Starting phenix.real_space_refine on Sun Mar 24 18:02:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf6_25863/03_2024/7tf6_25863.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf6_25863/03_2024/7tf6_25863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf6_25863/03_2024/7tf6_25863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf6_25863/03_2024/7tf6_25863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf6_25863/03_2024/7tf6_25863.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf6_25863/03_2024/7tf6_25863.pdb" } resolution = 2.15 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= 0.112 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: 6 Type Number sf(0) Gaussians Mg 24 5.21 5 S 204 5.16 5 C 27468 2.51 5 N 7296 2.21 5 O 8160 1.98 5 H 120 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 18": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43272 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "E" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "F" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "J" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "K" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "L" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "N" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "O" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "Q" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "R" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "S" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "T" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "U" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "V" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "W" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "X" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "L" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "N" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "O" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "S" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "T" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N LEU A 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU A 252 " occ=0.97 residue: pdb=" N LEU B 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU B 252 " occ=0.97 residue: pdb=" N LEU C 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU C 252 " occ=0.97 residue: pdb=" N LEU F 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU F 252 " occ=0.97 residue: pdb=" N LEU G 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU G 252 " occ=0.97 residue: pdb=" N LEU H 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU H 252 " occ=0.97 residue: pdb=" N LEU L 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU L 252 " occ=0.97 residue: pdb=" N LEU N 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU N 252 " occ=0.97 residue: pdb=" N LEU O 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU O 252 " occ=0.97 residue: pdb=" N LEU R 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU R 252 " occ=0.97 residue: pdb=" N LEU S 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU S 252 " occ=0.97 residue: pdb=" N LEU T 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU T 252 " occ=0.97 Time building chain proxies: 21.28, per 1000 atoms: 0.49 Number of scatterers: 43272 At special positions: 0 Unit cell: (150.48, 159.28, 124.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 204 16.00 Mg 24 11.99 O 8160 8.00 N 7296 7.00 C 27468 6.00 H 120 1.00 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: 17.63 Conformation dependent library (CDL) restraints added in 8.1 seconds 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10104 Finding SS restraints... Secondary structure from input PDB file: 226 helices and 24 sheets defined 44.1% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.38 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 56 through 64 removed outlier: 6.495A pdb=" N PHE A 62 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 63 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG A 64 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 109 through 123 removed outlier: 3.692A pdb=" N ASP A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 182 Processing helix chain 'A' and resid 206 through 227 Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.610A pdb=" N ARG A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.826A pdb=" N THR A 332 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 363 Processing helix chain 'A' and resid 378 through 386 Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 404 through 412 removed outlier: 3.969A pdb=" N LYS A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 432 removed outlier: 3.786A pdb=" N THR A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 442 Processing helix chain 'B' and resid 7 through 19 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 56 through 64 removed outlier: 6.501A pdb=" N PHE B 62 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 63 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG B 64 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 Processing helix chain 'B' and resid 109 through 122 Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 169 through 182 Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'B' and resid 270 through 283 Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.554A pdb=" N ARG B 300 " --> pdb=" O ASN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 332 removed outlier: 3.878A pdb=" N THR B 332 " --> pdb=" O GLY B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 363 Processing helix chain 'B' and resid 378 through 386 Processing helix chain 'B' and resid 393 through 402 Processing helix chain 'B' and resid 404 through 412 removed outlier: 3.977A pdb=" N LYS B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 432 removed outlier: 3.790A pdb=" N THR B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 442 Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 56 through 64 removed outlier: 6.516A pdb=" N PHE C 62 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 63 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 169 through 181 Processing helix chain 'C' and resid 206 through 227 Processing helix chain 'C' and resid 270 through 283 Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.581A pdb=" N ARG C 300 " --> pdb=" O ASN C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 332 removed outlier: 3.900A pdb=" N THR C 332 " --> pdb=" O GLY C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 363 Processing helix chain 'C' and resid 378 through 386 Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 404 through 412 removed outlier: 3.997A pdb=" N LYS C 408 " --> pdb=" O ASN C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 432 removed outlier: 3.784A pdb=" N THR C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 442 Processing helix chain 'D' and resid 4 through 8 removed outlier: 3.661A pdb=" N SER D 8 " --> pdb=" O GLY D 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.716A pdb=" N SER E 8 " --> pdb=" O GLY E 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 19 Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 56 through 64 removed outlier: 6.499A pdb=" N PHE F 62 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL F 63 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG F 64 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 79 Processing helix chain 'F' and resid 109 through 123 removed outlier: 3.691A pdb=" N ASP F 123 " --> pdb=" O LYS F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 182 Processing helix chain 'F' and resid 206 through 227 Processing helix chain 'F' and resid 270 through 283 Processing helix chain 'F' and resid 287 through 292 Processing helix chain 'F' and resid 296 through 301 removed outlier: 3.602A pdb=" N ARG F 300 " --> pdb=" O ASN F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 332 removed outlier: 3.850A pdb=" N THR F 332 " --> pdb=" O GLY F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 363 Processing helix chain 'F' and resid 378 through 386 Processing helix chain 'F' and resid 393 through 402 Processing helix chain 'F' and resid 404 through 412 removed outlier: 3.965A pdb=" N LYS F 408 " --> pdb=" O ASN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 432 removed outlier: 3.782A pdb=" N THR F 432 " --> pdb=" O ASP F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 442 Processing helix chain 'G' and resid 7 through 19 Processing helix chain 'G' and resid 43 through 49 Processing helix chain 'G' and resid 56 through 64 removed outlier: 6.503A pdb=" N PHE G 62 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL G 63 " --> pdb=" O GLU G 60 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG G 64 " --> pdb=" O GLY G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 79 Processing helix chain 'G' and resid 109 through 122 Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 169 through 182 Processing helix chain 'G' and resid 206 through 227 Processing helix chain 'G' and resid 270 through 283 Processing helix chain 'G' and resid 287 through 292 Processing helix chain 'G' and resid 296 through 301 removed outlier: 3.552A pdb=" N ARG G 300 " --> pdb=" O ASN G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 332 removed outlier: 3.877A pdb=" N THR G 332 " --> pdb=" O GLY G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 363 Processing helix chain 'G' and resid 378 through 386 Processing helix chain 'G' and resid 393 through 402 Processing helix chain 'G' and resid 404 through 412 removed outlier: 3.976A pdb=" N LYS G 408 " --> pdb=" O ASN G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 432 removed outlier: 3.808A pdb=" N THR G 432 " --> pdb=" O ASP G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 442 Processing helix chain 'H' and resid 7 through 19 Processing helix chain 'H' and resid 43 through 49 Processing helix chain 'H' and resid 56 through 64 removed outlier: 6.511A pdb=" N PHE H 62 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 63 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG H 64 " --> pdb=" O GLY H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 79 Processing helix chain 'H' and resid 109 through 122 Processing helix chain 'H' and resid 123 through 125 No H-bonds generated for 'chain 'H' and resid 123 through 125' Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'H' and resid 206 through 227 Processing helix chain 'H' and resid 270 through 283 Processing helix chain 'H' and resid 287 through 292 Processing helix chain 'H' and resid 296 through 301 removed outlier: 3.581A pdb=" N ARG H 300 " --> pdb=" O ASN H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 332 removed outlier: 3.851A pdb=" N THR H 332 " --> pdb=" O GLY H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 363 Processing helix chain 'H' and resid 378 through 386 Processing helix chain 'H' and resid 393 through 402 Processing helix chain 'H' and resid 404 through 412 removed outlier: 3.988A pdb=" N LYS H 408 " --> pdb=" O ASN H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 432 removed outlier: 3.782A pdb=" N THR H 432 " --> pdb=" O ASP H 428 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 442 Processing helix chain 'I' and resid 4 through 8 removed outlier: 3.719A pdb=" N SER I 8 " --> pdb=" O GLY I 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 8 removed outlier: 3.675A pdb=" N SER J 8 " --> pdb=" O GLY J 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 