cc_final: 0.6326 (mmmm) REVERT: K 403 LYS cc_start: 0.7238 (ptpt) cc_final: 0.6962 (ptpt) REVERT: L 55 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7218 (mp) REVERT: L 110 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: L 121 HIS cc_start: 0.7701 (p-80) cc_final: 0.7465 (p-80) outliers start: 113 outliers final: 18 residues processed: 622 average time/residue: 1.9939 time to fit residues: 1398.3864 Evaluate side-chains 503 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 468 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 363 MET 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 403 LYS 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 G residue 123 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 375 LYS 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 J residue 57 ARG Chi-restraints excluded: chain J residue 268 MET Chi-restraints excluded: chain J residue 313 GLU Chi-restraints excluded: chain K residue 123 THR 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 292 optimal weight: 0.2980 chunk 352 optimal weight: 4.9990 chunk 361 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 370 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN B 121 HIS B 320 ASN B 388 GLN C 314 GLN C 320 ASN C 393 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 GLN F 339 GLN F 385 GLN F 388 GLN F 393 ASN G 121 HIS G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 339 GLN 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 121 HIS ** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 388 GLN L 94 GLN L 312 ASN L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.148488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.120332 restraints weight = 32457.529| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.20 r_work: 0.3181 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32040 Z= 0.128 Angle : 0.492 5.073 43128 Z= 0.281 Chirality : 0.041 0.140 4764 Planarity : 0.004 0.057 5448 Dihedral : 5.129 173.315 4200 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.07 % Allowed : 11.01 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3732 helix: 1.21 (0.12), residues: 2028 sheet: -0.54 (0.21), residues: 624 loop : -0.63 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 121 PHE 0.019 0.002 PHE E 269 TYR 0.035 0.002 TYR J 28 ARG 0.008 0.000 ARG F 113 Details of bonding type rmsd hydrogen bonds : bond 0.05710 ( 1740) hydrogen bonds : angle 4.92032 ( 5040) covalent geometry : bond 0.00261 (32040) covalent geometry : angle 0.49234 (43128) *********************** 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 585 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 513 time to evaluate : 4.009 Fit side-chains REVERT: A 181 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7993 (tm-30) REVERT: A 326 ARG cc_start: 0.7382 (mmt90) cc_final: 0.7031 (mmt180) REVERT: A 372 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7817 (mtm180) REVERT: B 120 ASP cc_start: 0.7416 (p0) cc_final: 0.7116 (p0) REVERT: B 144 ARG cc_start: 0.8320 (mtt-85) cc_final: 0.8083 (mtt-85) REVERT: B 181 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: B 403 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.6997 (pttm) REVERT: C 55 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7060 (mp) REVERT: C 144 ARG cc_start: 0.8287 (mtt-85) cc_final: 0.8073 (mtt-85) REVERT: C 181 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7631 (pp20) REVERT: C 341 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8051 (mt-10) REVERT: C 357 LYS cc_start: 0.8124 (tppt) cc_final: 0.7412 (tttm) REVERT: D 119 PHE cc_start: 0.7529 (m-80) cc_final: 0.7047 (m-80) REVERT: D 181 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: D 290 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7798 (mm-30) REVERT: D 326 ARG cc_start: 0.7346 (mmt90) cc_final: 0.6965 (mmt180) REVERT: D 357 LYS cc_start: 0.8014 (tppt) cc_final: 0.7501 (tttt) REVERT: E 120 ASP cc_start: 0.7480 (p0) cc_final: 0.7113 (p0) REVERT: E 181 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: E 357 LYS cc_start: 0.8066 (tppt) cc_final: 0.7568 (tttp) REVERT: E 382 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7837 (mmtm) REVERT: E 401 LYS cc_start: 0.6437 (mmmm) cc_final: 0.6158 (mmmm) REVERT: F 121 HIS cc_start: 0.7789 (p-80) cc_final: 0.7582 (p-80) REVERT: F 185 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7098 (mp0) REVERT: F 326 ARG cc_start: 0.7204 (mmt90) cc_final: 0.7000 (mmt180) REVERT: F 402 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: G 326 ARG cc_start: 0.7360 (mmt90) cc_final: 0.7042 (mmt180) REVERT: G 357 LYS cc_start: 0.7712 (tttm) cc_final: 0.7353 (tttt) REVERT: H 181 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: I 55 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7140 (mp) REVERT: I 144 ARG cc_start: 0.8265 (mtt-85) cc_final: 0.7857 (mtt-85) REVERT: I 185 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7083 (mp0) REVERT: J 20 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8200 (ttmm) REVERT: