Starting phenix.real_space_refine on Fri Jul 26 05:12:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/07_2024/8pho_17669.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/07_2024/8pho_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/07_2024/8pho_17669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/07_2024/8pho_17669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/07_2024/8pho_17669.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/07_2024/8pho_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 Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 32172 Number of models: 1 Model: "" Number of chains: 24 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: 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: "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: 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: "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: 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: "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: 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: "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: 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: "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: 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: "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: 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: "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: 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: "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: 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: "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: 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: "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: 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: "L" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Time building chain proxies: 18.30, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 12.72 Conformation dependent library (CDL) restraints added in 5.7 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: 3.66 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: 11.15 Time building geometry restraints manager: 13.99 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: 100.69 - 106.89: 372 106.89 - 113.09: 16388 113.09 - 119.29: 9724 119.29 - 125.49: 16524 125.49 - 131.68: 120 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 2.440 nonbonded pdb=" O HOH D 502 " pdb=" O HOH D 533 " model vdw 2.128 2.440 nonbonded pdb=" O HOH J 502 " pdb=" O HOH J 533 " model vdw 2.128 2.440 nonbonded pdb=" O HOH A 502 " pdb=" O HOH A 533 " model vdw 2.128 2.440 nonbonded pdb=" O HOH I 502 " pdb=" O HOH I 533 " model vdw 2.128 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.220 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 84.770 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.170 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:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.920 ------------------------------------------------------------------------------- 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= 0.290 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 3.974 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: 1.9621 time to fit residues: 1542.1852 Evaluate side-chains 492 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 3.803 ------------------------------------------------------------------------------- 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: 0.0000 chunk 281 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 150 optimal weight: 0.0870 chunk 291 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 337 optimal weight: 8.9990 overall best weight: 2.2168 ------------------------------------------------------------------------------- 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 393 ASN D 94 GLN ** D 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN 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 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: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 32040 Z= 0.427 Angle : 1.277 36.405 43128 Z= 0.663 Chirality : 0.069 0.887 4764 Planarity : 0.018 0.437 5448 Dihedral : 5.912 139.914 4200 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.88 % Favored : 98.02 % Rotamer: Outliers : 3.13 % Allowed : 9.80 % Favored : 87.07 % 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: -1.15 (0.13), residues: 3732 helix: -0.43 (0.11), residues: 2004 sheet: -0.79 (0.20), residues: 624 loop : -1.01 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.055 0.005 HIS L 76 PHE 0.198 0.009 PHE H 119 TYR 0.252 0.008 TYR J 383 ARG 0.109 0.004 ARG I 372 *********************** 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 668 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 559 time to evaluate : 3.758 Fit side-chains REVERT: A 55 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7281 (mp) REVERT: A 121 HIS cc_start: 0.7524 (p90) cc_final: 0.7269 (p90) REVERT: A 326 ARG cc_start: 0.7248 (mmt90) cc_final: 0.6951 (mmt180) REVERT: A 372 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7745 (mtm180) REVERT: A 382 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7686 (mmmt) REVERT: B 157 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7575 (ptp90) REVERT: B 382 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7694 (mmmt) REVERT: C 55 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7464 (mp) REVERT: C 57 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.6362 (ttp80) REVERT: C 403 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6833 (pttm) REVERT: D 326 ARG cc_start: 0.7256 (mmt90) cc_final: 0.6945 (mmt180) REVERT: E 120 ASP cc_start: 0.7387 (p0) cc_final: 0.7131 (p0) REVERT: E 382 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7694 (mptt) REVERT: E 403 LYS cc_start: 0.6946 (ptmt) cc_final: 0.6674 (ptpt) REVERT: F 111 TYR cc_start: 0.8460 (m-10) cc_final: 0.8213 (m-10) REVERT: F 121 HIS cc_start: 0.7660 (p-80) cc_final: 0.7451 (p-80) REVERT: F 144 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.8068 (mtt-85) REVERT: F 185 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7316 (mp0) REVERT: F 393 ASN cc_start: 0.5823 (OUTLIER) cc_final: 0.5424 (p0) REVERT: G 110 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: G 121 HIS cc_start: 0.7540 (p-80) cc_final: 0.7239 (p90) REVERT: G 326 ARG cc_start: 0.7267 (mmt90) cc_final: 0.6995 (mmt180) REVERT: G 382 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7677 (mmmt) REVERT: H 181 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: H 375 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7861 (mmtm) REVERT: H 382 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7611 (mptt) REVERT: I 55 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7352 (mp) REVERT: I 121 HIS cc_start: 0.7553 (p-80) cc_final: 0.7339 (p-80) REVERT: I 185 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7132 (mp0) REVERT: I 357 LYS cc_start: 0.7963 (tppt) cc_final: 0.7530 (tmtt) REVERT: I 363 MET cc_start: 0.7454 (mtp) cc_final: 0.7023 (mmt) REVERT: I 391 SER cc_start: 0.6477 (OUTLIER) cc_final: 0.5812 (m) REVERT: J 57 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.6249 (ttp-170) REVERT: J 111 TYR cc_start: 0.8501 (m-10) cc_final: 0.8300 (m-10) REVERT: J 313 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: J 326 ARG cc_start: 0.7236 (mmt90) cc_final: 0.6931 (mmt180) REVERT: J 367 GLU cc_start: 0.7761 (mp0) cc_final: 0.7523 (mp0) REVERT: K 382 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7743 (mmmt) REVERT: K 401 LYS cc_start: 0.6579 (mmmm) cc_final: 0.6332 (mmmm) REVERT: K 403 LYS cc_start: 0.7149 (ptpt) cc_final: 0.6861 (ptpt) REVERT: L 55 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7431 (mp) REVERT: L 110 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: L 121 HIS cc_start: 0.7615 (p-80) cc_final: 0.7409 (p-80) outliers start: 109 outliers final: 18 residues processed: 611 average time/residue: 2.0174 time to fit residues: 1388.4846 Evaluate side-chains 502 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 469 time to evaluate : 4.041 ------------------------------------------------------------------------------- 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 157 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 ARG 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 G residue 170 ILE 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 313 GLU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 102 ILE 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 187 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 281 optimal weight: 7.9990 chunk 230 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 338 optimal weight: 4.9990 chunk 365 optimal weight: 8.9990 chunk 301 optimal weight: 4.9990 chunk 335 optimal weight: 1.9990 chunk 115 optimal weight: 0.0010 chunk 271 optimal weight: 0.6980 overall best weight: 0.8188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 320 ASN B 388 GLN C 61 GLN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 320 ASN C 388 GLN C 393 ASN D 94 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN E 121 HIS E 188 ASN E 314 GLN E 388 GLN F 314 GLN F 339 GLN 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 ** 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 388 GLN L 393 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 32040 Z= 0.125 Angle : 0.434 5.055 43128 Z= 0.249 Chirality : 0.039 0.135 4764 Planarity : 0.003 0.045 5448 Dihedral : 4.928 174.704 4200 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.47 % Allowed : 11.72 % Favored : 86.81 % 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: 0.77 (0.14), residues: 3732 helix: 1.51 (0.12), residues: 2016 sheet: -0.48 (0.21), residues: 624 loop : -0.65 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 121 PHE 0.015 0.001 PHE B 269 TYR 0.022 0.001 TYR L 177 ARG 0.008 0.000 ARG F 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 517 time to evaluate : 4.014 Fit side-chains revert: symmetry clash REVERT: A 119 PHE cc_start: 0.7527 (m-80) cc_final: 0.7116 (m-80) REVERT: A 326 ARG cc_start: 0.7275 (mmt90) cc_final: 0.6988 (mmt180) REVERT: B 120 ASP cc_start: 0.7183 (p0) cc_final: 0.6966 (p0) REVERT: B 144 ARG cc_start: 0.8242 (mtt-85) cc_final: 0.8007 (mtt-85) REVERT: B 181 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: B 382 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7552 (mmtm) REVERT: C 55 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7228 (mp) REVERT: C 181 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7486 (pp20) REVERT: C 357 LYS cc_start: 0.8061 (tppt) cc_final: 0.7628 (tttm) REVERT: C 388 GLN cc_start: 0.6830 (mt0) cc_final: 0.6621 (mt0) REVERT: D 119 PHE cc_start: 0.7578 (m-80) cc_final: 0.7174 (m-80) REVERT: D 181 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: D 326 ARG cc_start: 0.7264 (mmt90) cc_final: 0.6924 (mmt180) REVERT: D 357 LYS cc_start: 0.7883 (tppt) cc_final: 0.7558 (tttt) REVERT: E 120 ASP cc_start: 0.7329 (p0) cc_final: 0.6981 (p0) REVERT: E 181 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: E 357 LYS cc_start: 0.7955 (tppt) cc_final: 0.7672 (tttp) REVERT: F 185 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7164 (mp0) REVERT: F 402 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5956 (mp0) REVERT: G 181 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7242 (tp30) REVERT: G 326 ARG cc_start: 0.7283 (mmt90) cc_final: 0.6999 (mmt180) REVERT: H 119 PHE cc_start: 0.7446 (m-80) cc_final: 0.7078 (m-80) REVERT: H 181 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: I 55 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7349 (mp) REVERT: I 326 ARG cc_start: 0.7243 (mmt180) cc_final: 0.6964 (mmt180) REVERT: J 20 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8250 (ttmm) REVERT: J 119 PHE cc_start: 0.7663 (m-80) cc_final: 0.7263 (m-80) REVERT: J 326 ARG cc_start: 0.7266 (mmt90) cc_final: 0.6960 (mmt180) REVERT: K 120 ASP cc_start: 0.7438 (p0) cc_final: 0.7156 (p0) REVERT: K 144 ARG cc_start: 0.8251 (mtt-85) cc_final: 0.8045 (mtt-85) REVERT: K 357 LYS cc_start: 0.7596 (ttpp) cc_final: 0.7336 (tttp) REVERT: L 55 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7285 (mp) REVERT: L 121 HIS cc_start: 0.7630 (p-80) cc_final: 0.7396 (p-80) outliers start: 51 outliers final: 4 residues processed: 542 average time/residue: 2.0711 time to fit residues: 1262.9802 Evaluate side-chains 455 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 440 time to evaluate : 3.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 55 LEU 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 E residue 181 GLU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 181 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 J residue 20 LYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain L residue 55 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 161 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 339 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 177 optimal weight: 0.0980 chunk 321 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 121 HIS A 314 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN B 121 HIS B 314 GLN B 320 ASN C 314 GLN C 320 ASN C 393 ASN D 94 GLN D 121 HIS D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN E 121 HIS E 314 GLN F 314 GLN F 320 ASN F 393 ASN G 121 HIS G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32040 Z= 0.216 Angle : 0.531 4.945 43128 Z= 0.300 Chirality : 0.042 0.140 4764 Planarity : 0.004 0.055 5448 Dihedral : 5.276 177.743 4200 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.70 % Allowed : 12.24 % 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: 0.93 (0.14), residues: 3732 helix: 1.51 (0.12), residues: 2028 sheet: -0.13 (0.22), residues: 600 loop : -0.51 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 121 PHE 0.025 0.002 PHE E 269 TYR 0.026 0.002 TYR I 177 ARG 0.006 0.001 ARG B 74 *********************** 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 533 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 474 time to evaluate : 3.569 Fit side-chains REVERT: A 326 ARG cc_start: 0.7376 (mmt90) cc_final: 0.7024 (mmt180) REVERT: A 403 LYS cc_start: 0.7259 (ttpt) cc_final: 0.7024 (mtmm) REVERT: B 120 ASP cc_start: 0.7119 (p0) cc_final: 0.6786 (p0) REVERT: C 144 ARG cc_start: 0.8284 (mtt-85) cc_final: 0.7992 (mtt-85) REVERT: C 357 LYS cc_start: 0.8010 (tppt) cc_final: 0.7586 (tttm) REVERT: C 403 LYS cc_start: 0.7336 (ttpt) cc_final: 0.7043 (mtmm) REVERT: D 181 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: D 326 ARG cc_start: 0.7366 (mmt90) cc_final: 0.6995 (mmt180) REVERT: D 357 LYS cc_start: 0.7982 (tppt) cc_final: 0.7652 (tttt) REVERT: D 403 LYS cc_start: 0.7189 (ttpt) cc_final: 0.6986 (mtmm) REVERT: E 120 ASP cc_start: 0.7299 (p0) cc_final: 0.6933 (p0) REVERT: E 139 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7213 (tttm) REVERT: E 144 ARG cc_start: 0.8266 (mtt-85) cc_final: 0.7980 (mtt-85) REVERT: E 181 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: E 357 LYS cc_start: 0.8060 (tppt) cc_final: 0.7658 (tttp) REVERT: E 403 LYS cc_start: 0.7260 (ttpt) cc_final: 0.6743 (tttt) REVERT: F 185 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7178 (mp0) REVERT: F 402 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: G 326 ARG cc_start: 0.7370 (mmt90) cc_final: 0.6980 (mmt180) REVERT: H 181 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: H 357 LYS cc_start: 0.8047 (tppt) cc_final: 0.7628 (tttm) REVERT: J 20 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8201 (ttmm) REVERT: J 326 ARG cc_start: 0.7369 (mmt90) cc_final: 0.7001 (mmt180) REVERT: J 401 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.5915 (mmtp) REVERT: J 403 LYS cc_start: 0.7133 (ttpt) cc_final: 0.6880 (mtmm) REVERT: K 120 ASP cc_start: 0.7328 (p0) cc_final: 0.7009 (p0) REVERT: K 389 SER cc_start: 0.7571 (p) cc_final: 0.7304 (m) REVERT: L 121 HIS cc_start: 0.7693 (p-80) cc_final: 0.7449 (p-80) REVERT: L 357 LYS cc_start: 0.8051 (tppt) cc_final: 0.7632 (tttm) REVERT: L 403 LYS cc_start: 0.7367 (ttpt) cc_final: 0.7070 (mtmm) outliers start: 59 outliers final: 14 residues processed: 503 average time/residue: 1.9385 time to fit residues: 1102.3332 Evaluate side-chains 447 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 426 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain J residue 401 LYS Chi-restraints excluded: chain K residue 185 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 267 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 322 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 320 ASN C 121 HIS C 314 GLN C 320 ASN C 388 GLN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN E 388 GLN F 314 GLN F 320 ASN 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 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** L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32040 Z= 0.272 Angle : 0.574 5.049 43128 Z= 0.323 Chirality : 0.044 0.142 4764 Planarity : 0.004 0.049 5448 Dihedral : 5.533 176.052 4200 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.39 % Allowed : 11.47 % Favored : 86.15 % 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: 1.29 (0.12), residues: 2028 sheet: -0.09 (0.22), residues: 600 loop : -0.61 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 48 PHE 0.025 0.002 PHE E 269 TYR 0.027 0.002 TYR L 177 ARG 0.006 0.001 ARG B 74 *********************** 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 537 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 454 time to evaluate : 3.699 Fit side-chains REVERT: B 120 ASP cc_start: 0.7085 (p0) cc_final: 0.6745 (p0) REVERT: B 357 LYS cc_start: 0.8064 (tppt) cc_final: 0.7625 (tttm) REVERT: C 64 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7690 (t0) REVERT: C 144 ARG cc_start: 0.8305 (mtt-85) cc_final: 0.8099 (mtt-85) REVERT: C 403 LYS cc_start: 0.7398 (ttpt) cc_final: 0.7176 (mtmm) REVERT: D 181 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: D 357 LYS cc_start: 0.8047 (tppt) cc_final: 0.7696 (mmmt) REVERT: E 120 ASP cc_start: 0.7307 (p0) cc_final: 0.6954 (p0) REVERT: E 144 ARG cc_start: 0.8249 (mtt-85) cc_final: 0.7942 (mtt-85) REVERT: E 181 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: E 357 LYS cc_start: 0.8099 (tppt) cc_final: 0.7612 (ttpp) REVERT: E 388 GLN cc_start: 0.7158 (mt0) cc_final: 0.6949 (mt0) REVERT: F 64 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7625 (t0) REVERT: F 185 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7191 (mp0) REVERT: F 403 LYS cc_start: 0.7429 (ttpt) cc_final: 0.7148 (mtmm) REVERT: H 120 ASP cc_start: 0.7280 (p0) cc_final: 0.6870 (p0) REVERT: H 181 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: I 185 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: J 20 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8207 (ttmm) REVERT: J 401 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.5885 (mmtp) REVERT: J 403 LYS cc_start: 0.7341 (ttpt) cc_final: 0.7105 (mtmm) REVERT: K 120 ASP cc_start: 0.7308 (p0) cc_final: 0.6957 (p0) REVERT: K 157 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7766 (ptp90) REVERT: K 403 LYS cc_start: 0.7374 (ttpt) cc_final: 0.6801 (tttt) REVERT: L 64 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7673 (t0) outliers start: 83 outliers final: 28 residues processed: 500 average time/residue: 1.9628 time to fit residues: 1110.4141 Evaluate side-chains 474 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 436 time to evaluate : 3.