8 removed outlier: 3.660A pdb=" N SER K 8 " --> pdb=" O GLY K 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 19 Processing helix chain 'L' and resid 43 through 49 Processing helix chain 'L' and resid 56 through 64 removed outlier: 6.507A pdb=" N PHE L 62 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL L 63 " --> pdb=" O GLU L 60 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG L 64 " --> pdb=" O GLY L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 79 Processing helix chain 'L' and resid 109 through 122 Processing helix chain 'L' and resid 123 through 125 No H-bonds generated for 'chain 'L' and resid 123 through 125' Processing helix chain 'L' and resid 169 through 181 Processing helix chain 'L' and resid 206 through 227 Processing helix chain 'L' and resid 270 through 283 Processing helix chain 'L' and resid 287 through 292 Processing helix chain 'L' and resid 296 through 301 removed outlier: 3.602A pdb=" N ARG L 300 " --> pdb=" O ASN L 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 328 through 332 removed outlier: 3.853A pdb=" N THR L 332 " --> pdb=" O GLY L 329 " (cutoff:3.500A) Processing helix chain 'L' and resid 344 through 363 Processing helix chain 'L' and resid 378 through 386 Processing helix chain 'L' and resid 393 through 402 Processing helix chain 'L' and resid 404 through 412 removed outlier: 3.969A pdb=" N LYS L 408 " --> pdb=" O ASN L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 432 removed outlier: 3.791A pdb=" N THR L 432 " --> pdb=" O ASP L 428 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 442 Processing helix chain 'M' and resid 4 through 8 removed outlier: 3.697A pdb=" N SER M 8 " --> pdb=" O GLY M 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 19 Processing helix chain 'N' and resid 43 through 49 Processing helix chain 'N' and resid 56 through 64 removed outlier: 6.492A pdb=" N PHE N 62 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL N 63 " --> pdb=" O GLU N 60 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG N 64 " --> pdb=" O GLY N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 79 Processing helix chain 'N' and resid 109 through 122 Processing helix chain 'N' and resid 123 through 125 No H-bonds generated for 'chain 'N' and resid 123 through 125' Processing helix chain 'N' and resid 169 through 182 Processing helix chain 'N' and resid 206 through 227 Processing helix chain 'N' and resid 270 through 283 Processing helix chain 'N' and resid 287 through 292 Processing helix chain 'N' and resid 296 through 301 removed outlier: 3.554A pdb=" N ARG N 300 " --> pdb=" O ASN N 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 328 through 332 removed outlier: 3.876A pdb=" N THR N 332 " --> pdb=" O GLY N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 344 through 363 Processing helix chain 'N' and resid 378 through 386 Processing helix chain 'N' and resid 393 through 402 Processing helix chain 'N' and resid 404 through 412 removed outlier: 3.977A pdb=" N LYS N 408 " --> pdb=" O ASN N 404 " (cutoff:3.500A) Processing helix chain 'N' and resid 412 through 432 removed outlier: 3.807A pdb=" N THR N 432 " --> pdb=" O ASP N 428 " (cutoff:3.500A) Processing helix chain 'N' and resid 435 through 442 Processing helix chain 'O' and resid 7 through 19 Processing helix chain 'O' and resid 43 through 49 Processing helix chain 'O' and resid 56 through 64 removed outlier: 6.515A pdb=" N PHE O 62 " --> pdb=" O ILE O 59 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL O 63 " --> pdb=" O GLU O 60 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG O 64 " --> pdb=" O GLY O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 79 Processing helix chain 'O' and resid 109 through 122 Processing helix chain 'O' and resid 123 through 125 No H-bonds generated for 'chain 'O' and resid 123 through 125' Processing helix chain 'O' and resid 169 through 181 Processing helix chain 'O' and resid 206 through 227 Processing helix chain 'O' and resid 270 through 283 Processing helix chain 'O' and resid 287 through 292 Processing helix chain 'O' and resid 296 through 301 removed outlier: 3.581A pdb=" N ARG O 300 " --> pdb=" O ASN O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 328 through 332 removed outlier: 3.853A pdb=" N THR O 332 " --> pdb=" O GLY O 329 " (cutoff:3.500A) Processing helix chain 'O' and resid 344 through 363 Processing helix chain 'O' and resid 378 through 386 Processing helix chain 'O' and resid 393 through 402 Processing helix chain 'O' and resid 404 through 412 removed outlier: 3.986A pdb=" N LYS O 408 " --> pdb=" O ASN O 404 " (cutoff:3.500A) Processing helix chain 'O' and resid 412 through 432 removed outlier: 3.791A pdb=" N THR O 432 " --> pdb=" O ASP O 428 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 442 Processing helix chain 'P' and resid 4 through 8 removed outlier: 3.694A pdb=" N SER P 8 " --> pdb=" O GLY P 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 8 removed outlier: 3.714A pdb=" N SER Q 8 " --> pdb=" O GLY Q 5 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 19 Processing helix chain 'R' and resid 43 through 49 Processing helix chain 'R' and resid 56 through 64 removed outlier: 6.520A pdb=" N PHE R 62 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL R 63 " --> pdb=" O GLU R 60 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG R 64 " --> pdb=" O GLY R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 79 Processing helix chain 'R' and resid 109 through 122 Processing helix chain 'R' and resid 123 through 125 No H-bonds generated for 'chain 'R' and resid 123 through 125' Processing helix chain 'R' and resid 169 through 182 Processing helix chain 'R' and resid 206 through 227 Processing helix chain 'R' and resid 270 through 283 Processing helix chain 'R' and resid 287 through 292 Processing helix chain 'R' and resid 296 through 301 removed outlier: 3.600A pdb=" N ARG R 300 " --> pdb=" O ASN R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 328 through 332 removed outlier: 3.850A pdb=" N THR R 332 " --> pdb=" O GLY R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 363 Processing helix chain 'R' and resid 371 through 375 removed outlier: 3.505A pdb=" N TYR R 375 " --> pdb=" O GLN R 372 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 386 Processing helix chain 'R' and resid 393 through 402 Processing helix chain 'R' and resid 404 through 412 removed outlier: 3.970A pdb=" N LYS R 408 " --> pdb=" O ASN R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 412 through 432 removed outlier: 3.801A pdb=" N THR R 432 " --> pdb=" O ASP R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 442 Processing helix chain 'S' and resid 7 through 19 Processing helix chain 'S' and resid 43 through 49 Processing helix chain 'S' and resid 56 through 64 removed outlier: 6.505A pdb=" N PHE S 62 " --> pdb=" O ILE S 59 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL S 63 " --> pdb=" O GLU S 60 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG S 64 " --> pdb=" O GLY S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 79 Processing helix chain 'S' and resid 109 through 123 removed outlier: 3.685A pdb=" N ASP S 123 " --> pdb=" O LYS S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 182 Processing helix chain 'S' and resid 206 through 227 Processing helix chain 'S' and resid 270 through 283 Processing helix chain 'S' and resid 287 through 292 Processing helix chain 'S' and resid 296 through 301 removed outlier: 3.560A pdb=" N ARG S 300 " --> pdb=" O ASN S 296 " (cutoff:3.500A) Processing helix chain 'S' and resid 328 through 332 removed outlier: 3.851A pdb=" N THR S 332 " --> pdb=" O GLY S 329 " (cutoff:3.500A) Processing helix chain 'S' and resid 344 through 363 Processing helix chain 'S' and resid 378 through 386 Processing helix chain 'S' and resid 393 through 402 Processing helix chain 'S' and resid 404 through 412 removed outlier: 3.970A pdb=" N LYS S 408 " --> pdb=" O ASN S 404 " (cutoff:3.500A) Processing helix chain 'S' and resid 412 through 432 removed outlier: 3.812A pdb=" N THR S 432 " --> pdb=" O ASP S 428 " (cutoff:3.500A) Processing helix chain 'S' and resid 435 through 442 Processing helix chain 'T' and resid 7 through 19 Processing helix chain 'T' and resid 43 through 49 Processing helix chain 'T' and resid 56 through 64 removed outlier: 6.515A pdb=" N PHE T 62 " --> pdb=" O ILE T 59 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL T 63 " --> pdb=" O GLU T 60 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG T 64 " --> pdb=" O GLY T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 79 Processing helix chain 'T' and resid 109 through 122 Processing helix chain 'T' and resid 123 through 125 No H-bonds generated for 'chain 'T' and resid 123 through 125' Processing helix chain 'T' and resid 169 through 181 Processing helix chain 'T' and resid 206 through 227 Processing helix chain 'T' and resid 270 through 283 Processing helix chain 'T' and resid 287 through 292 Processing helix chain 'T' and resid 296 through 301 removed outlier: 3.577A pdb=" N ARG T 300 " --> pdb=" O ASN T 296 " (cutoff:3.500A) Processing helix chain 'T' and resid 328 through 332 removed outlier: 3.852A pdb=" N THR T 332 " --> pdb=" O GLY T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 344 through 363 Processing helix chain 'T' and resid 378 through 386 Processing helix chain 'T' and resid 393 through 402 Processing helix chain 'T' and resid 404 through 412 removed outlier: 3.994A pdb=" N LYS T 408 " --> pdb=" O ASN T 404 " (cutoff:3.500A) Processing helix chain 'T' and resid 412 through 432 removed outlier: 3.790A pdb=" N THR T 432 " --> pdb=" O ASP T 428 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 442 Processing helix chain 'U' and resid 4 through 8 removed outlier: 3.712A pdb=" N SER U 8 " --> pdb=" O GLY U 5 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 8 removed outlier: 3.687A pdb=" N SER V 8 " --> pdb=" O GLY V 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 8 removed outlier: 3.728A pdb=" N SER W 8 " --> pdb=" O GLY W 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 8 removed outlier: 3.724A pdb=" N SER X 8 " --> pdb=" O GLY X 5 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 34 through 40 current: chain 'A' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 70 through 74 current: chain 'A' and resid 90 through 99 Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 142 removed outlier: 5.268A pdb=" N GLU A 151 " --> pdb=" O LYS A 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 148 through 152 current: chain 'A' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 196 through 201 current: chain 'A' and resid 322 through 323 Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 34 through 40 current: chain 'B' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 70 through 74 current: chain 'B' and resid 90 through 99 Processing sheet with id=AA4, first strand: chain 'B' and resid 128 through 142 removed outlier: 7.111A pdb=" N LEU B 139 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU B 151 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LYS B 141 " --> pdb=" O THR B 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 148 through 152 current: chain 'B' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 196 through 201 current: chain 'B' and resid 322 through 323 Processing sheet with id=AA5, first strand: chain 'C' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 