J 181 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7944 (pp20) REVERT: J 326 ARG cc_start: 0.7369 (mmt90) cc_final: 0.6994 (mmt180) REVERT: J 399 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.6064 (mpp) REVERT: K 120 ASP cc_start: 0.7591 (p0) cc_final: 0.7248 (p0) REVERT: K 144 ARG cc_start: 0.8366 (mtt-85) cc_final: 0.8143 (mtt-85) REVERT: K 403 LYS cc_start: 0.7456 (ptpt) cc_final: 0.7020 (ptpt) REVERT: L 55 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7055 (mp) REVERT: L 121 HIS cc_start: 0.7724 (p-80) cc_final: 0.7480 (p-80) outliers start: 72 outliers final: 17 residues processed: 552 average time/residue: 2.0608 time to fit residues: 1283.4086 Evaluate side-chains 485 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 454 time to evaluate : 4.124 ------------------------------------------------------------------------------- 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 B residue 181 GLU Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 ARG 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 123 THR Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 170 ILE 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 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 L residue 55 LEU Chi-restraints excluded: chain L residue 57 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 213 optimal weight: 0.8980 chunk 348 optimal weight: 0.0370 chunk 6 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 287 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 321 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- 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** A 388 GLN B 121 HIS B 314 GLN B 320 ASN C 314 GLN C 320 ASN C 388 GLN C 393 ASN D 94 GLN D 121 HIS ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN E 121 HIS E 188 ASN E 314 GLN ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN F 314 GLN F 388 GLN F 393 ASN G 121 HIS G 314 GLN G 388 GLN G 393 ASN H 121 HIS H 314 GLN 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 = 0.3690 r_free = 0.3690 target = 0.148899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120768 restraints weight = 32457.130| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.21 r_work: 0.3189 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 32040 Z= 0.112 Angle : 0.452 4.218 43128 Z= 0.258 Chirality : 0.039 0.135 4764 Planarity : 0.003 0.041 5448 Dihedral : 5.020 179.434 4200 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.81 % Allowed : 12.13 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.14), residues: 3732 helix: 1.78 (0.12), residues: 2028 sheet: -0.18 (0.21), residues: 600 loop : -0.32 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 121 PHE 0.017 0.001 PHE B 269 TYR 0.022 0.001 TYR H 177 ARG 0.004 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.05156 ( 1740) hydrogen bonds : angle 4.68986 ( 5040) covalent geometry : bond 0.00223 (32040) covalent geometry : angle 0.45238 (43128) *********************** 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 526 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 463 time to evaluate : 3.860 Fit side-chains REVERT: A 181 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7930 (tm-30) REVERT: A 326 ARG cc_start: 0.7369 (mmt90) cc_final: 0.7031 (mmt180) REVERT: A 357 LYS cc_start: 0.7642 (tttm) cc_final: 0.7251 (tttt) REVERT: A 403 LYS cc_start: 0.7226 (ttpt) cc_final: 0.6971 (mtmm) REVERT: B 120 ASP cc_start: 0.7299 (p0) cc_final: 0.6944 (p0) REVERT: B 181 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: B 290 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7704 (mm-30) REVERT: B 403 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6916 (pttm) REVERT: C 55 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6943 (mp) REVERT: C 181 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7769 (pp20) REVERT: C 290 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7804 (mm-30) REVERT: C 341 GLU cc_start: 0.8214 (mt-10) cc_final: 0.8007 (mt-10) REVERT: C 357 LYS cc_start: 0.8105 (tppt) cc_final: 0.7416 (tttm) REVERT: C 403 LYS cc_start: 0.7391 (ttpt) cc_final: 0.7040 (mtmm) REVERT: D 181 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: D 290 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7785 (mm-30) REVERT: D 326 ARG cc_start: 0.7355 (mmt90) cc_final: 0.6978 (mmt180) REVERT: D 357 LYS cc_start: 0.8055 (tppt) cc_final: 0.7535 (tttt) REVERT: E 120 ASP cc_start: 0.7445 (p0) cc_final: 0.7056 (p0) REVERT: E 181 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: E 357 LYS cc_start: 0.8118 (tppt) cc_final: 0.7504 (tttm) REVERT: F 64 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7745 (t0) REVERT: F 121 HIS cc_start: 0.7841 (p-80) cc_final: 0.7602 (p-80) REVERT: F 269 PHE cc_start: 0.8428 (t80) cc_final: 0.8179 (t80) REVERT: F 290 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: F 402 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: G 326 ARG cc_start: 0.7356 (mmt90) cc_final: 0.7000 (mmt180) REVERT: H 144 