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 389 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 389 SER 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 389 SER 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 389 SER Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain J residue 401 LYS Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain L residue 64 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 389 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 4.9990 chunk 323 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 359 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 320 ASN C 121 HIS C 314 GLN C 320 ASN C 388 GLN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN E 320 ASN F 314 GLN F 388 GLN F 393 ASN G 314 GLN H 314 GLN H 393 ASN I 314 GLN I 388 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32040 Z= 0.197 Angle : 0.497 4.360 43128 Z= 0.283 Chirality : 0.041 0.142 4764 Planarity : 0.003 0.043 5448 Dihedral : 5.381 178.593 4200 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.07 % Allowed : 11.78 % Favored : 86.15 % 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: 0.94 (0.14), residues: 3732 helix: 1.50 (0.12), residues: 2028 sheet: -0.03 (0.22), residues: 600 loop : -0.52 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 76 PHE 0.020 0.002 PHE E 269 TYR 0.024 0.002 TYR K 177 ARG 0.004 0.000 ARG B 74 *********************** 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 532 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 460 time to evaluate : 3.915 Fit side-chains REVERT: A 326 ARG cc_start: 0.7372 (mmt90) cc_final: 0.6990 (mmt180) REVERT: A 341 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7876 (tt0) REVERT: A 357 LYS cc_start: 0.7905 (tppp) cc_final: 0.7595 (tttm) REVERT: B 120 ASP cc_start: 0.7085 (p0) cc_final: 0.6718 (p0) REVERT: B 121 HIS cc_start: 0.7883 (p-80) cc_final: 0.7422 (p-80) REVERT: B 403 LYS cc_start: 0.7701 (mtmm) cc_final: 0.7344 (mtmm) REVERT: C 144 ARG cc_start: 0.8296 (mtt-85) cc_final: 0.8014 (mtt-85) REVERT: C 403 LYS cc_start: 0.7403 (ttpt) cc_final: 0.7171 (mtmm) REVERT: D 181 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: D 326 ARG cc_start: 0.7387 (mmt90) cc_final: 0.6950 (mmt-90) REVERT: E 20 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8439 (mtmm) REVERT: E 120 ASP cc_start: 0.7313 (p0) cc_final: 0.6944 (p0) REVERT: E 181 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: E 403 LYS cc_start: 0.7392 (mtpp) cc_final: 0.7147 (mtmm) REVERT: F 64 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7614 (t0) REVERT: F 185 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7166 (mp0) REVERT: F 290 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7865 (mm-30) REVERT: F 403 LYS cc_start: 0.7451 (ttpt) cc_final: 0.7137 (mtmm) REVERT: G 326 ARG cc_start: 0.7361 (mmt90) cc_final: 0.6977 (mmt180) REVERT: H 120 ASP cc_start: 0.7302 (p0) cc_final: 0.6898 (p0) REVERT: H 181 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: I 185 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: J 20 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8201 (ttmm) REVERT: J 181 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7876 (pp20) REVERT: J 326 ARG cc_start: 0.7374 (mmt90) cc_final: 0.6989 (mmt180) REVERT: J 403 LYS cc_start: 0.7270 (ttpt) cc_final: 0.7063 (mtmm) REVERT: K 120 ASP cc_start: 0.7353 (p0) cc_final: 0.7012 (p0) REVERT: K 157 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7746 (ptp90) REVERT: K 403 LYS cc_start: 0.7390 (ttpt) cc_final: 0.6813 (tttt) outliers start: 72 outliers final: 28 residues processed: 505 average time/residue: 1.9902 time to fit residues: 1138.3693 Evaluate side-chains 477 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 439 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 389 SER 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 389 SER Chi-restraints excluded: chain E residue 20 LYS 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 123 THR Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 389 SER Chi-restraints excluded: chain L residue 64 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 389 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 358 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 B 320 ASN C 121 HIS C 314 GLN C 320 ASN C 388 GLN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN E 320 ASN E 393 ASN F 314 GLN F 320 ASN F 393 ASN G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN H 393 ASN I 314 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 HIS K 314 GLN L 314 GLN L 393 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 32040 Z= 0.293 Angle : 0.590 4.908 43128 Z= 0.331 Chirality : 0.044 0.148 4764 Planarity : 0.004 0.050 5448 Dihedral : 5.636 176.640 4200 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.21 % Allowed : 11.67 % Favored : 86.12 % 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: 0.53 (0.14), residues: 3732 helix: 1.20 (0.12), residues: 2016 sheet: -0.32 (0.22), residues: 624 loop : -0.69 (0.16), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 48 PHE 0.025 0.002 PHE L 269 TYR 0.027 0.002 TYR I 177 ARG 0.006 0.001 ARG H 144 *********************** 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 523 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 446 time to evaluate : 3.462 Fit side-chains REVERT: B 120 ASP cc_start: 0.7060 (p0) cc_final: 0.6684 (p0) REVERT: B 121 HIS cc_start: 0.7871 (p-80) cc_final: 0.7353 (p-80) REVERT: B 139 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7203 (tttm) REVERT: C 64 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7648 (t0) REVERT: C 403 LYS cc_start: 0.7447 (ttpt) cc_final: 0.7207 (mtmm) REVERT: D 181 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: D 357 LYS cc_start: 0.8045 (tppt) cc_final: 0.7641 (tttm) REVERT: E 120 ASP cc_start: 0.7315 (p0) cc_final: 0.6938 (p0) REVERT: E 121 HIS cc_start: 0.7848 (p-80) cc_final: 0.7473 (p90) REVERT: E 139 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7161 (tttm) REVERT: E 144 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.7951 (mtt-85) REVERT: E 181 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: E 403 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7148 (mtmm) REVERT: F 64 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7627 (t0) REVERT: F 185 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7305 (mp0) REVERT: H 120 ASP cc_start: 0.7287 (p0) cc_final: 0.6892 (p0) REVERT: H 181 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: I 185 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7591 (tt0) REVERT: J 20 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8193 (ttmm) REVERT: J 181 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8143 (pp20) REVERT: J 357 LYS cc_start: 0.8027 (mtmm) cc_final: 0.7621 (mttm) REVERT: J 401 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.5879 (mmtp) REVERT: J 403 LYS cc_start: 0.7339 (ttpt) cc_final: 0.7124 (mtmm) REVERT: K 120 ASP cc_start: 0.7339 (p0) cc_final: 0.6974 (p0) REVERT: K 121 HIS cc_start: 0.7851 (p90) cc_final: 0.7372 (p90) REVERT: K 139 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7302 (tttm) REVERT: K 157 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7773 (ptp90) REVERT: K 403 LYS cc_start: 0.7312 (ttpt) cc_final: 0.6788 (tttt) REVERT: L 64 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7661 (t0) outliers start: 77 outliers final: 27 residues processed: 494 average time/residue: 1.9072 time to fit residues: 1067.8744 Evaluate side-chains 478 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 436 time to evaluate : 4.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 389 SER 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 389 SER Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 403 LYS Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain J residue 401 LYS Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 139 LYS Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 389 SER Chi-restraints excluded: chain L residue 64 ASN Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 389 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 227 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 281 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 B 320 ASN C 121 HIS C 314 GLN C 388 GLN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN E 320 ASN E 393 ASN F 314 GLN F 393 ASN G 314 GLN H 314 GLN H 393 ASN I 314 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 HIS L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2475 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= 0.179 Angle : 0.485 4.260 43128 Z= 0.277 Chirality : 0.040 0.143 4764 Planarity : 0.003 0.038 5448 Dihedral : 5.391 178.584 4200 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.58 % Allowed : 12.30 % Favored : 86.12 % 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: 0.98 (0.14), residues: 3732 helix: 1.54 (0.12), residues: 2028 sheet: -0.04 (0.22), residues: 600 loop : -0.50 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 76 PHE 0.017 0.002 PHE E 269 TYR 0.024 0.002 TYR K 177 ARG 0.003 0.000 ARG F 144 *********************** 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 511 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 456 time to evaluate : 4.019 Fit side-chains REVERT: A 282 LYS cc_start: 0.8585 (mttm) cc_final: 0.8334 (mttm) REVERT: A 326 ARG cc_start: 0.7398 (mmt90) cc_final: 0.6995 (mmt180) REVERT: B 120 ASP cc_start: 0.7091 (p0) cc_final: 0.6734 (p0) REVERT: B 121 HIS cc_start: 0.7892 (p-80) cc_final: 0.7532 (p90) REVERT: C 403 LYS cc_start: 0.7440 (ttpt) cc_final: 0.7212 (mtmm) REVERT: D 181 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: D 326 ARG cc_start: 0.7382 (mmt90) cc_final: 0.6946 (mmt-90) REVERT: D 357 LYS cc_start: 0.8036 (tppt) cc_final: 0.7665 (tttm) REVERT: E 120 ASP cc_start: 0.7307 (p0) cc_final: 0.6940 (p0) REVERT: E 121 HIS cc_start: 0.7887 (p-80) cc_final: 0.7480 (p90) REVERT: E 181 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: E 403 LYS cc_start: 0.7410 (mtpp) cc_final: 0.7163 (mtmm) REVERT: F 64 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7611 (t0) REVERT: F 185 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7201 (mp0) REVERT: F 403 LYS cc_start: 0.7481 (ttpt) cc_final: 0.7214 (mtmm) REVERT: G 326 ARG cc_start: 0.7393 (mmt90) cc_final: 0.6992 (mmt180) REVERT: H 120 ASP cc_start: 0.7316 (p0) cc_final: 0.6878 (p0) REVERT: H 121 HIS cc_start: 0.7839 (p-80) cc_final: 0.7366 (p-80) REVERT: H 181 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: H 357 LYS cc_start: 0.8047 (tppt) cc_final: 0.7609 (tttm) REVERT: I 185 