34 through 40 current: chain 'C' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 70 through 74 current: chain 'C' and resid 90 through 99 Processing sheet with id=AA6, first strand: chain 'C' and resid 128 through 142 removed outlier: 7.061A pdb=" N LEU C 139 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU C 151 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS C 141 " --> pdb=" O THR C 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 148 through 152 current: chain 'C' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 196 through 201 current: chain 'C' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'F' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 34 through 40 current: chain 'F' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 70 through 74 current: chain 'F' and resid 90 through 99 Processing sheet with id=AA8, first strand: chain 'F' and resid 128 through 142 removed outlier: 5.289A pdb=" N GLU F 151 " --> pdb=" O LYS F 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 148 through 152 current: chain 'F' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 196 through 201 current: chain 'F' and resid 322 through 323 Processing sheet with id=AA9, first strand: chain 'G' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 34 through 40 current: chain 'G' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 70 through 74 current: chain 'G' and resid 90 through 99 Processing sheet with id=AB1, first strand: chain 'G' and resid 128 through 142 removed outlier: 7.113A pdb=" N LEU G 139 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU G 151 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LYS G 141 " --> pdb=" O THR G 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 148 through 152 current: chain 'G' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 196 through 201 current: chain 'G' and resid 322 through 323 Processing sheet with id=AB2, first strand: chain 'H' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 34 through 40 current: chain 'H' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 70 through 74 current: chain 'H' and resid 90 through 99 Processing sheet with id=AB3, first strand: chain 'H' and resid 128 through 142 removed outlier: 5.331A pdb=" N GLU H 151 " --> pdb=" O LYS H 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 148 through 152 current: chain 'H' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 196 through 201 current: chain 'H' and resid 322 through 323 Processing sheet with id=AB4, first strand: chain 'L' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 34 through 40 current: chain 'L' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 70 through 74 current: chain 'L' and resid 90 through 99 Processing sheet with id=AB5, first strand: chain 'L' and resid 128 through 142 removed outlier: 5.281A pdb=" N GLU L 151 " --> pdb=" O LYS L 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 148 through 152 current: chain 'L' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 196 through 201 current: chain 'L' and resid 322 through 323 Processing sheet with id=AB6, first strand: chain 'N' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 34 through 40 current: chain 'N' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 70 through 74 current: chain 'N' and resid 90 through 99 Processing sheet with id=AB7, first strand: chain 'N' and resid 128 through 142 removed outlier: 7.109A pdb=" N LEU N 139 " --> pdb=" O GLU N 151 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU N 151 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LYS N 141 " --> pdb=" O THR N 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 148 through 152 current: chain 'N' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 196 through 201 current: chain 'N' and resid 322 through 323 Processing sheet with id=AB8, first strand: chain 'O' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 34 through 40 current: chain 'O' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 70 through 74 current: chain 'O' and resid 90 through 99 Processing sheet with id=AB9, first strand: chain 'O' and resid 128 through 142 removed outlier: 7.062A pdb=" N LEU O 139 " --> pdb=" O GLU O 151 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU O 151 " --> pdb=" O LEU O 139 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS O 141 " --> pdb=" O THR O 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 148 through 152 current: chain 'O' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 196 through 201 current: chain 'O' and resid 322 through 323 Processing sheet with id=AC1, first strand: chain 'R' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 34 through 40 current: chain 'R' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 70 through 74 current: chain 'R' and resid 90 through 99 Processing sheet with id=AC2, first strand: chain 'R' and resid 128 through 142 removed outlier: 5.271A pdb=" N GLU R 151 " --> pdb=" O LYS R 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 148 through 152 current: chain 'R' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 196 through 201 current: chain 'R' and resid 322 through 323 Processing sheet with id=AC3, first strand: chain 'S' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 34 through 40 current: chain 'S' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 70 through 74 current: chain 'S' and resid 90 through 99 Processing sheet with id=AC4, first strand: chain 'S' and resid 128 through 142 removed outlier: 7.117A pdb=" N LEU S 139 " --> pdb=" O GLU S 151 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU S 151 " --> pdb=" O LEU S 139 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS S 141 " --> pdb=" O THR S 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 148 through 152 current: chain 'S' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 196 through 201 current: chain 'S' and resid 322 through 323 Processing sheet with id=AC5, first strand: chain 'T' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 34 through 40 current: chain 'T' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 70 through 74 current: chain 'T' and resid 90 through 99 Processing sheet with id=AC6, first strand: chain 'T' and resid 128 through 142 removed outlier: 7.058A pdb=" N LEU T 139 " --> pdb=" O GLU T 151 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU T 151 " --> pdb=" O LEU T 139 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LYS T 141 " --> pdb=" O THR T 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 148 through 152 current: chain 'T' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 196 through 201 current: chain 'T' and resid 322 through 323 1545 hydrogen bonds defined for protein. 4413 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: 14.71 Time building geometry restraints manager: 18.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.13: 120 1.13 - 1.30: 7452 1.30 - 1.47: 17226 1.47 - 1.64: 19074 1.64 - 1.81: 348 Bond restraints: 44220 Sorted by residual: bond pdb=" NE2 GLN O 503 " pdb="HE21 GLN O 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" NE2 GLN R 503 " pdb="HE21 GLN R 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" NE2 GLN H 503 " pdb="HE21 GLN H 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" NE2 GLN B 503 " pdb="HE21 GLN B 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.08e+01 bond pdb=" NE2 GLN S 503 " pdb="HE21 GLN S 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.08e+01 ... (remaining 44215 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.97: 1428 106.97 - 113.72: 23749 113.72 - 120.48: 17341 120.48 - 127.24: 16955 127.24 - 134.00: 491 Bond angle restraints: 59964 Sorted by residual: angle pdb=" N SER G 57 " pdb=" CA SER G 57 " pdb=" C SER G 57 " ideal model delta sigma weight residual 113.18 109.53 3.65 1.21e+00 6.83e-01 9.08e+00 angle pdb=" CA GLY L 412 " pdb=" C GLY L 412 " pdb=" O GLY L 412 " ideal model delta sigma weight residual 122.24 119.70 2.54 8.70e-01 1.32e+00 8.55e+00 angle pdb=" CA GLY A 412 " pdb=" C GLY A 412 " pdb=" O GLY A 412 " ideal model delta sigma weight residual 122.24 119.71 2.53 8.70e-01 1.32e+00 8.49e+00 angle pdb=" CA GLY R 412 " pdb=" C GLY R 412 " pdb=" O GLY R 412 " ideal model delta sigma weight residual 122.24 119.73 2.51 8.70e-01 1.32e+00 8.33e+00 angle pdb=" CA GLY F 412 " pdb=" C GLY F 412 " pdb=" O GLY F 412 " ideal model delta sigma weight residual 122.24 119.75 2.49 8.70e-01 1.32e+00 8.22e+00 ... (remaining 59959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 23511 18.00 - 36.01: 2137 36.01 - 54.01: 631 54.01 - 72.02: 191 72.02 - 90.02: 62 Dihedral angle restraints: 26532 sinusoidal: 10872 harmonic: 15660 Sorted by residual: dihedral pdb=" CA PRO R 163 " pdb=" C PRO R 163 " pdb=" N THR R 164 " pdb=" CA THR R 164 " ideal model delta harmonic sigma weight residual -180.00 -155.15 -24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA PRO H 163 " pdb=" C PRO H 163 " pdb=" N THR H 164 " pdb=" CA THR H 164 " ideal model delta harmonic sigma weight residual 180.00 -155.49 -24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA PRO O 163 " pdb=" C PRO O 163 " pdb=" N THR O 164 " pdb=" CA THR O 164 " ideal model delta harmonic sigma weight residual -180.00 -155.52 -24.48 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 26529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3685 0.026 - 0.052: 1553 0.052 - 0.077: 763 0.077 - 0.103: 229 0.103 - 0.129: 214 Chirality restraints: 6444 Sorted by residual: chirality pdb=" CA ILE A 334 " pdb=" N ILE A 334 " pdb=" C ILE A 334 " pdb=" CB ILE A 334 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE L 334 " pdb=" N ILE L 334 " pdb=" C ILE L 334 " pdb=" CB ILE L 334 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA PRO R 293 " pdb=" N PRO R 293 " pdb=" C PRO R 293 " pdb=" CB PRO R 293 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 6441 not shown) Planarity restraints: 7860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN H 503 " 0.122 2.00e-02 2.50e+03 1.17e-01 2.06e+02 pdb=" CD GLN H 503 " -0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN H 503 " -0.116 2.00e-02 2.50e+03 pdb=" NE2 GLN H 503 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN H 503 " -0.163 2.00e-02 2.50e+03 pdb="HE22 GLN H 503 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN O 503 " -0.122 2.00e-02 2.50e+03 1.17e-01 2.06e+02 pdb=" CD GLN O 503 " 0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN O 503 " 0.116 2.00e-02 2.50e+03 pdb=" NE2 GLN O 503 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN O 503 " 0.163 2.00e-02 2.50e+03 pdb="HE22 GLN O 503 " -0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN R 503 " 0.122 2.00e-02 2.50e+03 1.17e-01 2.06e+02 pdb=" CD GLN R 503 " -0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN R 503 " -0.116 2.00e-02 2.50e+03 pdb=" NE2 GLN R 503 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN R 503 " -0.162 2.00e-02 2.50e+03 pdb="HE22 GLN R 503 " 0.166 2.00e-02 2.50e+03 ... (remaining 7857 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 130 2.27 - 2.85: 15352 2.85 - 3.43: 48433 3.43 - 4.02: 88664 4.02 - 4.60: 132220 Nonbonded interactions: 284799 Sorted by model distance: nonbonded pdb=" O GLY G 243 " pdb=" H1 GLN G 503 " model vdw 1.686 1.850 nonbonded pdb=" O GLY O 243 " pdb=" H1 GLN O 503 " model vdw 1.687 1.850 nonbonded pdb=" O GLY N 243 " pdb=" H1 GLN N 503 " model vdw 1.687 1.850 nonbonded pdb=" O GLY S 243 " pdb=" H1 GLN S 503 " model vdw 1.692 1.850 nonbonded pdb=" O GLY B 243 " pdb=" H1 GLN B 503 " model vdw 1.694 1.850 ... (remaining 284794 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 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.97 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.020 Extract box with map and model: 15.800 Check model and map are aligned: 0.590 Set scattering table: 0.340 Process input model: 108.450 Find NCS groups from input model: 3.420 Set up NCS constraints: 0.520 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:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 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 : 0.002 0.033 44100 Z= 0.155 Angle : 0.505 5.756 59700 Z= 0.285 Chirality : 0.040 0.129 6444 Planarity : 0.003 0.034 7860 Dihedral : 16.471 90.021 16416 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.34 % Allowed : 14.42 % Favored : 84.24 % 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: 0.26 (0.12), residues: 5316 helix: 1.25 (0.11), residues: 2244 sheet: -1.18 (0.16), residues: 924 loop : -0.20 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 427 HIS 0.002 0.001 HIS S 197 PHE 0.011 0.001 PHE B 287 TYR 0.018 0.001 TYR O 203 ARG 0.007 0.000 ARG W 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 923 time to evaluate : 4.729 Fit side-chains REVERT: A 13 LYS cc_start: 0.6176 (ttmm) cc_final: 0.5737 (ttpt) REVERT: A 16 GLU cc_start: 0.6706 (tp30) cc_final: 0.6271 (tm-30) REVERT: A 52 MET cc_start: 0.7233 (mmm) cc_final: 0.6676 (mmm) REVERT: A 66 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6927 (mt-10) REVERT: A 119 LYS cc_start: 0.6649 (ttpt) cc_final: 0.6342 (tttm) REVERT: A 120 GLU cc_start: 0.6347 (pt0) cc_final: 0.5702 (mt-10) REVERT: A 122 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6323 (mt-10) REVERT: A 128 ASP cc_start: 0.6851 (m-30) cc_final: 0.6597 (m-30) REVERT: A 151 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6440 (mt-10) REVERT: A 155 ASP cc_start: 0.6566 (t0) cc_final: 0.6337 (t70) REVERT: A 173 ASP cc_start: 0.6956 (m-30) cc_final: 0.6546 (m-30) REVERT: A 184 ASP cc_start: 0.7262 (m-30) cc_final: 0.6963 (m-30) REVERT: A 201 PHE cc_start: 0.6809 (m-80) cc_final: 0.5949 (m-80) REVERT: A 203 TYR cc_start: 0.6273 (p90) cc_final: 0.5732 (p90) REVERT: A 225 ARG cc_start: 0.6475 (ttp-170) cc_final: 0.5923 (ttt180) REVERT: A 257 GLU cc_start: 0.6253 (tm-30) cc_final: 0.5725 (pp20) REVERT: A 271 GLU cc_start: 0.6323 (tp30) cc_final: 0.6001 (tp30) REVERT: A 282 LYS cc_start: 0.6528 (tptm) cc_final: 0.5925 (tttm) REVERT: A 354 GLU cc_start: 0.7178 (tp30) cc_final: 0.6962 (mm-30) REVERT: A 365 LYS cc_start: 0.6394 (mmtm) cc_final: 0.5609 (tttm) REVERT: A 399 LYS cc_start: 0.6726 (ttmt) cc_final: 0.5966 (ttmm) REVERT: A 409 LYS cc_start: 0.6285 (ttmm) cc_final: 0.5871 (tttt) REVERT: A 418 GLN cc_start: 0.6860 (mm110) cc_final: 0.6634 (mm110) REVERT: A 428 ASP cc_start: 0.7182 (t70) cc_final: 0.6580 (m-30) REVERT: A 445 GLN cc_start: 0.6331 (tt0) cc_final: 0.5437 (tp40) REVERT: B 13 LYS cc_start: 0.5987 (ttmm) cc_final: 0.5228 (tttp) REVERT: B 16 GLU cc_start: 0.6417 (tp30) cc_final: 0.5752 (tt0) REVERT: B 66 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6500 (mt-10) REVERT: B 75 ASP cc_start: 0.6440 (t0) cc_final: 0.6151 (t0) REVERT: B 120 GLU cc_start: 0.6490 (pt0) cc_final: 0.5426 (mm-30) REVERT: B 128 ASP cc_start: 0.7007 (m-30) cc_final: 0.6778 (m-30) REVERT: B 151 GLU cc_start: 0.6476 (mt-10) cc_final: 0.5707 (mm-30) REVERT: B 169 ASN cc_start: 0.5515 (OUTLIER) cc_final: 0.5113 (m-40) REVERT: B 173 ASP cc_start: 0.6778 (m-30) cc_final: 0.6508 (m-30) REVERT: B 201 PHE cc_start: 0.6892 (m-80) cc_final: 0.5946 (m-80) REVERT: B 225 ARG cc_start: 0.6211 (ttp-170) cc_final: 0.5989 (ttm170) REVERT: B 257 GLU cc_start: 0.6537 (tm-30) cc_final: 0.6175 (tm-30) REVERT: B 270 THR cc_start: 0.6962 (m) cc_final: 0.6414 (p) REVERT: B 271 GLU cc_start: 0.6235 (tp30) cc_final: 0.5931 (tp30) REVERT: B 330 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7633 (mt) REVERT: B 365 LYS cc_start: 0.6631 (mmtm) cc_final: 0.5845 (tttm) REVERT: B 409 LYS cc_start: 0.6442 (ttmm) cc_final: 0.5917 (tttt) REVERT: B 418 GLN cc_start: 0.7034 (mm-40) cc_final: 0.6829 (mm-40) REVERT: B 421 ASN cc_start: 0.6108 (m-40) cc_final: 0.4762 (t0) REVERT: B 428 ASP cc_start: 0.7044 (t70) cc_final: 0.6432 (t0) REVERT: B 445 GLN cc_start: 0.6949 (tt0) cc_final: 0.5988 (tp40) REVERT: C 13 LYS cc_start: 0.5969 (ttmm) cc_final: 0.5259 (tttp) REVERT: C 16 GLU cc_start: 0.6727 (tp30) cc_final: 0.6358 (tm-30) REVERT: C 21 ARG cc_start: 0.6693 (mtp85) cc_final: 0.6484 (mmm160) REVERT: C 53 MET cc_start: 0.7303 (mtm) cc_final: 0.6830 (mtp) REVERT: C 66 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6555 (mt-10) REVERT: C 119 LYS cc_start: 0.6032 (tptp) cc_final: 0.5444 (tttm) REVERT: C 120 GLU cc_start: 0.6318 (pt0) cc_final: 0.5327 (mm-30) REVERT: C 122 GLU cc_start: 0.6542 (mt-10) cc_final: 0.6251 (mt-10) REVERT: C 128 ASP cc_start: 0.6937 (m-30) cc_final: 0.6687 (m-30) REVERT: C 151 GLU cc_start: 0.6618 (mt-10) cc_final: 0.5771 (mm-30) REVERT: C 155 ASP cc_start: 0.6577 (t0) cc_final: 0.6046 (t70) REVERT: C 173 ASP cc_start: 0.6725 (m-30) cc_final: 0.6348 (m-30) REVERT: C 184 ASP cc_start: 0.7206 (m-30) cc_final: 0.6960 (m-30) REVERT: C 201 PHE cc_start: 0.7116 (m-80) cc_final: 0.6336 (m-80) REVERT: C 225 ARG cc_start: 0.6522 (ttt180) cc_final: 0.6097 (ttt180) REVERT: C 257 GLU cc_start: 0.6264 (tm-30) cc_final: 0.5786 (pp20) REVERT: C 270 THR cc_start: 0.6997 (m) cc_final: 0.6499 (p) REVERT: C 271 GLU cc_start: 0.5812 (tp30) cc_final: 0.5404 (tp30) REVERT: C 354 GLU cc_start: 0.7310 (tp30) cc_final: 0.7038 (mm-30) REVERT: C 365 LYS cc_start: 0.6271 (tppt) cc_final: 0.5495 (tttm) REVERT: C 388 GLN cc_start: 0.6358 (mt0) cc_final: 0.6158 (mt0) REVERT: C 399 LYS cc_start: 0.6518 (ttmt) cc_final: 0.5714 (ttmm) REVERT: C 405 GLU cc_start: 0.5708 (mm-30) cc_final: 0.5224 (tm-30) REVERT: C 408 LYS cc_start: 0.6765 (tttt) cc_final: 0.6472 (ttpp) REVERT: C 409 LYS cc_start: 0.6534 (ttmm) cc_final: 0.6208 (ttpt) REVERT: C 421 ASN cc_start: 0.5864 (m-40) cc_final: 0.4565 (t0) REVERT: C 428 ASP cc_start: 0.6993 (t70) cc_final: 0.6328 (m-30) REVERT: C 436 GLU cc_start: 0.5564 (pm20) cc_final: 0.5038 (pm20) REVERT: C 443 MET cc_start: 0.6590 (ttp) cc_final: 0.6248 (ttt) REVERT: C 445 GLN cc_start: 0.6662 (tt0) cc_final: 0.5610 (tp40) REVERT: D 4 ARG cc_start: 0.6243 (tmt170) cc_final: 0.5763 (tpt90) REVERT: E 11 ILE cc_start: 0.6662 (mt) cc_final: 0.6417 (mp) REVERT: F 13 LYS cc_start: 0.6174 (ttmm) cc_final: 0.5742 (ttpt) REVERT: F 16 GLU cc_start: 0.6684 (tp30) cc_final: 0.6268 (tm-30) REVERT: F 21 ARG cc_start: 0.6639 (mtp85) cc_final: 0.6267 (mmp-170) REVERT: F 52 MET cc_start: 0.7223 (mmm) cc_final: 0.6662 (mmm) REVERT: F 66 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6939 (mt-10) REVERT: F 119 LYS cc_start: 0.6637 (ttpt) cc_final: 0.6078 (tttt) REVERT: F 120 GLU cc_start: 0.6268 (pt0) cc_final: 0.5616 (mt-10) REVERT: F 122 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6309 (mt-10) REVERT: F 128 ASP cc_start: 0.6829 (m-30) cc_final: 0.6584 (m-30) REVERT: F 151 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6369 (mt-10) REVERT: F 155 ASP cc_start: 0.6560 (t0) cc_final: 0.6321 (t70) REVERT: F 173 ASP cc_start: 0.6906 (m-30) cc_final: 0.6458 (m-30) REVERT: F 184 ASP cc_start: 0.7180 (m-30) cc_final: 0.6872 (m-30) REVERT: F 201 PHE cc_start: 0.6902 (m-80) cc_final: 0.6081 (m-80) REVERT: F 225 ARG cc_start: 0.6390 (ttp-170) cc_final: 0.5980 (ttt180) REVERT: F 257 GLU cc_start: 0.6450 (tm-30) cc_final: 0.5913 (pp20) REVERT: F 270 THR cc_start: 0.7012 (m) cc_final: 0.6324 (p) REVERT: F 271 GLU cc_start: 0.6028 (tp30) cc_final: 0.5622 (tp30) REVERT: F 282 LYS cc_start: 0.6528 (tptm) cc_final: 0.5918 (tttm) REVERT: F 354 GLU cc_start: 0.7120 (tp30) cc_final: 0.6910 (mm-30) REVERT: F 365 LYS cc_start: 0.6383 (mmtm) cc_final: 0.5598 (tttm) REVERT: F 399 LYS cc_start: 0.6712 (ttmt) cc_final: 0.5951 (ttmm) REVERT: F 409 LYS cc_start: 0.6276 (ttmm) cc_final: 0.5864 (tttt) REVERT: F 418 GLN cc_start: 0.6851 (mm110) cc_final: 0.6626 (mm110) REVERT: F 428 ASP cc_start: 0.7202 (t70) cc_final: 0.6574 (m-30) REVERT: F 445 GLN cc_start: 0.6341 (tt0) cc_final: 0.5443 (tp40) REVERT: G 16 GLU cc_start: 0.6588 (tp30) cc_final: 0.5915 (tt0) REVERT: G 17 GLU cc_start: 0.6394 (mt-10) cc_final: 0.6152 (mt-10) REVERT: G 51 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6554 (mt-10) REVERT: G 66 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6362 (mt-10) REVERT: G 75 ASP cc_start: 0.6451 (t0) cc_final: 0.6135 (t0) REVERT: G 120 GLU cc_start: 0.6358 (pt0) cc_final: 0.5288 (mm-30) REVERT: G 122 GLU cc_start: 0.6694 (mt-10) cc_final: 0.6365 (mt-10) REVERT: G 128 ASP cc_start: 0.7021 (m-30) cc_final: 0.6781 (m-30) REVERT: G 151 GLU cc_start: 0.6506 (mt-10) cc_final: 0.5738 (mm-30) REVERT: G 173 ASP cc_start: 0.6780 (m-30) cc_final: 0.6510 (m-30) REVERT: G 201 PHE cc_start: 0.6946 (m-80) cc_final: 0.6001 (m-80) REVERT: G 225 ARG cc_start: 0.6241 (ttp-170) cc_final: 0.6003 (ttm170) REVERT: G 257 GLU cc_start: 0.6538 (tm-30) cc_final: 0.6179 (tm-30) REVERT: G 270 THR cc_start: 0.6943 (m) cc_final: 0.6378 (p) REVERT: G 271 GLU cc_start: 0.6201 (tp30) cc_final: 0.5862 (tp30) REVERT: G 330 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7640 (mt) REVERT: G 347 MET cc_start: 0.7336 (mtp) cc_final: 0.6928 (mtp) REVERT: G 365 LYS cc_start: 0.6635 (mmtm) cc_final: 0.5844 (tttm) REVERT: G 409 LYS cc_start: 0.6445 (ttmm) cc_final: 0.5901 (tttt) REVERT: G 421 ASN cc_start: 0.6123 (m-40) cc_final: 0.4790 (t0) REVERT: G 428 ASP cc_start: 0.7052 (t70) cc_final: 0.6761 (t0) REVERT: G 436 GLU cc_start: 0.5428 (pm20) cc_final: 0.5060 (pm20) REVERT: G 445 GLN cc_start: 0.6754 (tt0) cc_final: 0.6497 (tt0) REVERT: H 13 LYS cc_start: 0.5983 (ttmm) cc_final: 0.5283 (tttp) REVERT: H 16 GLU cc_start: 0.6745 (tp30) cc_final: 0.6329 (tm-30) REVERT: H 21 ARG cc_start: 0.6706 (mtp85) cc_final: 0.6488 (mmm160) REVERT: H 53 MET cc_start: 0.7379 (mtm) cc_final: 0.6886 (mtp) REVERT: H 66 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6562 (mt-10) REVERT: H 119 LYS cc_start: 0.6077 (tptp) cc_final: 0.5520 (tttm) REVERT: H 120 GLU cc_start: 0.6312 (pt0) cc_final: 0.5340 (mm-30) REVERT: H 128 ASP cc_start: 0.6937 (m-30) cc_final: 0.6692 (m-30) REVERT: H 151 GLU cc_start: 0.6617 (mt-10) cc_final: 0.5754 (mm-30) REVERT: H 155 ASP cc_start: 0.6587 (t0) cc_final: 0.6155 (t70) REVERT: H 173 ASP cc_start: 0.6727 (m-30) cc_final: 0.6360 (m-30) REVERT: H 184 ASP cc_start: 0.7133 (m-30) cc_final: 0.6913 (m-30) REVERT: H 201 PHE cc_start: 0.7046 (m-80) cc_final: 0.6258 (m-80) REVERT: H 225 ARG cc_start: 0.6576 (ttp-170) cc_final: 0.6204 (ttt180) REVERT: H 257 GLU cc_start: 0.6251 (tm-30) cc_final: 0.5789 (pp20) REVERT: H 270 THR cc_start: 0.6937 (m) cc_final: 0.6461 (p) REVERT: H 271 GLU cc_start: 0.5801 (tp30) cc_final: 0.5392 (tp30) REVERT: H 354 GLU cc_start: 0.7307 (tp30) cc_final: 0.7042 (mm-30) REVERT: H 365 LYS cc_start: 0.6275 (tppt) cc_final: 0.5499 (tttm) REVERT: H 388 GLN cc_start: 0.6363 (mt0) cc_final: 0.6162 (mt0) REVERT: H 399 LYS cc_start: 0.6514 (ttmt) cc_final: 0.5710 (ttmm) REVERT: H 408 LYS cc_start: 0.6751 (tttt) cc_final: 0.6468 (ttpp) REVERT: H 409 LYS cc_start: 0.6537 (ttmm) cc_final: 0.6033 (ttpt) REVERT: H 421 ASN cc_start: 0.5873 (m-40) cc_final: 0.4575 (t0) REVERT: H 428 ASP cc_start: 0.6928 (t0) cc_final: 0.6301 (m-30) REVERT: H 436 GLU cc_start: 0.5561 (pm20) cc_final: 0.5067 (pm20) REVERT: H 443 MET cc_start: 0.6579 (ttp) cc_final: 0.6343 (ttt) REVERT: H 445 GLN cc_start: 0.6630 (tt0) cc_final: 0.5628 (tp40) REVERT: I 4 ARG cc_start: 0.6227 (tmt170) cc_final: 0.5790 (tpt90) REVERT: K 3 ASN cc_start: 0.6578 (p0) cc_final: 0.6046 (p0) REVERT: K 4 ARG cc_start: 0.6389 (tmt170) cc_final: 0.5992 (tpt90) REVERT: L 13 LYS cc_start: 0.6129 (ttmm) cc_final: 0.5705 (ttpt) REVERT: L 16 GLU cc_start: 0.6742 (tp30) cc_final: 0.6330 (tm-30) REVERT: L 52 MET cc_start: 0.7130 (mmm) cc_final: 0.6608 (mmm) REVERT: L 66 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6945 (mt-10) REVERT: L 119 LYS cc_start: 0.6496 (ttpt) cc_final: 0.6012 (tttt) REVERT: L 120 GLU cc_start: 0.6399 (pt0) cc_final: 0.5766 (mt-10) REVERT: L 122 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6302 (mt-10) REVERT: L 128 ASP cc_start: 0.6898 (m-30) cc_final: 0.6640 (m-30) REVERT: L 151 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6412 (mt-10) REVERT: L 155 ASP cc_start: 0.6559 (t0) cc_final: 0.6308 (t70) REVERT: L 173 ASP cc_start: 0.6903 (m-30) cc_final: 0.6451 (m-30) REVERT: L 184 ASP cc_start: 0.7182 (m-30) cc_final: 0.6868 (m-30) REVERT: L 201 PHE cc_start: 0.6886 (m-80) cc_final: 0.6103 (m-80) REVERT: L 225 ARG cc_start: 0.6452 (ttp-170) cc_final: 0.5981 (ttt180) REVERT: L 257 GLU cc_start: 0.6383 (tm-30) cc_final: 0.5774 (pp20) REVERT: L 270 THR cc_start: 0.7009 (m) cc_final: 0.6323 (p) REVERT: L 271 GLU cc_start: 0.6085 (tp30) cc_final: 0.5716 (tp30) REVERT: L 282 LYS cc_start: 0.6547 (tptm) cc_final: 0.5940 (tttm) REVERT: L 354 GLU cc_start: 0.7163 (tp30) cc_final: 0.6945 (mm-30) REVERT: L 365 LYS cc_start: 0.6387 (mmtm) cc_final: 0.5602 (tttm) REVERT: L 399 LYS cc_start: 0.6759 (ttmt) cc_final: 0.5989 (ttmm) REVERT: L 409 LYS cc_start: 0.6289 (ttmm) cc_final: 0.5877 (tttt) REVERT: L 418 GLN cc_start: 0.6842 (mm110) cc_final: 0.6607 (mm-40) REVERT: L 428 ASP cc_start: 0.7204 (t70) cc_final: 0.6598 (m-30) REVERT: L 445 GLN cc_start: 0.6265 (tt0) cc_final: 0.5412 (tp40) REVERT: M 3 ASN cc_start: 0.6684 (p0) cc_final: 0.6210 (p0) REVERT: N 13 LYS cc_start: 0.5988 (ttmm) cc_final: 0.5238 (tttp) REVERT: N 16 GLU cc_start: 0.6424 (tp30) cc_final: 0.5749 (tt0) REVERT: N 51 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6548 (mt-10) REVERT: N 66 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6334 (mt-10) REVERT: N 75 ASP cc_start: 0.6475 (t0) cc_final: 0.6162 (t0) REVERT: N 120 GLU cc_start: 0.6405 (pt0) cc_final: 0.5416 (mm-30) REVERT: N 122 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6351 (mt-10) REVERT: N 128 ASP cc_start: 0.7001 (m-30) cc_final: 0.6772 (m-30) REVERT: N 151 GLU cc_start: 0.6479 (mt-10) cc_final: 0.5711 (mm-30) REVERT: N 173 ASP cc_start: 0.6795 (m-30) cc_final: 0.6498 (m-30) REVERT: N 201 PHE cc_start: 0.6959 (m-80) cc_final: 0.6015 (m-80) REVERT: N 225 ARG cc_start: 0.6209 (ttp-170) cc_final: 0.5971 (ttm170) REVERT: N 257 GLU cc_start: 0.6532 (tm-30) cc_final: 0.6172 (tm-30) REVERT: N 270 THR cc_start: 0.6956 (m) cc_final: 0.6409 (p) REVERT: N 271 GLU cc_start: 0.6231 (tp30) cc_final: 0.5923 (tp30) REVERT: N 330 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7626 (mt) REVERT: N 365 LYS cc_start: 0.6635 (mmtm) cc_final: 0.5889 (tttm) REVERT: N 409 LYS cc_start: 0.6448 (ttmm) cc_final: 0.5902 (tttt) REVERT: N 421 ASN cc_start: 0.6111 (m-40) cc_final: 0.4773 (t0) REVERT: N 428 ASP cc_start: 0.7036 (t70) cc_final: 0.6425 (t0) REVERT: N 445 GLN cc_start: 0.6792 (tt0) cc_final: 0.5842 (tp40) REVERT: O 13 LYS cc_start: 0.5950 (ttmm) cc_final: 0.5250 (tttp) REVERT: O 16 GLU cc_start: 0.6731 (tp30) cc_final: 0.6316 (tm-30) REVERT: O 21 ARG cc_start: 0.6699 (mtp85) cc_final: 0.6488 (mmm160) REVERT: O 51 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6651 (mt-10) REVERT: O 53 MET cc_start: 0.7287 (mtm) cc_final: 0.6822 (mtp) REVERT: O 66 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6567 (mt-10) REVERT: O 119 LYS cc_start: 0.6087 (tptp) cc_final: 0.5493 (tttm) REVERT: O 120 GLU cc_start: 0.6312 (pt0) cc_final: 0.5342 (mm-30) REVERT: O 122 GLU cc_start: 0.6556 (mt-10) cc_final: 0.6266 (mt-10) REVERT: O 128 ASP cc_start: 0.6932 (m-30) cc_final: 0.6684 (m-30) REVERT: O 151 GLU cc_start: 0.6607 (mt-10) cc_final: 0.5737 (mm-30) REVERT: O 155 ASP cc_start: 0.6585 (t0) cc_final: 0.6157 (t70) REVERT: O 173 ASP cc_start: 0.6715 (m-30) cc_final: 0.6336 (m-30) REVERT: O 184 ASP cc_start: 0.7192 (m-30) cc_final: 0.6991 (m-30) REVERT: O 201 PHE cc_start: 0.7045 (m-80) cc_final: 0.6278 (m-80) REVERT: O 225 ARG cc_start: 0.6524 (ttt180) cc_final: 0.5986 (ttt180) REVERT: O 257 GLU cc_start: 0.6391 (tm-30) cc_final: 0.5950 (pp20) REVERT: O 270 THR cc_start: 0.6933 (m) cc_final: 0.6458 (p) REVERT: O 271 GLU cc_start: 0.5811 (tp30) cc_final: 0.5401 (tp30) REVERT: O 354 GLU cc_start: 0.7306 (tp30) cc_final: 0.7067 (tp30) REVERT: O 365 LYS cc_start: 0.6273 (tppt) cc_final: 0.5499 (tttm) REVERT: O 388 GLN cc_start: 0.6370 (mt0) cc_final: 0.6167 (mt0) REVERT: O 399 LYS cc_start: 0.6511 (ttmt) cc_final: 0.5708 (ttmm) REVERT: O 408 LYS cc_start: 0.6772 (tttt) cc_final: 0.6487 (ttpp) REVERT: O 409 LYS cc_start: 0.6494 (ttmm) cc_final: 0.5954 (ttpt) REVERT: O 421 ASN cc_start: 0.5852 (m-40) cc_final: 0.4562 (t0) REVERT: O 428 ASP cc_start: 0.7002 (t70) cc_final: 0.6321 (m-30) REVERT: O 436 GLU cc_start: 0.6476 (tp30) cc_final: 0.6041 (tp30) REVERT: O 443 MET cc_start: 0.6620 (ttp) cc_final: 0.6277 (ttt) REVERT: O 445 GLN cc_start: 0.6642 (tt0) cc_final: 0.5622 (tp40) REVERT: P 4 ARG cc_start: 0.6216 (tmt170) cc_final: 0.5878 (tpt90) REVERT: Q 4 ARG cc_start: 0.6235 (tmt170) cc_final: 0.5998 (tpt90) REVERT: R 13 LYS cc_start: 0.6136 (ttmm) cc_final: 0.5712 (ttpt) REVERT: R 16 GLU cc_start: 0.6734 (tp30) cc_final: 0.6284 (tm-30) REVERT: R 51 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6718 (mt-10) REVERT: R 52 MET cc_start: 0.7305 (mmm) cc_final: 0.6629 (mmm) REVERT: R 66 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6991 (mt-10) REVERT: R 70 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7475 (mtt) REVERT: R 119 LYS cc_start: 0.6556 (ttpt) cc_final: 0.6082 (tttt) REVERT: R 120 GLU cc_start: 0.6266 (pt0) cc_final: 0.5201 (mm-30) REVERT: R 122 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6272 (mt-10) REVERT: R 128 ASP cc_start: 0.6847 (m-30) cc_final: 0.6596 (m-30) REVERT: R 151 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6500 (mt-10) REVERT: R 155 ASP cc_start: 0.6593 (t0) cc_final: 0.6341 (t70) REVERT: R 168 GLU cc_start: 0.4287 (OUTLIER) cc_final: 0.3928 (pp20) REVERT: R 173 ASP cc_start: 0.6894 (m-30) cc_final: 0.6428 (m-30) REVERT: R 184 ASP cc_start: 0.7205 (m-30) cc_final: 0.6891 (m-30) REVERT: R 201 PHE cc_start: 0.6903 (m-80) cc_final: 0.6107 (m-80) REVERT: R 203 TYR cc_start: 0.6344 (p90) cc_final: 0.5808 (p90) REVERT: R 225 ARG cc_start: 0.6507 (ttp-170) cc_final: 0.6097 (ttt180) REVERT: R 257 GLU cc_start: 0.6362 (tm-30) cc_final: 0.5839 (pp20) REVERT: R 270 THR cc_start: 0.7005 (m) cc_final: 0.6311 (p) REVERT: R 271 GLU cc_start: 0.6010 (tp30) cc_final: 0.5637 (tp30) REVERT: R 282 LYS cc_start: 0.6529 (tptm) cc_final: 0.5922 (tttm) REVERT: R 354 GLU cc_start: 0.7104 (tp30) cc_final: 0.6887 (mm-30) REVERT: R 365 LYS cc_start: 0.6390 (mmtm) cc_final: 0.5603 (tttm) REVERT: R 399 LYS cc_start: 0.6724 (ttmt) cc_final: 0.5969 (ttmm) REVERT: R 409 LYS cc_start: 0.6282 (ttmm) cc_final: 0.5870 (tttt) REVERT: R 418 GLN cc_start: 0.6852 (mm110) cc_final: 0.6617 (mm-40) REVERT: R 428 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6591 (m-30) REVERT: R 445 GLN cc_start: 0.6374 (tt0) cc_final: 0.5510 (tp40) REVERT: S 16 GLU cc_start: 0.6439 (tp30) cc_final: 0.5749 (tt0) REVERT: S 51 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6516 (mt-10) REVERT: S 66 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6396 (mt-10) REVERT: S 75 ASP cc_start: 0.6506 (t0) cc_final: 0.6236 (t0) REVERT: S 120 GLU cc_start: 0.6498 (pt0) cc_final: 0.5430 (mm-30) REVERT: S 122 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6377 (mt-10) REVERT: S 128 ASP cc_start: 0.6864 (m-30) cc_final: 0.6578 (m-30) REVERT: S 151 GLU cc_start: 0.6528 (mt-10) cc_final: 0.5727 (mm-30) REVERT: S 169 ASN cc_start: 0.5515 (OUTLIER) cc_final: 0.5251 (m-40) REVERT: S 173 ASP cc_start: 0.6765 (m-30) cc_final: 0.6469 (m-30) REVERT: S 201 PHE cc_start: 0.6792 (m-80) cc_final: 0.5822 (m-80) REVERT: S 225 ARG cc_start: 0.6262 (ttp-170) cc_final: 0.5876 (ttt180) REVERT: S 257 GLU cc_start: 0.6494 (tm-30) cc_final: 0.6187 (tm-30) REVERT: S 270 THR cc_start: 0.6966 (m) cc_final: 0.6421 (p) REVERT: S 271 GLU cc_start: 0.6249 (tp30) cc_final: 0.5785 (tp30) REVERT: S 330 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7610 (mt) REVERT: S 365 LYS cc_start: 0.6774 (mmtm) cc_final: 0.5982 (tttm) REVERT: S 409 LYS cc_start: 0.6429 (ttmm) cc_final: 0.5871 (tttt) REVERT: S 421 ASN cc_start: 0.6149 (m-40) cc_final: 0.4819 (t0) REVERT: S 428 ASP cc_start: 0.7023 (t70) cc_final: 0.6391 (t0) REVERT: S 445 GLN cc_start: 0.6779 (tt0) cc_final: 0.6504 (tt0) REVERT: T 13 LYS cc_start: 0.5960 (ttmm) cc_final: 0.5255 (tttp) REVERT: T 16 GLU cc_start: 0.6752 (tp30) cc_final: 0.6377 (tm-30) REVERT: T 21 ARG cc_start: 0.6203 (mmm-85) cc_final: 0.5746 (mmm160) REVERT: T 53 MET cc_start: 0.7286 (mtm) cc_final: 0.6824 (mtp) REVERT: T 66 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6534 (mt-10) REVERT: T 119 LYS cc_start: 0.6060 (tptp) cc_final: 0.5463 (tttm) REVERT: T 120 GLU cc_start: 0.6333 (pt0) cc_final: 0.5344 (mm-30) REVERT: T 122 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6251 (mt-10) REVERT: T 128 ASP cc_start: 0.6929 (m-30) cc_final: 0.6678 (m-30) REVERT: T 151 GLU cc_start: 0.6610 (mt-10) cc_final: 0.5741 (mm-30) REVERT: T 155 ASP cc_start: 0.6579 (t0) cc_final: 0.6175 (t70) REVERT: T 173 ASP cc_start: 0.6765 (m-30) cc_final: 0.6408 (m-30) REVERT: T 184 ASP cc_start: 0.7179 (m-30) cc_final: 0.6930 (m-30) REVERT: T 201 PHE cc_start: 0.7026 (m-80) cc_final: 0.6244 (m-80) REVERT: T 225 ARG cc_start: 0.6491 (ttt180) cc_final: 0.6097 (ttt180) REVERT: T 270 THR cc_start: 0.6984 (m) cc_final: 0.6487 (p) REVERT: T 271 GLU cc_start: 0.5802 (tp30) cc_final: 0.5455 (tp30) REVERT: T 354 GLU cc_start: 0.7306 (tp30) cc_final: 0.7043 (mm-30) REVERT: T 365 LYS cc_start: 0.6281 (tppt) cc_final: 0.5505 (tttm) REVERT: T 399 LYS cc_start: 0.6512 (ttmt) cc_final: 0.5709 (ttmm) REVERT: T 405 GLU cc_start: 0.5710 (mm-30) cc_final: 0.5227 (tm-30) REVERT: T 408 LYS cc_start: 0.6778 (tttt) cc_final: 0.6487 (ttpp) REVERT: T 409 LYS cc_start: 0.6518 (ttmm) cc_final: 0.6074 (ttpt) REVERT: T 421 ASN cc_start: 0.5850 (m-40) cc_final: 0.4554 (t0) REVERT: T 428 ASP cc_start: 0.6950 (t0) cc_final: 0.6306 (m-30) REVERT: T 436 GLU cc_start: 0.6416 (tp30) cc_final: 0.5968 (tp30) REVERT: T 443 MET cc_start: 0.6619 (ttp) cc_final: 0.6276 (ttt) REVERT: T 445 GLN cc_start: 0.6624 (tt0) cc_final: 0.5622 (tp40) REVERT: U 4 ARG cc_start: 0.6251 (tmt170) cc_final: 0.5887 (tpt90) REVERT: V 11 ILE cc_start: 0.6707 (mt) cc_final: 0.6506 (mp) REVERT: X 3 ASN cc_start: 0.6631 (p0) cc_final: 0.6125 (p0) outliers start: 62 outliers final: 32 residues processed: 965 average time/residue: 1.6545 time to fit residues: 1929.4829 Evaluate side-chains 830 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 789 time to evaluate : 4.