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.8050 (mtt-85) REVERT: H 181 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: H 357 LYS cc_start: 0.8064 (tppt) cc_final: 0.7483 (tttp) REVERT: I 55 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7021 (mp) REVERT: I 144 ARG cc_start: 0.8284 (mtt-85) cc_final: 0.7914 (mtt-85) REVERT: I 290 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: J 20 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8217 (ttmm) REVERT: J 181 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7927 (pp20) REVERT: J 326 ARG cc_start: 0.7336 (mmt90) cc_final: 0.6977 (mmt180) REVERT: J 399 MET cc_start: 0.6391 (OUTLIER) cc_final: 0.6081 (tpt) REVERT: K 120 ASP cc_start: 0.7495 (p0) cc_final: 0.7132 (p0) REVERT: K 144 ARG cc_start: 0.8359 (mtt-85) cc_final: 0.8127 (mtt-85) REVERT: K 339 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8245 (mp-120) REVERT: K 357 LYS cc_start: 0.8080 (tppt) cc_final: 0.7523 (tttp) REVERT: L 121 HIS cc_start: 0.7779 (p-80) cc_final: 0.7516 (p-80) REVERT: L 403 LYS cc_start: 0.7351 (ttpt) cc_final: 0.7008 (mtmm) outliers start: 63 outliers final: 14 residues processed: 499 average time/residue: 1.9868 time to fit residues: 1119.4597 Evaluate side-chains 459 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 426 time to evaluate : 3.682 ------------------------------------------------------------------------------- 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 B residue 181 GLU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 290 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 123 THR Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 402 GLU 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 290 GLU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 89 LEU 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 339 GLN Chi-restraints excluded: chain L residue 57 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 164 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 104 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 314 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 314 GLN C 320 ASN C 388 GLN C 393 ASN D 94 GLN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN E 121 HIS E 314 GLN E 388 GLN F 314 GLN F 320 ASN F 388 GLN F 393 ASN G 121 HIS G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 GLN ** H 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 314 GLN I 320 ASN 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 314 GLN L 188 ASN L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.117061 restraints weight = 31966.464| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.19 r_work: 0.3129 rms_B_bonded: 1.71 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: 0.8398 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32040 Z= 0.193 Angle : 0.585 5.089 43128 Z= 0.328 Chirality : 0.044 0.148 4764 Planarity : 0.004 0.054 5448 Dihedral : 5.517 179.415 4200 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.33 % Allowed : 11.09 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3732 helix: 1.38 (0.12), residues: 2028 sheet: -0.15 (0.22), residues: 600 loop : -0.49 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 76 PHE 0.025 0.002 PHE E 269 TYR 0.028 0.002 TYR L 177 ARG 0.007 0.001 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.07005 ( 1740) hydrogen bonds : angle 5.12186 ( 5040) covalent geometry : bond 0.00438 (32040) covalent geometry : angle 0.58460 (43128) *********************** 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 527 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 446 time to evaluate : 4.038 Fit side-chains REVERT: B 120 ASP cc_start: 0.7294 (p0) cc_final: 0.6917 (p0) REVERT: B 144 ARG cc_start: 0.8305 (mtt-85) cc_final: 0.8051 (mtt-85) REVERT: B 290 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: B 403 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7056 (pttm) REVERT: C 64 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7760 (t0) REVERT: C 341 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8117 (mt-10) REVERT: D 181 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: D 290 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7931 (mm-30) REVERT: D 403 LYS cc_start: 0.7422 (ttpt) cc_final: 0.7212 (mtmm) REVERT: E 120 ASP cc_start: 0.7451 (p0) cc_final: 0.7058 (p0) REVERT: E 144 ARG cc_start: 0.8264 (mtt-85) cc_final: 0.8041 (mtt-85) REVERT: E 181 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: E 388 GLN cc_start: 0.7153 (mt0) cc_final: 0.6950 (mt0) REVERT: F 64 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7804 (t0) REVERT: F 121 HIS cc_start: 0.7917 (p-80) cc_final: 0.7685 (p-80) REVERT: F 403 LYS cc_start: 0.7510 (ttpt) cc_final: 0.7304 (mtmm) REVERT: G 357 LYS cc_start: 0.7667 (tttm) cc_final: 0.7431 (tttt) REVERT: H 105 GLU cc_start: 0.7810 (pt0) cc_final: 0.7449 (tp30) REVERT: H 120 ASP cc_start: 0.7488 (p0) cc_final: 0.7058 (p0) REVERT: H 144 ARG cc_start: 0.8301 (mtt-85) cc_final: 0.8064 (mtt-85) REVERT: H 181 