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: J 20 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8119 (ttmm) REVERT: J 181 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7973 (pp20) REVERT: J 326 ARG cc_start: 0.7377 (mmt90) cc_final: 0.6977 (mmt180) REVERT: J 401 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.5866 (mmtp) REVERT: J 403 LYS cc_start: 0.7274 (ttpt) cc_final: 0.7046 (mtmm) REVERT: K 120 ASP cc_start: 0.7326 (p0) cc_final: 0.6937 (p0) REVERT: K 121 HIS cc_start: 0.7830 (p90) cc_final: 0.7402 (p90) REVERT: K 157 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7740 (ptp90) REVERT: K 403 LYS cc_start: 0.7345 (ttpt) cc_final: 0.6818 (tttt) outliers start: 55 outliers final: 23 residues processed: 488 average time/residue: 1.9752 time to fit residues: 1092.4011 Evaluate side-chains 476 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 444 time to evaluate : 3.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 401 LYS Chi-restraints excluded: chain K residue 157 ARG Chi-restraints excluded: chain K residue 389 SER Chi-restraints excluded: chain L residue 64 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 389 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 0.9990 chunk 343 optimal weight: 4.9990 chunk 313 optimal weight: 5.9990 chunk 334 optimal weight: 0.6980 chunk 201 optimal weight: 7.9990 chunk 145 optimal weight: 0.6980 chunk 262 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 301 optimal weight: 1.9990 chunk 316 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 314 GLN C 121 HIS C 314 GLN C 388 GLN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 HIS E 314 GLN E 320 ASN E 393 ASN F 314 GLN F 393 ASN G 314 GLN H 314 GLN H 393 ASN I 314 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 HIS L 314 GLN L 393 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 32040 Z= 0.152 Angle : 0.458 4.339 43128 Z= 0.262 Chirality : 0.039 0.139 4764 Planarity : 0.003 0.036 5448 Dihedral : 5.274 178.941 4200 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.26 % Allowed : 12.79 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.14), residues: 3732 helix: 1.74 (0.12), residues: 2028 sheet: 0.01 (0.23), residues: 600 loop : -0.39 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 76 PHE 0.017 0.001 PHE E 269 TYR 0.022 0.001 TYR H 177 ARG 0.006 0.000 ARG H 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 448 time to evaluate : 3.664 Fit side-chains REVERT: A 282 LYS cc_start: 0.8567 (mttm) cc_final: 0.8318 (mttm) REVERT: A 326 ARG cc_start: 0.7381 (mmt90) cc_final: 0.6988 (mmt180) REVERT: A 357 LYS cc_start: 0.7874 (tppp) cc_final: 0.7560 (tttt) REVERT: B 120 ASP cc_start: 0.7168 (p0) cc_final: 0.6810 (p0) REVERT: B 121 HIS cc_start: 0.7882 (p-80) cc_final: 0.7520 (p90) REVERT: B 139 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7162 (tttm) REVERT: B 357 LYS cc_start: 0.8035 (tppt) cc_final: 0.7604 (tttm) REVERT: C 120 ASP cc_start: 0.7276 (p0) cc_final: 0.6926 (p0) REVERT: C 403 LYS cc_start: 0.7412 (ttpt) cc_final: 0.7131 (mtmm) REVERT: D 326 ARG cc_start: 0.7366 (mmt90) cc_final: 0.6970 (mmt180) REVERT: D 357 LYS cc_start: 0.8023 (tppt) cc_final: 0.7644 (tttm) REVERT: E 120 ASP cc_start: 0.7321 (p0) cc_final: 0.6960 (p0) REVERT: E 121 HIS cc_start: 0.7866 (p90) cc_final: 0.7445 (p90) REVERT: E 144 ARG cc_start: 0.8245 (mtt-85) cc_final: 0.7949 (mtt-85) REVERT: E 181 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: E 403 LYS cc_start: 0.7408 (mtpp) cc_final: 0.7170 (mtmm) REVERT: F 185 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7181 (mp0) REVERT: F 290 GLU cc_start: 0.8155 (mp0) cc_final: 0.7905 (mm-30) REVERT: F 403 LYS cc_start: 0.7436 (ttpt) cc_final: 0.7160 (mtmm) REVERT: G 326 ARG cc_start: 0.7378 (mmt90) cc_final: 0.6985 (mmt180) REVERT: H 120 ASP cc_start: 0.7305 (p0) cc_final: 0.6926 (p0) REVERT: H 181 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: I 290 GLU cc_start: 0.8143 (mp0) cc_final: 0.7875 (mm-30) REVERT: J 181 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7802 (pp20) REVERT: J 326 ARG cc_start: 0.7379 (mmt90) cc_final: 0.6982 (mmt180) REVERT: J 357 LYS cc_start: 0.7799 (ptmm) cc_final: 0.7599 (ptpp) REVERT: J 401 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.5853 (mmtp) REVERT: J 403 LYS cc_start: 0.7261 (ttpt) cc_final: 0.7025 (mtmm) REVERT: K 120 ASP cc_start: 0.7335 (p0) cc_final: 0.6962 (p0) REVERT: K 121 HIS cc_start: 0.7868 (p90) cc_final: 0.7414 (p90) REVERT: K 403 LYS cc_start: 0.7343 (ttpt) cc_final: 0.6710 (tttt) REVERT: L 357 LYS cc_start: 0.8014 (tppt) cc_final: 0.7574 (tttm) outliers start: 44 outliers final: 18 residues processed: 475 average time/residue: 1.9529 time to fit residues: 1050.1911 Evaluate side-chains 466 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 443 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 401 LYS Chi-restraints excluded: chain K residue 389 SER Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 389 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 8.9990 chunk 353 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 167 optimal weight: 10.0000 chunk 245 optimal weight: 0.9980 chunk 370 optimal weight: 0.9990 chunk 341 optimal weight: 1.9990 chunk 295 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 314 GLN C 121 HIS C 314 GLN C 388 GLN C 393 ASN D 314 GLN E 314 GLN E 393 ASN F 314 GLN F 393 ASN G 314 GLN H 314 GLN H 393 ASN I 314 GLN I 393 ASN J 314 GLN J 320 ASN L 121 HIS L 314 GLN L 393 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 32040 Z= 0.135 Angle : 0.438 4.553 43128 Z= 0.250 Chirality : 0.039 0.138 4764 Planarity : 0.003 0.035 5448 Dihedral : 5.161 179.260 4200 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.86 % Allowed : 13.42 % Favored : 85.72 % 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: 1.42 (0.14), residues: 3732 helix: 1.92 (0.12), residues: 2028 sheet: 0.06 (0.23), residues: 600 loop : -0.30 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 76 PHE 0.014 0.001 PHE B 269 TYR 0.020 0.001 TYR K 177 ARG 0.004 0.000 ARG F 144 ********************** 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 fitting. rotamer outliers: 30 poor density : 448 time to evaluate : 3.651 Fit side-chains REVERT: A 326 ARG cc_start: 0.7358 (mmt90) cc_final: 0.6997 (mmt180) REVERT: A 357 LYS cc_start: 0.7862 (tppp) cc_final: 0.7541 (tttt) REVERT: B 120 ASP cc_start: 0.7169 (p0) cc_final: 0.6801 (p0) REVERT: B 121 HIS cc_start: 0.7882 (p-80) cc_final: 0.7509 (p90) REVERT: B 357 LYS cc_start: 0.8055 (tppt) cc_final: 0.7618 (tttm) REVERT: C 120 ASP cc_start: 0.7290 (p0) cc_final: 0.6955 (p0) REVERT: C 403 LYS cc_start: 0.7394 (ttpt) cc_final: 0.7105 (mtmm) REVERT: C 406 SER cc_start: 0.7216 (m) cc_final: 0.6586 (t) REVERT: D 326 ARG cc_start: 0.7329 (mmt90) cc_final: 0.6966 (mmt180) REVERT: D 357 LYS cc_start: 0.8022 (tppt) cc_final: 0.7564 (tttt) REVERT: E 120 ASP cc_start: 0.7336 (p0) cc_final: 0.6961 (p0) REVERT: E 121 HIS cc_start: 0.7843 (p90) cc_final: 0.7402 (p90) REVERT: E 144 ARG cc_start: 0.8237 (mtt-85) cc_final: 0.7913 (mtt-85) REVERT: E 181 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: E 403 LYS cc_start: 0.7400 (mtpp) cc_final: 0.7161 (mtmm) REVERT: F 290 GLU cc_start: 0.8087 (mp0) cc_final: 0.7848 (mm-30) REVERT: F 403 LYS cc_start: 0.7360 (ttpt) cc_final: 0.7081 (mtmm) REVERT: G 326 ARG cc_start: 0.7365 (mmt90) cc_final: 0.7003 (mmt180) REVERT: H 120 ASP cc_start: 0.7295 (p0) cc_final: 0.6896 (p0) REVERT: H 121 HIS cc_start: 0.7890 (p-80) cc_final: 0.7514 (p90) REVERT: H 181 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: I 290 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: J 181 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7795 (pp20) REVERT: J 326 ARG cc_start: 0.7372 (mmt90) cc_final: 0.6999 (mmt180) REVERT: J 357 LYS cc_start: 0.7833 (ptmm) cc_final: 0.7604 (ptpp) REVERT: J 401 LYS cc_start: 0.6479 (OUTLIER) cc_final: 0.5848 (mmtp) REVERT: J 403 LYS cc_start: 0.7306 (ttpt) cc_final: 0.7050 (mtmm) REVERT: K 120 ASP cc_start: 0.7264 (p0) cc_final: 0.6902 (p0) REVERT: K 121 HIS cc_start: 0.7850 (p90) cc_final: 0.7379 (p90) REVERT: K 389 SER cc_start: 0.7607 (OUTLIER) cc_final: 0.7112 (m) REVERT: K 403 LYS cc_start: 0.7275 (ttpt) cc_final: 0.6655 (tttt) REVERT: L 357 LYS cc_start: 0.8008 (tppt) cc_final: 0.7578 (tttm) outliers start: 30 outliers final: 12 residues processed: 466 average time/residue: 1.9316 time to fit residues: 1022.0657 Evaluate side-chains 454 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 436 time to evaluate : 4.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 401 LYS Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 389 SER Chi-restraints excluded: chain L residue 389 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 0.0170 chunk 314 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 272 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 295 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 121 HIS B 314 GLN C 121 HIS C 314 GLN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN E 393 ASN F 314 GLN F 393 ASN G 314 GLN H 314 GLN H 393 ASN I 314 GLN I 393 ASN J 314 GLN K 314 GLN L 121 HIS L 314 GLN L 393 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119858 restraints weight = 32149.977| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.16 r_work: 0.3171 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: 0.8353 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 32040 Z= 0.142 Angle : 0.447 5.911 43128 Z= 0.255 Chirality : 0.039 0.137 4764 Planarity : 0.003 0.035 5448 Dihedral : 5.184 179.035 4200 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.06 % Allowed : 13.45 % Favored : 85.49 % 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: 1.42 (0.14), residues: 3732 helix: 1.91 (0.12), residues: 2028 sheet: 0.07 (0.23), residues: 600 loop : -0.29 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 76 PHE 0.016 0.001 PHE E 269 TYR 0.021 0.001 TYR H 177 ARG 0.006 0.000 ARG C 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16165.69 seconds wall clock time: 282 minutes 39.16 seconds (16959.16 seconds total)