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: H 375 LYS cc_start: 0.8363 (tptt) cc_final: 0.8035 (tptm) REVERT: J 20 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8220 (ttmm) REVERT: J 181 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7974 (pp20) REVERT: J 357 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7738 (mmmt) REVERT: K 120 ASP cc_start: 0.7484 (p0) cc_final: 0.7115 (p0) REVERT: K 403 LYS cc_start: 0.7381 (ttpt) cc_final: 0.6864 (tttt) REVERT: L 64 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7779 (t0) REVERT: L 121 HIS cc_start: 0.7887 (p-80) cc_final: 0.7640 (p-80) REVERT: L 372 ARG cc_start: 0.8142 (mmm-85) cc_final: 0.7886 (mmt90) REVERT: L 403 LYS cc_start: 0.7449 (ttpt) cc_final: 0.7215 (mtmm) outliers start: 81 outliers final: 27 residues processed: 493 average time/residue: 1.9494 time to fit residues: 1091.5087 Evaluate side-chains 454 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 416 time to evaluate : 3.662 ------------------------------------------------------------------------------- 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 89 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain 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 181 GLU Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 185 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 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 K residue 89 LEU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 64 ASN Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 11 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 234 optimal weight: 5.9990 chunk 263 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 302 optimal weight: 0.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** A 388 GLN B 314 GLN B 320 ASN C 314 GLN C 320 ASN C 388 GLN C 393 ASN D 314 GLN E 121 HIS E 320 ASN E 393 ASN F 314 GLN F 388 GLN F 393 ASN G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 121 HIS I 314 GLN I 388 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.147164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118899 restraints weight = 32239.552| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.19 r_work: 0.3158 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 32040 Z= 0.128 Angle : 0.479 4.225 43128 Z= 0.273 Chirality : 0.040 0.139 4764 Planarity : 0.003 0.040 5448 Dihedral : 5.287 178.314 4200 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.55 % Allowed : 11.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.14), residues: 3732 helix: 1.65 (0.12), residues: 2028 sheet: -0.05 (0.22), residues: 600 loop : -0.37 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 121 PHE 0.019 0.002 PHE E 269 TYR 0.023 0.001 TYR H 177 ARG 0.004 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.05652 ( 1740) hydrogen bonds : angle 4.80201 ( 5040) covalent geometry : bond 0.00268 (32040) covalent geometry : angle 0.47856 (43128) *********************** 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 511 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 457 time to evaluate : 4.098 Fit side-chains REVERT: A 326 ARG cc_start: 0.7429 (mmt90) cc_final: 0.7016 (mmt180) REVERT: A 357 LYS cc_start: 0.7663 (tttm) cc_final: 0.7313 (tttt) REVERT: B 120 ASP cc_start: 0.7379 (p0) cc_final: 0.6986 (p0) REVERT: B 144 ARG cc_start: 0.8287 (mtt-85) cc_final: 0.8035 (mtt-85) REVERT: B 290 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: C 144 ARG cc_start: 0.8253 (mtt-85) cc_final: 0.7971 (mtt-85) REVERT: D 181 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: D 185 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: D 290 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7859 (mm-30) REVERT: D 326 ARG cc_start: 0.7431 (mmt90) cc_final: 0.7013 (mmt180) REVERT: D 357 LYS cc_start: 0.8142 (tppt) cc_final: 0.7653 (tttt) REVERT: D 403 LYS cc_start: 0.7394 (ttpt) cc_final: 0.7188 (mtmm) REVERT: E 120 ASP cc_start: 0.7481 (p0) cc_final: 0.7071 (p0) REVERT: E 144 ARG cc_start: 0.8249 (mtt-85) cc_final: 0.8025 (mtt-85) REVERT: E 181 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: E 357 LYS cc_start: 0.8143 (tppt) cc_final: 0.7497 (tttm) REVERT: E 388 GLN cc_start: 0.7087 (mt0) cc_final: 0.6876 (mt0) REVERT: F 64 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7795 (t0) REVERT: F 121 HIS cc_start: 0.7928 (p-80) cc_final: 0.7722 (p-80) REVERT: F 403 LYS cc_start: 0.7483 (ttpt) cc_final: 0.7251 (mtmm) REVERT: G 326 ARG cc_start: 0.7410 (mmt90) cc_final: 0.7000 (mmt180) REVERT: G 357 LYS cc_start: 0.7636 (tttm) cc_final: 0.7410 (tttt) REVERT: H 105 GLU cc_start: 0.7849 (pt0) cc_final: 0.7492 (tp30) REVERT: H 144 ARG cc_start: 0.8301 (mtt-85) cc_final: 0.8054 (mtt-85) REVERT: H 181 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: I 144 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.8089 (mtt-85) REVERT: J 20 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8220 (ttmm) REVERT: J 181 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7861 (pp20) REVERT: J 326 ARG cc_start: 0.7393 (mmt90) cc_final: 0.6983 (mmt180) REVERT: J 357 LYS cc_start: 0.7927 (mmmm) cc_final: 0.7586 (tttm) REVERT: J 399 MET cc_start: 0.6562 (ttp) cc_final: 0.6140 (tpt) REVERT: K 120 ASP cc_start: 0.7502 (p0) cc_final: 0.7111 (p0) REVERT: K 403 LYS cc_start: 0.7454 (ttpt) cc_final: 0.6870 (tttt) REVERT: L 144 ARG cc_start: 0.8251 (mtt-85) cc_final: 0.8022 (mtt-85) REVERT: L 269 PHE cc_start: 0.8462 (t80) cc_final: 0.8238 (t80) REVERT: L 403 LYS cc_start: 0.7400 (ttpt) cc_final: 0.7190 (mtmm) outliers start: 54 outliers final: 21 residues processed: 488 average time/residue: 1.9703 time to fit residues: 1088.6551 Evaluate side-chains 465 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 435 time to evaluate : 3.572 ------------------------------------------------------------------------------- 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 B residue 290 GLU 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 64 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 185 GLU 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 E residue 185 GLU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 170 ILE 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 H residue 185 GLU Chi-restraints excluded: chain I residue 57 ARG 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 K residue 123 THR Chi-restraints excluded: chain L residue 57 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 239 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 314 GLN C 320 ASN C 393 ASN D 314 GLN E 121 HIS E 314 GLN E 320 ASN E 393 ASN F 314 GLN F 320 ASN F 393 ASN G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 121 HIS I 314 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN 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 = 0.3638 r_free = 0.3638 target = 0.144494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116214 restraints weight = 32286.680| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.15 r_work: 0.3115 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2538 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= 0.198 Angle : 0.590 4.950 43128 Z= 0.331 Chirality : 0.044 0.146 4764 Planarity : 0.004 0.048 5448 Dihedral : 5.637 177.269 4200 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.98 % Allowed : 11.61 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3732 helix: 1.28 (0.12), residues: 2028 sheet: -0.10 (0.22), residues: 600 loop : -0.56 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS K 121 PHE 0.024 0.002 PHE G 269 TYR 0.027 0.002 TYR L 177 ARG 0.005 0.001 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.07107 ( 1740) hydrogen bonds : angle 5.13517 ( 5040) covalent geometry : bond 0.00452 (32040) covalent geometry : angle 0.59006 (43128) *********************** 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 505 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 436 time to evaluate : 3.679 Fit side-chains REVERT: B 120 ASP cc_start: 0.7373 (p0) cc_final: 0.6957 (p0) REVERT: B 121 HIS cc_start: 0.8041 (p-80) cc_final: 0.7648 (p90) REVERT: B 290 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: B 403 LYS cc_start: 0.7328 (ptmt) cc_final: 0.6910 (mtmm) REVERT: D 181 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: D 290 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7983 (mm-30) REVERT: D 357 LYS cc_start: 0.8179 (tppt) cc_final: 0.7592 (tttm) REVERT: D 403 LYS cc_start: 0.7435 (ttpt) cc_final: 0.7207 (mtmm) REVERT: E 120 ASP cc_start: 0.7448 (p0) cc_final: 0.7074 (p0) REVERT: E 121 HIS cc_start: 0.8007 (p90) cc_final: 0.7616 (p90) REVERT: E 144 ARG cc_start: 0.8302 (mtt-85) cc_final: 0.8064 (mtt-85) REVERT: E 181 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: F 64 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7819 (t0) REVERT: F 121 HIS cc_start: 0.8025 (p-80) cc_final: 0.7815 (p-80) REVERT: F 185 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: F 403 LYS cc_start: 0.7556 (ttpt) cc_final: 0.7313 (mtmm) REVERT: G 357 LYS cc_start: 0.7663 (tttm) cc_final: 0.7307 (tttt) REVERT: H 105 GLU cc_start: 0.7835 (pt0) cc_final: 0.7463 (tp30) REVERT: H 120 ASP cc_start: 0.7478 (p0) cc_final: 0.7038 (p0) REVERT: H 144 ARG cc_start: 0.8340 (mtt-85) cc_final: 0.8105 (mtt-85) REVERT: H 181 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: I 185 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: J 20 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8223 (ttmm) REVERT: J 181 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8121 (pp20) REVERT: K 120 ASP cc_start: 0.7471 (p0) cc_final: 0.7086 (p0) REVERT: K 403 LYS cc_start: 0.7408 (ttpt) cc_final: 0.6869 (tttt) REVERT: L 372 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7941 (mmt90) REVERT: L 403 LYS cc_start: 0.7453 (ttpt) cc_final: 0.7220 (mtmm) outliers start: 69 outliers final: 23 residues processed: 481 average time/residue: 1.9701 time to fit residues: 1074.9867 Evaluate side-chains 459 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 426 time to evaluate : 3.967 ------------------------------------------------------------------------------- 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 290 GLU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 185 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 123 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 185 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 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 L residue 57 ARG Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 6.9990 chunk 265 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 191 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.0030 chunk 1 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN C 314 GLN C 388 GLN C 393 ASN D 314 GLN E 314 GLN E 393 ASN F 314 GLN F 388 GLN F 393 ASN G 314 GLN G 388 GLN G 393 ASN H 314 GLN H 388 GLN I 121 HIS I 314 GLN I 388 GLN I 393 ASN J 314 GLN J 320 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN L 188 ASN L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.149830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121439 restraints weight = 32447.567| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.19 r_work: 0.3197 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32040 Z= 0.100 Angle : 0.434 5.675 43128 Z= 0.249 Chirality : 0.038 0.137 4764 Planarity : 0.003 0.039 5448 Dihedral : 5.130 179.777 4200 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.98 % Allowed : 12.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.14), residues: 3732 helix: 1.95 (0.12), residues: 2028 sheet: 0.04 (0.23), residues: 600 loop : -0.24 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS K 121 PHE 0.014 0.001 PHE E 189 TYR 0.019 0.001 TYR K 177 ARG 0.004 0.000 ARG F 144 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 1740) hydrogen bonds : angle 4.46754 ( 5040) covalent geometry : bond 0.00196 (32040) covalent geometry : angle 0.43434 (43128) *********************** 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 479 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 445 time to evaluate : 3.806 Fit side-chains REVERT: A 326 ARG cc_start: 0.7390 (mmt90) cc_final: 0.6993 (mmt180) REVERT: A 357 LYS cc_start: 0.7874 (tttt) cc_final: 0.7632 (tttm) REVERT: B 120 ASP cc_start: 0.7382 (p0) cc_final: 0.6932 (p0) REVERT: B 121 HIS cc_start: 0.8069 (p-80) cc_final: 0.7654 (p-80) REVERT: B 144 ARG cc_start: 0.8208 (mtt-85) cc_final: 0.8002 (mtt-85) REVERT: B 290 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: B 403 LYS cc_start: 0.7304 (ptmt) cc_final: 0.6716 (ptpt) REVERT: C 121 HIS cc_start: 0.7733 (p-80) cc_final: 0.7520 (p-80) REVERT: C 269 PHE cc_start: 0.8515 (t80) cc_final: 0.8245 (t80) REVERT: C 290 GLU cc_start: 0.8083 (mp0) cc_final: 0.7736 (mm-30) REVERT: D 181 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: D 290 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7750 (mm-30) REVERT: D 326 ARG cc_start: 0.7401 (mmt90) cc_final: 0.7003 (mmt180) REVERT: D 357 LYS cc_start: 0.8118 (tppt) cc_final: 0.7521 (tttm) REVERT: D 403 LYS cc_start: 0.7317 (ttpt) cc_final: 0.7103 (mtmm) REVERT: E 120 ASP cc_start: 0.7500 (p0) cc_final: 0.7101 (p0) REVERT: E 121 HIS cc_start: 0.8007 (p90) cc_final: 0.7573 (p90) REVERT: E 144 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7991 (mtt-85) REVERT: E 181 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: F 269 PHE cc_start: 0.8528 (t80) cc_final: 0.8274 (t80) REVERT: F 403 LYS cc_start: 0.7457 (ttpt) cc_final: 0.7213 (mtmm) REVERT: G 326 ARG cc_start: 0.7389 (mmt90) cc_final: 0.7002 (mmt180) REVERT: H 105 GLU cc_start: 0.7828 (pt0) cc_final: 0.7538 (tp30) REVERT: H 144 ARG cc_start: 0.8294 (mtt-85) cc_final: 0.8067 (mtt-85) REVERT: H 181 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: I 144 ARG cc_start: 0.8349 (mtt-85) cc_final: 0.7974 (mtt-85) REVERT: I 269 PHE cc_start: 0.8519 (t80) cc_final: 0.8283 (t80) REVERT: I 290 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7757 (mm-30) REVERT: J 181 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7875 (pp20) REVERT: J 326 ARG cc_start: 0.7399 (mmt90) cc_final: 0.6999 (mmt180) REVERT: J 357 LYS cc_start: 0.7939 (mmmm) cc_final: 0.7462 (tttm) REVERT: J 399 MET cc_start: 0.6469 (ttp) cc_final: 0.6123 (tpt) REVERT: K 120 ASP cc_start: 0.7511 (p0) cc_final: 0.7153 (p0) REVERT: K 357 LYS cc_start: 0.8117 (tppt) cc_final: 0.7520 (tttp) REVERT: K 403 LYS cc_start: 0.7360 (ttpt) cc_final: 0.6794 (tttt) REVERT: L 269 PHE cc_start: 0.8465 (t80) cc_final: 0.8225 (t80) REVERT: L 290 GLU cc_start: 0.8051 (mp0) cc_final: 0.7718 (mm-30) REVERT: L 357 LYS cc_start: 0.8096 (tppt) cc_final: 0.7463 (tttm) REVERT: L 403 LYS cc_start: 0.7419 (ttpt) cc_final: 0.7181 (mtmm) outliers start: 34 outliers final: 1 residues processed: 465 average time/residue: 1.9465 time to fit residues: 1024.1692 Evaluate side-chains 431 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 423 time to evaluate : 3.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain B residue 290 GLU 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 H residue 181 GLU Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain J residue 181 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 86 optimal weight: 9.9990 chunk 258 optimal weight: 0.5980 chunk 310 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 chunk 272 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 281 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 314 GLN C 393 ASN D 314 GLN E 314 GLN E 320 ASN E 393 ASN F 314 GLN F 393 ASN G 314 GLN G 393 ASN H 314 GLN I 121 HIS I 314 GLN I 393 ASN J 314 GLN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN L 121 HIS L 314 GLN L 393 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.119634 restraints weight = 32226.015| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.16 r_work: 0.3170 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 32040 Z= 0.119 Angle : 0.474 6.118 43128 Z= 0.269 Chirality : 0.040 0.136 4764 Planarity : 0.003 0.036 5448 Dihedral : 5.210 179.137 4200 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.95 % Allowed : 13.62 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.14), residues: 3732 helix: 1.91 (0.12), residues: 2028 sheet: 0.03 (0.23), residues: 600 loop : -0.23 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS K 121 PHE 0.017 0.001 PHE E 269 TYR 0.022 0.001 TYR H 177 ARG 0.006 0.000 ARG K 144 Details of bonding type rmsd hydrogen bonds : bond 0.05306 ( 1740) hydrogen bonds : angle 4.61616 ( 5040) covalent geometry : bond 0.00246 (32040) covalent geometry : angle 0.47388 (43128) *********************** 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 474 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 441 time to evaluate : 3.689 Fit side-chains REVERT: A 326 ARG cc_start: 0.7418 (mmt90) cc_final: 0.7023 (mmt180) REVERT: B 120 ASP cc_start: 0.7374 (p0) cc_final: 0.6916 (p0) REVERT: B 121 HIS cc_start: 0.8018 (p-80) cc_final: 0.7608 (p-80) REVERT: B 144 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.8039 (mtt-85) REVERT: B 290 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7759 (mm-30) REVERT: B 403 LYS cc_start: 0.7309 (ptmt) cc_final: 0.6736 (ptpt) REVERT: C 120 ASP cc_start: 0.7426 (p0) cc_final: 0.7089 (p0) REVERT: D 290 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7825 (mm-30) REVERT: D 326 ARG cc_start: 0.7424 (mmt90) cc_final: 0.7023 (mmt180) REVERT: D 357 LYS cc_start: 0.8123 (tppt) cc_final: 0.7514 (tttm) REVERT: D 392 PHE cc_start: 0.7507 (m-80) cc_final: 0.7246 (m-80) REVERT: D 403 LYS cc_start: 0.7373 (ttpt) cc_final: 0.7155 (mtmm) REVERT: E 120 ASP cc_start: 0.7489 (p0) cc_final: 0.7097 (p0) REVERT: E 121 HIS cc_start: 0.7972 (p90) cc_final: 0.7563 (p90) REVERT: E 144 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.8032 (mtt-85) REVERT: E 181 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: E 357 LYS cc_start: 0.8134 (tppt) cc_final: 0.7486 (tttm) REVERT: F 403 LYS cc_start: 0.7465 (ttpt) cc_final: 0.7208 (mtmm) REVERT: G 326 ARG cc_start: 0.7418 (mmt90) cc_final: 0.7027 (mmt180) REVERT: H 105 GLU cc_start: 0.7819 (pt0) cc_final: 0.7530 (tp30) REVERT: H 120 ASP cc_start: 0.7510 (p0) cc_final: 0.7076 (p0) REVERT: H 144 ARG cc_start: 0.8314 (mtt-85) cc_final: 0.8072 (mtt-85) REVERT: H 181 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: I 144 ARG cc_start: 0.8354 (mtt-85) cc_final: 0.8083 (mtt-85) REVERT: I 290 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7924 (mm-30) REVERT: J 181 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7845 (pp20) REVERT: J 326 ARG cc_start: 0.7414 (mmt90) cc_final: 0.7009 (mmt180) REVERT: J 357 LYS cc_start: 0.7944 (mmmm) cc_final: 0.7475 (tttm) REVERT: J 399 MET cc_start: 0.6547 (ttp) cc_final: 0.6208 (tpt) REVERT: K 120 ASP cc_start: 0.7493 (p0) cc_final: 0.7137 (p0) REVERT: K 357 LYS cc_start: 0.8127 (tppt) cc_final: 0.7544 (tttp) REVERT: K 403 LYS cc_start: 0.7303 (ttpt) cc_final: 0.6745 (tttt) REVERT: L 269 PHE cc_start: 0.8528 (t80) cc_final: 0.8278 (t80) REVERT: L 357 LYS cc_start: 0.8092 (tppt) cc_final: 0.7472 (tttm) REVERT: L 403 LYS cc_start: 0.7435 (ttpt) cc_final: 0.7151 (mtmm) REVERT: L 406 SER cc_start: 0.7208 (m) cc_final: 0.6556 (t) outliers start: 33 outliers final: 5 residues processed: 459 average time/residue: 1.9626 time to fit residues: 1023.1418 Evaluate side-chains 435 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 424 time to evaluate : 4.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 355 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 146 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 319 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 353 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 121 HIS B 314 GLN B 388 GLN C 121 HIS C 314 GLN C 320 ASN C 393 ASN D 314 GLN E 314 GLN E 320 ASN E 388 GLN E 393 ASN F 314 GLN F 320 ASN F 393 ASN G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 ASN H 314 GLN H 388 GLN I 121 HIS I 314 GLN I 393 ASN J 314 GLN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN L 121 HIS L 188 ASN L 314 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 = 0.3634 r_free = 0.3634 target = 0.144209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.115793 restraints weight = 32200.559| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.17 r_work: 0.3101 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 32040 Z= 0.243 Angle : 0.663 8.389 43128 Z= 0.367 Chirality : 0.047 0.169 4764 Planarity : 0.005 0.057 5448 Dihedral : 5.757 176.592 4200 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.98 % Allowed : 13.48 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3732 helix: 1.21 (0.12), residues: 2016 sheet: -0.35 (0.22), residues: 624 loop : -0.61 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS K 121 PHE 0.029 0.003 PHE E 269 TYR 0.029 0.003 TYR L 177 ARG 0.007 0.001 ARG K 144 Details of bonding type rmsd hydrogen bonds : bond 0.07648 ( 1740) hydrogen bonds : angle 5.23002 ( 5040) covalent geometry : bond 0.00568 (32040) covalent geometry : angle 0.66309 (43128) ********************** 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 478 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 444 time to evaluate : 3.682 Fit side-chains REVERT: B 55 LEU cc_start: 0.7718 (tp) cc_final: 0.7488 (tp) REVERT: B 120 ASP cc_start: 0.7202 (p0) cc_final: 0.6785 (p0) REVERT: B 121 HIS cc_start: 0.8061 (p90) cc_final: 0.7516 (p-80) REVERT: B 144 ARG cc_start: 0.8300 (mtt-85) cc_final: 0.8062 (mtt-85) REVERT: B 290 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: B 403 LYS cc_start: 0.7298 (ptmt) cc_final: 0.6917 (mtmm) REVERT: C 64 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7864 (t0) REVERT: D 290 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: D 357 LYS cc_start: 0.8198 (tppt) cc_final: 0.7611 (tttm) REVERT: E 120 ASP cc_start: 0.7461 (p0) cc_final: 0.7084 (p0) REVERT: E 121 HIS cc_start: 0.8069 (p90) cc_final: 0.7607 (p90) REVERT: E 144 ARG cc_start: 0.8302 (mtt-85) cc_final: 0.8055 (mtt-85) REVERT: E 181 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: F 64 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7832 (t0) REVERT: F 403 LYS cc_start: 0.7575 (ttpt) cc_final: 0.7354 (mtmm) REVERT: H 55 LEU cc_start: 0.7734 (tp) cc_final: 0.7513 (tp) REVERT: H 105 GLU cc_start: 0.7818 (pt0) cc_final: 0.7465 (tp30) REVERT: H 120 ASP cc_start: 0.7478 (p0) cc_final: 0.7043 (p0) REVERT: H 144 ARG cc_start: 0.8340 (mtt-85) cc_final: 0.8106 (mtt-85) REVERT: H 181 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: H 357 LYS cc_start: 0.8137 (tppt) cc_final: 0.7497 (ttpp) REVERT: I 185 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: J 181 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8181 (pp20) REVERT: J 357 LYS cc_start: 0.7986 (mmmm) cc_final: 0.7509 (tttm) REVERT: K 120 ASP cc_start: 0.7464 (p0) cc_final: 0.7114 (p0) REVERT: K 282 LYS cc_start: 0.8743 (mttm) cc_final: 0.8529 (mtmm) REVERT: K 403 LYS cc_start: 0.7419 (ttpt) cc_final: 0.6863 (tttt) REVERT: L 64 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7853 (t0) REVERT: L 403 LYS cc_start: 0.7525 (ttpt) cc_final: 0.7301 (mtmm) REVERT: L 406 SER cc_start: 0.7229 (m) cc_final: 0.6594 (t) outliers start: 34 outliers final: 7 residues processed: 470 average time/residue: 1.9124 time to fit residues: 1020.8272 Evaluate side-chains 446 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 430 time to evaluate : 3.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 64 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 95 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 chunk 357 optimal weight: 0.2980 chunk 315 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 344 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 chunk 255 optimal weight: 0.1980 chunk 42 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN C 121 HIS C 314 GLN C 393 ASN E 314 GLN E 320 ASN E 388 GLN E 393 ASN F 314 GLN F 393 ASN G 393 ASN H 314 GLN I 121 HIS I 314 GLN I 393 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN L 121 HIS L 188 ASN L 314 GLN L 393 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.118686 restraints weight = 32185.810| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.16 r_work: 0.3157 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32040 Z= 0.128 Angle : 0.493 6.953 43128 Z= 0.280 Chirality : 0.040 0.141 4764 Planarity : 0.003 0.037 5448 Dihedral : 5.383 178.991 4200 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 0.63 % Allowed : 13.76 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.14), residues: 3732 helix: 1.63 (0.12), residues: 2028 sheet: -0.05 (0.22), residues: 600 loop : -0.36 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS K 121 PHE 0.019 0.002 PHE H 269 TYR 0.022 0.001 TYR K 177 ARG 0.009 0.000 ARG K 144 Details of bonding type rmsd hydrogen bonds : bond 0.05585 ( 1740) hydrogen bonds : angle 4.76940 ( 5040) covalent geometry : bond 0.00267 (32040) covalent geometry : angle 0.49264 (43128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29021.95 seconds wall clock time: 500 minutes 19.36 seconds (30019.36 seconds total)