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 169 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 68 SER Chi-restraints excluded: chain N residue 169 ASN Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain O residue 36 ASN Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 169 ASN Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 169 ASN Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain T residue 36 ASN Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 169 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 0.9990 chunk 400 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 269 optimal weight: 0.5980 chunk 213 optimal weight: 4.9990 chunk 413 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 251 optimal weight: 9.9990 chunk 308 optimal weight: 10.0000 chunk 479 optimal weight: 9.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 362 ASN A 421 ASN B 36 ASN B 418 GLN ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 ASN F 36 ASN F 421 ASN G 36 ASN G 413 ASN G 418 GLN ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN L 36 ASN L 362 ASN L 421 ASN N 36 ASN N 418 GLN ** O 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 228 ASN R 36 ASN R 421 ASN S 36 ASN S 413 ASN T 228 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 44100 Z= 0.116 Angle : 0.409 4.425 59700 Z= 0.219 Chirality : 0.039 0.142 6444 Planarity : 0.003 0.030 7860 Dihedral : 6.173 60.737 5933 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.07 % Allowed : 14.08 % Favored : 83.85 % 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: 0.61 (0.12), residues: 5316 helix: 1.59 (0.11), residues: 2340 sheet: -1.23 (0.16), residues: 864 loop : -0.09 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 427 HIS 0.004 0.001 HIS T 197 PHE 0.009 0.001 PHE S 287 TYR 0.018 0.001 TYR G 298 ARG 0.003 0.000 ARG M 4 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 818 time to evaluate : 5.370 Fit side-chains REVERT: A 16 GLU cc_start: 0.6619 (tp30) cc_final: 0.6199 (tm-30) REVERT: A 52 MET cc_start: 0.7406 (mmm) cc_final: 0.6838 (mmm) REVERT: A 66 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6932 (mt-10) REVERT: A 119 LYS cc_start: 0.6533 (ttpt) cc_final: 0.6070 (tttt) REVERT: A 120 GLU cc_start: 0.6264 (pt0) cc_final: 0.5255 (mm-30) REVERT: A 122 GLU cc_start: 0.6611 (mt-10) cc_final: 0.6367 (mt-10) REVERT: A 128 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6818 (m-30) REVERT: A 151 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6433 (mt-10) REVERT: A 184 ASP cc_start: 0.7143 (m-30) cc_final: 0.6868 (m-30) REVERT: A 201 PHE cc_start: 0.7061 (m-80) cc_final: 0.6827 (m-80) REVERT: A 225 ARG cc_start: 0.6643 (ttp-170) cc_final: 0.6163 (ttt180) REVERT: A 254 LYS cc_start: 0.7179 (ptmt) cc_final: 0.6826 (ptmm) REVERT: A 271 GLU cc_start: 0.5958 (tp30) cc_final: 0.5563 (tp30) REVERT: A 354 GLU cc_start: 0.7222 (tp30) cc_final: 0.6991 (mm-30) REVERT: A 365 LYS cc_start: 0.6242 (mmtm) cc_final: 0.5475 (tttm) REVERT: A 399 LYS cc_start: 0.6609 (ttmt) cc_final: 0.5874 (ttmm) REVERT: A 409 LYS cc_start: 0.6243 (ttmm) cc_final: 0.5844 (tttt) REVERT: A 418 GLN cc_start: 0.6856 (mm110) cc_final: 0.6591 (mm110) REVERT: A 428 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6524 (t0) REVERT: A 445 GLN cc_start: 0.6428 (tt0) cc_final: 0.5596 (tp40) REVERT: B 16 GLU cc_start: 0.6304 (tp30) cc_final: 0.5770 (tm-30) REVERT: B 120 GLU cc_start: 0.6177 (pt0) cc_final: 0.5220 (mm-30) REVERT: B 122 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6531 (mt-10) REVERT: B 128 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6962 (m-30) REVERT: B 151 GLU cc_start: 0.6498 (mt-10) cc_final: 0.5723 (mm-30) REVERT: B 155 ASP cc_start: 0.6706 (t0) cc_final: 0.6111 (t70) REVERT: B 173 ASP cc_start: 0.6474 (m-30) cc_final: 0.6232 (m-30) REVERT: B 201 PHE cc_start: 0.6992 (m-80) cc_final: 0.6089 (m-80) REVERT: B 271 GLU cc_start: 0.6025 (tp30) cc_final: 0.5728 (tp30) REVERT: B 365 LYS cc_start: 0.6581 (mmtm) cc_final: 0.5736 (tttm) REVERT: B 409 LYS cc_start: 0.6275 (ttmm) cc_final: 0.5896 (tttt) REVERT: B 421 ASN cc_start: 0.6086 (m-40) cc_final: 0.4791 (t0) REVERT: B 428 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6474 (t0) REVERT: B 445 GLN cc_start: 0.6949 (tt0) cc_final: 0.6723 (tt0) REVERT: C 13 LYS cc_start: 0.5966 (ttmm) cc_final: 0.5336 (tttp) REVERT: C 16 GLU cc_start: 0.6458 (tp30) cc_final: 0.6095 (tm-30) REVERT: C 53 MET cc_start: 0.7307 (mtm) cc_final: 0.6820 (mtp) REVERT: C 66 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6562 (mt-10) REVERT: C 119 LYS cc_start: 0.6194 (tptp) cc_final: 0.5746 (tttt) REVERT: C 120 GLU cc_start: 0.6168 (pt0) cc_final: 0.5239 (mm-30) REVERT: C 122 GLU cc_start: 0.6455 (mt-10) cc_final: 0.6151 (mt-10) REVERT: C 128 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6835 (m-30) REVERT: C 151 GLU cc_start: 0.6532 (mt-10) cc_final: 0.5712 (mm-30) REVERT: C 155 ASP cc_start: 0.6676 (t0) cc_final: 0.6136 (t70) REVERT: C 173 ASP cc_start: 0.6493 (m-30) cc_final: 0.6123 (m-30) REVERT: C 184 ASP cc_start: 0.7108 (m-30) cc_final: 0.6879 (m-30) REVERT: C 201 PHE cc_start: 0.7120 (m-80) cc_final: 0.6841 (m-80) REVERT: C 225 ARG cc_start: 0.6281 (ttt180) cc_final: 0.5931 (ttt180) REVERT: C 270 THR cc_start: 0.6685 (m) cc_final: 0.6064 (p) REVERT: C 271 GLU cc_start: 0.5612 (tp30) cc_final: 0.5120 (tp30) REVERT: C 327 SER cc_start: 0.6958 (m) cc_final: 0.6735 (t) REVERT: C 354 GLU cc_start: 0.7244 (tp30) cc_final: 0.6958 (mm-30) REVERT: C 365 LYS cc_start: 0.6324 (tppt) cc_final: 0.5464 (tttm) REVERT: C 388 GLN cc_start: 0.6542 (mt0) cc_final: 0.5943 (mm-40) REVERT: C 399 LYS cc_start: 0.6504 (ttmt) cc_final: 0.5753 (ttmm) REVERT: C 408 LYS cc_start: 0.6736 (tttt) cc_final: 0.6478 (ttpp) REVERT: C 409 LYS cc_start: 0.6493 (ttmm) cc_final: 0.5984 (ttmt) REVERT: C 421 ASN cc_start: 0.5825 (m-40) cc_final: 0.4624 (t0) REVERT: C 428 ASP cc_start: 0.6986 (t70) cc_final: 0.6393 (m-30) REVERT: C 436 GLU cc_start: 0.5573 (pm20) cc_final: 0.5063 (pm20) REVERT: C 443 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.6201 (ttt) REVERT: C 445 GLN cc_start: 0.6577 (tt0) cc_final: 0.5586 (tp40) REVERT: D 4 ARG cc_start: 0.5934 (tmt170) cc_final: 0.5629 (tpt90) REVERT: E 11 ILE cc_start: 0.6557 (mt) cc_final: 0.6349 (mp) REVERT: F 16 GLU cc_start: 0.6627 (tp30) cc_final: 0.6221 (tm-30) REVERT: F 21 ARG cc_start: 0.6606 (mtp85) cc_final: 0.6234 (mmp-170) REVERT: F 52 MET cc_start: 0.7418 (mmm) cc_final: 0.6875 (mmm) REVERT: F 66 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6952 (mt-10) REVERT: F 119 LYS cc_start: 0.6521 (ttpt) cc_final: 0.6261 (tttm) REVERT: F 120 GLU cc_start: 0.6256 (pt0) cc_final: 0.5247 (mm-30) REVERT: F 122 GLU cc_start: 0.6578 (mt-10) cc_final: 0.6328 (mt-10) REVERT: F 128 ASP cc_start: 0.7073 (m-30) cc_final: 0.6835 (m-30) REVERT: F 151 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6364 (mt-10) REVERT: F 155 ASP cc_start: 0.6565 (t0) cc_final: 0.6360 (t70) REVERT: F 173 ASP cc_start: 0.6838 (m-30) cc_final: 0.6504 (m-30) REVERT: F 184 ASP cc_start: 0.7162 (m-30) cc_final: 0.6886 (m-30) REVERT: F 201 PHE cc_start: 0.7099 (m-80) cc_final: 0.6084 (m-80) REVERT: F 225 ARG cc_start: 0.6490 (ttp-170) cc_final: 0.6003 (ttt180) REVERT: F 254 LYS cc_start: 0.7250 (ptmt) cc_final: 0.6753 (ptmm) REVERT: F 257 GLU cc_start: 0.6341 (tm-30) cc_final: 0.5749 (pp20) REVERT: F 270 THR cc_start: 0.6603 (m) cc_final: 0.5732 (p) REVERT: F 271 GLU cc_start: 0.5784 (tp30) cc_final: 0.5383 (tp30) REVERT: F 354 GLU cc_start: 0.7218 (tp30) cc_final: 0.6985 (mm-30) REVERT: F 365 LYS cc_start: 0.6230 (mmtm) cc_final: 0.5461 (tttm) REVERT: F 399 LYS cc_start: 0.6591 (ttmt) cc_final: 0.5844 (ttmm) REVERT: F 409 LYS cc_start: 0.6239 (ttmm) cc_final: 0.5838 (tttt) REVERT: F 418 GLN cc_start: 0.6848 (mm110) cc_final: 0.6583 (mm110) REVERT: F 428 ASP cc_start: 0.7128 (t70) cc_final: 0.6493 (t0) REVERT: F 445 GLN cc_start: 0.6438 (tt0) cc_final: 0.5603 (tp40) REVERT: G 51 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6499 (mt-10) REVERT: G 120 GLU cc_start: 0.6176 (pt0) cc_final: 0.5216 (mm-30) REVERT: G 122 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6286 (mt-10) REVERT: G 128 ASP cc_start: 0.7266 (m-30) cc_final: 0.7016 (m-30) REVERT: G 151 GLU cc_start: 0.6473 (mt-10) cc_final: 0.5715 (mm-30) REVERT: G 155 ASP cc_start: 0.6697 (t0) cc_final: 0.6100 (t70) REVERT: G 173 ASP cc_start: 0.6476 (m-30) cc_final: 0.6236 (m-30) REVERT: G 201 PHE cc_start: 0.6991 (m-80) cc_final: 0.6088 (m-80) REVERT: G 271 GLU cc_start: 0.6022 (tp30) cc_final: 0.5620 (tp30) REVERT: G 365 LYS cc_start: 0.6589 (mmtm) cc_final: 0.5744 (tttm) REVERT: G 409 LYS cc_start: 0.6281 (ttmm) cc_final: 0.5902 (tttt) REVERT: G 421 ASN cc_start: 0.6136 (m-40) cc_final: 0.4826 (t0) REVERT: G 428 ASP cc_start: 0.7040 (t70) cc_final: 0.6777 (t0) REVERT: G 443 MET cc_start: 0.6287 (ttt) cc_final: 0.6013 (ttp) REVERT: G 445 GLN cc_start: 0.6749 (tt0) cc_final: 0.6489 (tt0) REVERT: H 13 LYS cc_start: 0.5979 (ttmm) cc_final: 0.5348 (tttp) REVERT: H 16 GLU cc_start: 0.6457 (tp30) cc_final: 0.6062 (tm-30) REVERT: H 53 MET cc_start: 0.7353 (mtm) cc_final: 0.6880 (mtp) REVERT: H 66 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6575 (mt-10) REVERT: H 119 LYS cc_start: 0.6218 (tptp) cc_final: 0.5761 (tttt) REVERT: H 120 GLU cc_start: 0.6179 (pt0) cc_final: 0.5262 (mm-30) REVERT: H 122 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6651 (mt-10) REVERT: H 128 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6783 (m-30) REVERT: H 151 GLU cc_start: 0.6561 (mt-10) cc_final: 0.5728 (mm-30) REVERT: H 155 ASP cc_start: 0.6575 (t0) cc_final: 0.6100 (t70) REVERT: H 173 ASP cc_start: 0.6458 (m-30) cc_final: 0.6102 (m-30) REVERT: H 201 PHE cc_start: 0.7206 (m-80) cc_final: 0.6846 (m-80) REVERT: H 225 ARG cc_start: 0.6304 (ttp-170) cc_final: 0.6039 (ttt180) REVERT: H 270 THR cc_start: 0.6675 (m) cc_final: 0.6056 (p) REVERT: H 271 GLU cc_start: 0.5583 (tp30) cc_final: 0.5090 (tp30) REVERT: H 327 SER cc_start: 0.6956 (m) cc_final: 0.6726 (t) REVERT: H 354 GLU cc_start: 0.7241 (tp30) cc_final: 0.6955 (mm-30) REVERT: H 365 LYS cc_start: 0.6298 (tppt) cc_final: 0.5455 (tttm) REVERT: H 399 LYS cc_start: 0.6492 (ttmt) cc_final: 0.5739 (ttmm) REVERT: H 408 LYS cc_start: 0.6729 (tttt) cc_final: 0.6465 (ttpp) REVERT: H 409 LYS cc_start: 0.6500 (ttmm) cc_final: 0.5990 (ttmt) REVERT: H 421 ASN cc_start: 0.5837 (m-40) cc_final: 0.4635 (t0) REVERT: H 428 ASP cc_start: 0.6983 (t0) cc_final: 0.6359 (m-30) REVERT: H 436 GLU cc_start: 0.5604 (pm20) cc_final: 0.5101 (pm20) REVERT: H 443 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6315 (ttt) REVERT: H 445 GLN cc_start: 0.6607 (tt0) cc_final: 0.5626 (tp40) REVERT: I 4 ARG cc_start: 0.5918 (tmt170) cc_final: 0.5667 (tpt90) REVERT: K 4 ARG cc_start: 0.6038 (tmt170) cc_final: 0.5514 (tpt90) REVERT: L 16 GLU cc_start: 0.6604 (tp30) cc_final: 0.6180 (tm-30) REVERT: L 52 MET cc_start: 0.7247 (mmm) cc_final: 0.6707 (mmm) REVERT: L 66 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6948 (mt-10) REVERT: L 119 LYS cc_start: 0.6391 (ttpt) cc_final: 0.6170 (tttm) REVERT: L 120 GLU cc_start: 0.6312 (pt0) cc_final: 0.5293 (mm-30) REVERT: L 122 GLU cc_start: 0.6544 (mt-10) cc_final: 0.6242 (mt-10) REVERT: L 128 ASP cc_start: 0.6960 (m-30) cc_final: 0.6700 (m-30) REVERT: L 151 GLU cc_start: 0.6658 (mt-10) cc_final: 0.6342 (mt-10) REVERT: L 155 ASP cc_start: 0.6563 (t0) cc_final: 0.6349 (t70) REVERT: L 173 ASP cc_start: 0.6840 (m-30) cc_final: 0.6479 (m-30) REVERT: L 184 ASP cc_start: 0.7125 (m-30) cc_final: 0.6826 (m-30) REVERT: L 201 PHE cc_start: 0.7102 (m-80) cc_final: 0.6074 (m-80) REVERT: L 225 ARG cc_start: 0.6607 (ttp-170) cc_final: 0.6199 (ttt180) REVERT: L 254 LYS cc_start: 0.7231 (ptmt) cc_final: 0.6775 (ptmm) REVERT: L 270 THR cc_start: 0.6624 (m) cc_final: 0.5764 (p) REVERT: L 271 GLU cc_start: 0.5740 (tp30) cc_final: 0.5417 (tp30) REVERT: L 354 GLU cc_start: 0.7212 (tp30) cc_final: 0.6977 (mm-30) REVERT: L 365 LYS cc_start: 0.6233 (mmtm) cc_final: 0.5461 (tttm) REVERT: L 399 LYS cc_start: 0.6635 (ttmt) cc_final: 0.5880 (ttmm) REVERT: L 409 LYS cc_start: 0.6250 (ttmm) cc_final: 0.5849 (tttt) REVERT: L 418 GLN cc_start: 0.6838 (mm110) cc_final: 0.6573 (mm110) REVERT: L 428 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6494 (t0) REVERT: L 445 GLN cc_start: 0.6306 (tt0) cc_final: 0.5498 (tp40) REVERT: N 16 GLU cc_start: 0.6289 (tp30) cc_final: 0.5755 (tm-30) REVERT: N 51 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6428 (mt-10) REVERT: N 120 GLU cc_start: 0.6148 (pt0) cc_final: 0.5183 (mm-30) REVERT: N 122 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6263 (mt-10) REVERT: N 128 ASP cc_start: 0.7192 (m-30) cc_final: 0.6958 (m-30) REVERT: N 151 GLU cc_start: 0.6502 (mt-10) cc_final: 0.5727 (mm-30) REVERT: N 168 GLU cc_start: 0.4193 (OUTLIER) cc_final: 0.3970 (tm-30) REVERT: N 169 ASN cc_start: 0.5108 (OUTLIER) cc_final: 0.4886 (m-40) REVERT: N 173 ASP cc_start: 0.6473 (m-30) cc_final: 0.6238 (m-30) REVERT: N 201 PHE cc_start: 0.6985 (m-80) cc_final: 0.6084 (m-80) REVERT: N 271 GLU cc_start: 0.6029 (tp30) cc_final: 0.5731 (tp30) REVERT: N 365 LYS cc_start: 0.6594 (mmtm) cc_final: 0.5763 (tttm) REVERT: N 409 LYS cc_start: 0.6284 (ttmm) cc_final: 0.5907 (tttt) REVERT: N 421 ASN cc_start: 0.6162 (m-40) cc_final: 0.4858 (t0) REVERT: N 428 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6467 (t0) REVERT: N 445 GLN cc_start: 0.6715 (tt0) cc_final: 0.6474 (tt0) REVERT: O 13 LYS cc_start: 0.5940 (ttmm) cc_final: 0.5314 (tttp) REVERT: O 16 GLU cc_start: 0.6441 (tp30) cc_final: 0.6046 (tm-30) REVERT: O 51 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6815 (mt-10) REVERT: O 53 MET cc_start: 0.7295 (mtm) cc_final: 0.6815 (mtp) REVERT: O 66 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6556 (mt-10) REVERT: O 119 LYS cc_start: 0.6233 (tptp) cc_final: 0.5772 (tttt) REVERT: O 120 GLU cc_start: 0.6188 (pt0) cc_final: 0.5262 (mm-30) REVERT: O 122 GLU cc_start: 0.6471 (mt-10) cc_final: 0.6180 (mt-10) REVERT: O 128 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6792 (m-30) REVERT: O 151 GLU cc_start: 0.6551 (mt-10) cc_final: 0.5718 (mm-30) REVERT: O 155 ASP cc_start: 0.6571 (t0) cc_final: 0.6101 (t70) REVERT: O 173 ASP cc_start: 0.6478 (m-30) cc_final: 0.6098 (m-30) REVERT: O 184 ASP cc_start: 0.7156 (m-30) cc_final: 0.6938 (m-30) REVERT: O 201 PHE cc_start: 0.7204 (m-80) cc_final: 0.6844 (m-80) REVERT: O 225 ARG cc_start: 0.6333 (ttt180) cc_final: 0.5958 (ttt180) REVERT: O 270 THR cc_start: 0.6667 (m) cc_final: 0.6048 (p) REVERT: O 271 GLU cc_start: 0.5579 (tp30) cc_final: 0.5085 (tp30) REVERT: O 327 SER cc_start: 0.6953 (m) cc_final: 0.6724 (t) REVERT: O 354 GLU cc_start: 0.7240 (tp30) cc_final: 0.6957 (mm-30) REVERT: O 365 LYS cc_start: 0.6265 (tppt) cc_final: 0.5442 (tttm) REVERT: O 399 LYS cc_start: 0.6494 (ttmt) cc_final: 0.5739 (ttmm) REVERT: O 408 LYS cc_start: 0.6710 (tttt) cc_final: 0.6445 (ttpp) REVERT: O 409 LYS cc_start: 0.6487 (ttmm) cc_final: 0.5979 (ttmt) REVERT: O 421 ASN cc_start: 0.5819 (m-40) cc_final: 0.4617 (t0) REVERT: O 428 ASP cc_start: 0.6999 (t70) cc_final: 0.6399 (m-30) REVERT: O 436 GLU cc_start: 0.6212 (tp30) cc_final: 0.5805 (tp30) REVERT: O 443 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.6194 (ttt) REVERT: O 445 GLN cc_start: 0.6608 (tt0) cc_final: 0.5618 (tp40) REVERT: P 4 ARG cc_start: 0.6187 (tmt170) cc_final: 0.5737 (tpt90) REVERT: Q 4 ARG cc_start: 0.6117 (tmt170) cc_final: 0.5865 (tpt90) REVERT: R 16 GLU cc_start: 0.6616 (tp30) cc_final: 0.6203 (tm-30) REVERT: R 51 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6678 (mt-10) REVERT: R 52 MET cc_start: 0.7347 (mmm) cc_final: 0.6654 (mmm) REVERT: R 66 GLU cc_start: 0.7332 (mt-10) cc_final: 0.7000 (mt-10) REVERT: R 70 MET cc_start: 0.8011 (mtt) cc_final: 0.7712 (mtt) REVERT: R 119 LYS cc_start: 0.6514 (ttpt) cc_final: 0.6043 (tttt) REVERT: R 120 GLU cc_start: 0.6214 (pt0) cc_final: 0.5244 (mm-30) REVERT: R 122 GLU cc_start: 0.6545 (mt-10) cc_final: 0.6241 (mt-10) REVERT: R 128 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6853 (m-30) REVERT: R 151 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6417 (mt-10) REVERT: R 155 ASP cc_start: 0.6574 (t0) cc_final: 0.6331 (t70) REVERT: R 173 ASP cc_start: 0.6861 (m-30) cc_final: 0.6514 (m-30) REVERT: R 184 ASP cc_start: 0.7129 (m-30) cc_final: 0.6847 (m-30) REVERT: R 201 PHE cc_start: 0.7053 (m-80) cc_final: 0.6112 (m-80) REVERT: R 225 ARG cc_start: 0.6489 (ttp-170) cc_final: 0.5997 (ttt180) REVERT: R 254 LYS cc_start: 0.7256 (ptmt) cc_final: 0.6798 (ptmm) REVERT: R 270 THR cc_start: 0.6598 (m) cc_final: 0.5724 (p) REVERT: R 271 GLU cc_start: 0.5740 (tp30) cc_final: 0.5358 (tp30) REVERT: R 354 GLU cc_start: 0.7211 (tp30) cc_final: 0.6978 (mm-30) REVERT: R 365 LYS cc_start: 0.6243 (mmtm) cc_final: 0.5469 (tttm) REVERT: R 399 LYS cc_start: 0.6606 (ttmt) cc_final: 0.5862 (ttmm) REVERT: R 409 LYS cc_start: 0.6245 (ttmm) cc_final: 0.5843 (tttt) REVERT: R 418 GLN cc_start: 0.6849 (mm110) cc_final: 0.6590 (mm110) REVERT: R 428 ASP cc_start: 0.7213 (t70) cc_final: 0.6771 (t0) REVERT: R 445 GLN cc_start: 0.6501 (tt0) cc_final: 0.5662 (tp40) REVERT: S 51 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6495 (mt-10) REVERT: S 120 GLU cc_start: 0.6278 (pt0) cc_final: 0.5225 (mm-30) REVERT: S 128 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6785 (m-30) REVERT: S 151 GLU cc_start: 0.6499 (mt-10) cc_final: 0.5709 (mm-30) REVERT: S 155 ASP cc_start: 0.6757 (t0) cc_final: 0.6158 (t70) REVERT: S 173 ASP cc_start: 0.6457 (m-30) cc_final: 0.6210 (m-30) REVERT: S 201 PHE cc_start: 0.6977 (m-80) cc_final: 0.6078 (m-80) REVERT: S 225 ARG cc_start: 0.6457 (ttp-170) cc_final: 0.6101 (ttt180) REVERT: S 271 GLU cc_start: 0.6067 (tp30) cc_final: 0.5613 (tp30) REVERT: S 365 LYS cc_start: 0.6549 (mmtm) cc_final: 0.5779 (tttm) REVERT: S 409 LYS cc_start: 0.6289 (ttmm) cc_final: 0.5907 (tttt) REVERT: S 421 ASN cc_start: 0.6109 (m-40) cc_final: 0.4798 (t0) REVERT: S 428 ASP cc_start: 0.7129 (t70) cc_final: 0.6498 (t0) REVERT: S 445 GLN cc_start: 0.6751 (tt0) cc_final: 0.6501 (tt0) REVERT: T 13 LYS cc_start: 0.5956 (ttmm) cc_final: 0.5323 (tttp) REVERT: T 16 GLU cc_start: 0.6459 (tp30) cc_final: 0.6093 (tm-30) REVERT: T 21 ARG cc_start: 0.6240 (mmm-85) cc_final: 0.5747 (mmm160) REVERT: T 53 MET cc_start: 0.7304 (mtm) cc_final: 0.6826 (mtp) REVERT: T 119 LYS cc_start: 0.6224 (tptp) cc_final: 0.5763 (tttt) REVERT: T 120 GLU cc_start: 0.6177 (pt0) cc_final: 0.5261 (mm-30) REVERT: T 122 GLU cc_start: 0.6461 (mt-10) cc_final: 0.6158 (mt-10) REVERT: T 128 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6826 (m-30) REVERT: T 151 GLU cc_start: 0.6550 (mt-10) cc_final: 0.5721 (mm-30) REVERT: T 155 ASP cc_start: 0.6564 (t0) cc_final: 0.6098 (t70) REVERT: T 173 ASP cc_start: 0.6484 (m-30) cc_final: 0.6161 (m-30) REVERT: T 184 ASP cc_start: 0.7099 (m-30) cc_final: 0.6867 (m-30) REVERT: T 201 PHE cc_start: 0.7135 (m-80) cc_final: 0.6865 (m-80) REVERT: T 225 ARG cc_start: 0.6253 (ttt180) cc_final: 0.5914 (ttt180) REVERT: T 270 THR cc_start: 0.6672 (m) cc_final: 0.6043 (p) REVERT: T 271 GLU cc_start: 0.5579 (tp30) cc_final: 0.5087 (tp30) REVERT: T 327 SER cc_start: 0.6955 (m) cc_final: 0.6724 (t) REVERT: T 354 GLU cc_start: 0.7242 (tp30) cc_final: 0.6957 (mm-30) REVERT: T 365 LYS cc_start: 0.6269 (tppt) cc_final: 0.5445 (tttm) REVERT: T 399 LYS cc_start: 0.6493 (ttmt) cc_final: 0.5739 (ttmm) REVERT: T 408 LYS cc_start: 0.6733 (tttt) cc_final: 0.6476 (ttpp) REVERT: T 409 LYS cc_start: 0.6480 (ttmm) cc_final: 0.5993 (ttmt) REVERT: T 421 ASN cc_start: 0.5815 (m-40) cc_final: 0.4614 (t0) REVERT: T 428 ASP cc_start: 0.7039 (t0) cc_final: 0.6393 (m-30) REVERT: T 436 GLU cc_start: 0.6268 (tp30) cc_final: 0.5811 (tp30) REVERT: T 443 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.6193 (ttt) REVERT: T 445 GLN cc_start: 0.6567 (tt0) cc_final: 0.5623 (tp40) REVERT: U 4 ARG cc_start: 0.5994 (tmt170) cc_final: 0.5687 (tpt90) REVERT: W 3 ASN cc_start: 0.6820 (p0) cc_final: 0.6304 (p0) outliers start: 96 outliers final: 35 residues processed: 860 average time/residue: 1.6451 time to fit residues: 1711.1649 Evaluate side-chains 842 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 789 time to evaluate : 4.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 53 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 169 ASN Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 443 MET Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain L residue 428 ASP Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 53 MET Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain N residue 169 ASN Chi-restraints excluded: chain N residue 428 ASP Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 169 ASN Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 443 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 169 ASN Chi-restraints excluded: chain R residue 366 VAL Chi-restraints excluded: chain S residue 10 ASP Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 53 MET Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain T residue 169 ASN Chi-restraints excluded: chain T residue 277 THR Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain T residue 443 MET Chi-restraints excluded: chain V residue 2 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 0.2980 chunk 148 optimal weight: 10.0000 chunk 399 optimal weight: 8.9990 chunk 326 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 480 optimal weight: 7.9990 chunk 518 optimal weight: 7.9990 chunk 427 optimal weight: 10.0000 chunk 476 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 385 optimal weight: 10.0000 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 189 HIS A 445 GLN B 36 ASN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS B 418 GLN B 445 GLN C 36 ASN C 189 HIS C 413 ASN C 445 GLN F 36 ASN F 169 ASN F 189 HIS F 445 GLN G 36 ASN G 169 ASN G 189 HIS G 413 ASN H 36 ASN H 189 HIS H 413 ASN H 445 GLN L 36 ASN L 169 ASN L 189 HIS N 36 ASN N 169 ASN N 189 HIS N 413 ASN O 36 ASN O 189 HIS ** O 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 413 ASN O 445 GLN R 36 ASN R 169 ASN R 189 HIS R 445 GLN S 36 ASN S 169 ASN S 189 HIS S 413 ASN T 36 ASN T 189 HIS T 413 ASN T 445 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 44100 Z= 0.413 Angle : 0.698 7.723 59700 Z= 0.381 Chirality : 0.051 0.227 6444 Planarity : 0.006 0.055 7860 Dihedral : 6.862 59.650 5896 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.22 % Rotamer: Outliers : 3.20 % Allowed : 12.28 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.03 (0.11), residues: 5316 helix: 1.10 (0.11), residues: 2280 sheet: -1.74 (0.15), residues: 744 loop : -0.35 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP R 427 HIS 0.008 0.002 HIS O 197 PHE 0.026 0.003 PHE H 287 TYR 0.040 0.003 TYR S 298 ARG 0.009 0.001 ARG M 4 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 769 time to evaluate : 5.384 Fit side-chains REVERT: A 16 GLU cc_start: 0.6750 (tp30) cc_final: 0.6195 (tm-30) REVERT: A 52 MET cc_start: 0.7337 (mmm) cc_final: 0.6766 (mmm) REVERT: A 109 ASP cc_start: 0.6835 (t0) cc_final: 0.6558 (t0) REVERT: A 119 LYS cc_start: 0.6493 (ttpt) cc_final: 0.6084 (tttt) REVERT: A 120 GLU cc_start: 0.6105 (pt0) cc_final: 0.5158 (mm-30) REVERT: A 128 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6775 (m-30) REVERT: A 151 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6477 (mt-10) REVERT: A 184 ASP cc_start: 0.7119 (m-30) cc_final: 0.6820 (m-30) REVERT: A 225 ARG cc_start: 0.6446 (ttp-170) cc_final: 0.6146 (ttm170) REVERT: A 246 MET cc_start: 0.7064 (ttp) cc_final: 0.6666 (ttp) REVERT: A 254 LYS cc_start: 0.7467 (ptmt) cc_final: 0.7257 (ptmt) REVERT: A 271 GLU cc_start: 0.5595 (tp30) cc_final: 0.5308 (tp30) REVERT: A 365 LYS cc_start: 0.6065 (mmtm) cc_final: 0.5337 (tttm) REVERT: A 409 LYS cc_start: 0.6258 (ttmm) cc_final: 0.5794 (tttt) REVERT: A 418 GLN cc_start: 0.6729 (mm110) cc_final: 0.6478 (mm-40) REVERT: A 436 GLU cc_start: 0.5708 (OUTLIER) cc_final: 0.5391 (pm20) REVERT: A 443 MET cc_start: 0.6855 (tpp) cc_final: 0.6332 (tpp) REVERT: A 445 GLN cc_start: 0.6534 (tt0) cc_final: 0.5744 (tp40) REVERT: B 16 GLU cc_start: 0.6420 (tp30) cc_final: 0.5991 (tm-30) REVERT: B 109 ASP cc_start: 0.6808 (t0) cc_final: 0.6232 (t0) REVERT: B 120 GLU cc_start: 0.6228 (pt0) cc_final: 0.5164 (mm-30) REVERT: B 122 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6397 (mt-10) REVERT: B 151 GLU cc_start: 0.6543 (mt-10) cc_final: 0.5727 (mm-30) REVERT: B 155 ASP cc_start: 0.6417 (t0) cc_final: 0.5922 (t70) REVERT: B 168 GLU cc_start: 0.4955 (OUTLIER) cc_final: 0.4621 (tt0) REVERT: B 201 PHE cc_start: 0.7001 (m-80) cc_final: 0.6055 (m-80) REVERT: B 226 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6613 (tttt) REVERT: B 365 LYS cc_start: 0.6443 (mmtm) cc_final: 0.5663 (tttm) REVERT: B 409 LYS cc_start: 0.6265 (ttmm) cc_final: 0.5869 (tttt) REVERT: B 421 ASN cc_start: 0.6319 (m-40) cc_final: 0.4958 (t0) REVERT: B 436 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5364 (pm20) REVERT: B 445 GLN cc_start: 0.6894 (tt0) cc_final: 0.6676 (tt0) REVERT: C 13 LYS cc_start: 0.6021 (ttmm) cc_final: 0.5405 (tttp) REVERT: C 16 GLU cc_start: 0.6704 (tp30) cc_final: 0.6332 (tm-30) REVERT: C 21 ARG cc_start: 0.7045 (mmm160) cc_final: 0.6834 (mmp-170) REVERT: C 119 LYS cc_start: 0.6081 (tptp) cc_final: 0.5586 (tttt) REVERT: C 120 GLU cc_start: 0.6188 (pt0) cc_final: 0.5358 (mm-30) REVERT: C 121 MET cc_start: 0.6510 (ttp) cc_final: 0.6281 (ttp) REVERT: C 122 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6411 (mt-10) REVERT: C 128 ASP cc_start: 0.7180 (m-30) cc_final: 0.6968 (m-30) REVERT: C 151 GLU cc_start: 0.6601 (mt-10) cc_final: 0.5731 (mm-30) REVERT: C 155 ASP cc_start: 0.6714 (t0) cc_final: 0.6209 (t70) REVERT: C 168 GLU cc_start: 0.4731 (OUTLIER) cc_final: 0.4067 (tm-30) REVERT: C 201 PHE cc_start: 0.7367 (m-80) cc_final: 0.7127 (m-80) REVERT: C 266 GLU cc_start: 0.5978 (OUTLIER) cc_final: 0.5541 (mp0) REVERT: C 270 THR cc_start: 0.6868 (m) cc_final: 0.6253 (p) REVERT: C 271 GLU cc_start: 0.5642 (tp30) cc_final: 0.5319 (tp30) REVERT: C 354 GLU cc_start: 0.7135 (tp30) cc_final: 0.6878 (mm-30) REVERT: C 365 LYS cc_start: 0.6347 (tppt) cc_final: 0.5453 (tttm) REVERT: C 388 GLN cc_start: 0.6520 (mt0) cc_final: 0.6005 (mm-40) REVERT: C 408 LYS cc_start: 0.6737 (tttt) cc_final: 0.6443 (ttpp) REVERT: C 409 LYS cc_start: 0.6544 (ttmm) cc_final: 0.6018 (ttpt) REVERT: C 421 ASN cc_start: 0.6079 (m-40) cc_final: 0.4777 (t0) REVERT: C 436 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.5308 (pm20) REVERT: C 445 GLN cc_start: 0.6621 (tt0) cc_final: 0.5737 (tp40) REVERT: F 16 GLU cc_start: 0.6754 (tp30) cc_final: 0.6210 (tm-30) REVERT: F 21 ARG cc_start: 0.6768 (mtp85) cc_final: 0.6418 (mmp-170) REVERT: F 52 MET cc_start: 0.7331 (mmm) cc_final: 0.6748 (mmm) REVERT: F 109 ASP cc_start: 0.6834 (t0) cc_final: 0.6556 (t0) REVERT: F 119 LYS cc_start: 0.6447 (ttpt) cc_final: 0.6064 (tttt) REVERT: F 120 GLU cc_start: 0.6125 (pt0) cc_final: 0.5185 (mm-30) REVERT: F 128 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6749 (m-30) REVERT: F 151 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6329 (mt-10) REVERT: F 168 GLU cc_start: 0.4600 (OUTLIER) cc_final: 0.4154 (tt0) REVERT: F 173 ASP cc_start: 0.6683 (m-30) cc_final: 0.6343 (m-30) REVERT: F 184 ASP cc_start: 0.7144 (m-30) cc_final: 0.6850 (m-30) REVERT: F 225 ARG cc_start: 0.6383 (ttp-170) cc_final: 0.6154 (ttm170) REVERT: F 254 LYS cc_start: 0.7554 (ptmt) cc_final: 0.7354 (ptmt) REVERT: F 270 THR cc_start: 0.6814 (m) cc_final: 0.5931 (p) REVERT: F 271 GLU cc_start: 0.5633 (tp30) cc_final: 0.5263 (tp30) REVERT: F 365 LYS cc_start: 0.6058 (mmtm) cc_final: 0.5334 (tttm) REVERT: F 409 LYS cc_start: 0.6250 (ttmm) cc_final: 0.5785 (tttt) REVERT: F 418 GLN cc_start: 0.6721 (mm110) cc_final: 0.6469 (mm-40) REVERT: F 436 GLU cc_start: 0.5713 (OUTLIER) cc_final: 0.5267 (pm20) REVERT: F 443 MET cc_start: 0.6834 (tpp) cc_final: 0.6508 (tpp) REVERT: F 445 GLN cc_start: 0.6547 (tt0) cc_final: 0.5753 (tp40) REVERT: G 16 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.5707 (tm-30) REVERT: G 120 GLU cc_start: 0.6230 (pt0) cc_final: 0.5164 (mm-30) REVERT: G 122 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6321 (mt-10) REVERT: G 151 GLU cc_start: 0.6541 (mt-10) cc_final: 0.5725 (mm-30) REVERT: G 155 ASP cc_start: 0.6404 (t0) cc_final: 0.5907 (t70) REVERT: G 168 GLU cc_start: 0.5020 (OUTLIER) cc_final: 0.4380 (pp20) REVERT: G 169 ASN cc_start: 0.5723 (OUTLIER) cc_final: 0.4502 (m-40) REVERT: G 201 PHE cc_start: 0.7007 (m-80) cc_final: 0.6071 (m-80) REVERT: G 226 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6569 (tttt) REVERT: G 266 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5544 (mp0) REVERT: G 365 LYS cc_start: 0.6448 (mmtm) cc_final: 0.5672 (tttm) REVERT: G 409 LYS cc_start: 0.6273 (ttmm) cc_final: 0.5876 (tttt) REVERT: G 421 ASN cc_start: 0.6333 (m-40) cc_final: 0.4982 (t0) REVERT: G 436 GLU cc_start: 0.6029 (OUTLIER) cc_final: 0.5376 (pm20) REVERT: G 443 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6141 (tpp) REVERT: H 13 LYS cc_start: 0.6036 (ttmm) cc_final: 0.5418 (tttp) REVERT: H 16 GLU cc_start: 0.6701 (tp30) cc_final: 0.6329 (tm-30) REVERT: H 21 ARG cc_start: 0.7048 (mmm160) cc_final: 0.6838 (mmp-170) REVERT: H 119 LYS cc_start: 0.6095 (tptp) cc_final: 0.5582 (tttt) REVERT: H 120 GLU cc_start: 0.6071 (pt0) cc_final: 0.5258 (mm-30) REVERT: H 121 MET cc_start: 0.6555 (ttp) cc_final: 0.6310 (ttp) REVERT: H 122 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6716 (mt-10) REVERT: H 128 ASP cc_start: 0.7180 (m-30) cc_final: 0.6968 (m-30) REVERT: H 151 GLU cc_start: 0.6647 (mt-10) cc_final: 0.5756 (mm-30) REVERT: H 155 ASP cc_start: 0.6629 (t0) cc_final: 0.6147 (t70) REVERT: H 168 GLU cc_start: 0.4766 (OUTLIER) cc_final: 0.4434 (tm-30) REVERT: H 201 PHE cc_start: 0.7363 (m-80) cc_final: 0.7119 (m-80) REVERT: H 225 ARG cc_start: 0.6498 (ttt180) cc_final: 0.6254 (ttm170) REVERT: H 270 THR cc_start: 0.6841 (m) cc_final: 0.6198 (p) REVERT: H 271 GLU cc_start: 0.5629 (tp30) cc_final: 0.5108 (tp30) REVERT: H 354 GLU cc_start: 0.7129 (tp30) cc_final: 0.6871 (mm-30) REVERT: H 365 LYS cc_start: 0.6343 (tppt) cc_final: 0.5445 (tttm) REVERT: H 388 GLN cc_start: 0.6580 (mt0) cc_final: 0.6160 (mm-40) REVERT: H 408 LYS cc_start: 0.6739 (tttt) cc_final: 0.6445 (ttpp) REVERT: H 409 LYS cc_start: 0.6547 (ttmm) cc_final: 0.6024 (ttpt) REVERT: H 421 ASN cc_start: 0.6073 (m-40) cc_final: 0.4783 (t0) REVERT: H 436 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.5378 (pm20) REVERT: H 445 GLN cc_start: 0.6626 (tt0) cc_final: 0.5722 (tp40) REVERT: K 4 ARG cc_start: 0.6226 (tmt170) cc_final: 0.6012 (tpt90) REVERT: L 16 GLU cc_start: 0.6737 (tp30) cc_final: 0.6264 (tm-30) REVERT: L 52 MET cc_start: 0.7224 (mmm) cc_final: 0.6809 (mmm) REVERT: L 109 ASP cc_start: 0.6822 (t0) cc_final: 0.6551 (t0) REVERT: L 119 LYS cc_start: 0.6398 (ttpt) cc_final: 0.6022 (tttt) REVERT: L 120 GLU cc_start: 0.6136 (pt0) cc_final: 0.5211 (mm-30) REVERT: L 128 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6675 (m-30) REVERT: L 151 GLU cc_start: 0.6652 (mt-10) cc_final: 0.6367 (mt-10) REVERT: L 168 GLU cc_start: 0.4581 (OUTLIER) cc_final: 0.4155 (tt0) REVERT: L 173 ASP cc_start: 0.6686 (m-30) cc_final: 0.6343 (m-30) REVERT: L 184 ASP cc_start: 0.7100 (m-30) cc_final: 0.6792 (m-30) REVERT: L 225 ARG cc_start: 0.6440 (ttp-170) cc_final: 0.6132 (ttm170) REVERT: L 270 THR cc_start: 0.6824 (m) cc_final: 0.5944 (p) REVERT: L 271 GLU cc_start: 0.5660 (tp30) cc_final: 0.5322 (tp30) REVERT: L 365 LYS cc_start: 0.6063 (mmtm) cc_final: 0.5336 (tttm) REVERT: L 409 LYS cc_start: 0.6264 (ttmm) cc_final: 0.5798 (tttt) REVERT: L 418 GLN cc_start: 0.6710 (mm110) cc_final: 0.6458 (mm-40) REVERT: L 436 GLU cc_start: 0.6195 (tp30) cc_final: 0.5103 (pm20) REVERT: L 443 MET cc_start: 0.6804 (tpp) cc_final: 0.6321 (tpp) REVERT: L 445 GLN cc_start: 0.6517 (tt0) cc_final: 0.5751 (tp40) REVERT: N 16 GLU cc_start: 0.6417 (tp30) cc_final: 0.5986 (tm-30) REVERT: N 109 ASP cc_start: 0.6807 (t0) cc_final: 0.6234 (t0) REVERT: N 120 GLU cc_start: 0.6082 (pt0) cc_final: 0.5030 (mm-30) REVERT: N 122 GLU cc_start: 0.6616 (mt-10) cc_final: 0.6238 (mt-10) REVERT: N 151 GLU cc_start: 0.6543 (mt-10) cc_final: 0.5707 (mm-30) REVERT: N 155 ASP cc_start: 0.6402 (t0) cc_final: 0.5991 (t70) REVERT: N 168 GLU cc_start: 0.4810 (OUTLIER) cc_final: 0.3986 (tt0) REVERT: N 201 PHE cc_start: 0.7001 (m-80) cc_final: 0.6065 (m-80) REVERT: N 226 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6578 (tttt) REVERT: N 365 LYS cc_start: 0.6444 (mmtm) cc_final: 0.5673 (tttm) REVERT: N 409 LYS cc_start: 0.6276 (ttmm) cc_final: 0.5880 (tttt) REVERT: N 421 ASN cc_start: 0.6415 (m-40) cc_final: 0.5045 (t0) REVERT: O 13 LYS cc_start: 0.5999 (ttmm) cc_final: 0.5364 (tttp) REVERT: O 16 GLU cc_start: 0.6685 (tp30) cc_final: 0.6314 (tm-30) REVERT: O 21 ARG cc_start: 0.7054 (mmm160) cc_final: 0.6843 (mmp-170) REVERT: O 53 MET cc_start: 0.7352 (mtm) cc_final: 0.6886 (mtp) REVERT: O 119 LYS cc_start: 0.6122 (tptp) cc_final: 0.5615 (tttt) REVERT: O 120 GLU cc_start: 0.6210 (pt0) cc_final: 0.5381 (mm-30) REVERT: O 121 MET cc_start: 0.6533 (ttp) cc_final: 0.6304 (ttp) REVERT: O 122 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6427 (mt-10) REVERT: O 128 ASP cc_start: 0.7176 (m-30) cc_final: 0.6963 (m-30) REVERT: O 151 GLU cc_start: 0.6620 (mt-10) cc_final: 0.5749 (mm-30) REVERT: O 155 ASP cc_start: 0.6623 (t0) cc_final: 0.6144 (t70) REVERT: O 168 GLU cc_start: 0.4772 (OUTLIER) cc_final: 0.4442 (tm-30) REVERT: O 201 PHE cc_start: 0.7356 (m-80) cc_final: 0.7111 (m-80) REVERT: O 225 ARG cc_start: 0.6511 (ttt180) cc_final: 0.5907 (ttt180) REVERT: O 270 THR cc_start: 0.6837 (m) cc_final: 0.6193 (p) REVERT: O 271 GLU cc_start: 0.5624 (tp30) cc_final: 0.5102 (tp30) REVERT: O 354 GLU cc_start: 0.7128 (tp30) cc_final: 0.6893 (mm-30) REVERT: O 365 LYS cc_start: 0.6340 (tppt) cc_final: 0.5444 (tttm) REVERT: O 388 GLN cc_start: 0.6586 (mt0) cc_final: 0.6166 (mm-40) REVERT: O 408 LYS cc_start: 0.6732 (tttt) cc_final: 0.6438 (ttpp) REVERT: O 409 LYS cc_start: 0.6537 (ttmm) cc_final: 0.5963 (ttmt) REVERT: O 421 ASN cc_start: 0.6057 (m-40) cc_final: 0.4764 (t0) REVERT: O 436 GLU cc_start: 0.6151 (tp30) cc_final: 0.4921 (pm20) REVERT: O 445 GLN cc_start: 0.6628 (tt0) cc_final: 0.5723 (tp40) REVERT: P 4 ARG cc_start: 0.6185 (tmt170) cc_final: 0.5624 (tpt90) REVERT: Q 4 ARG cc_start: 0.6112 (tmt170) cc_final: 0.5780 (tpt90) REVERT: R 16 GLU cc_start: 0.6747 (tp30) cc_final: 0.6196 (tm-30) REVERT: R 52 MET cc_start: 0.7244 (mmm) cc_final: 0.6776 (mmm) REVERT: R 70 MET cc_start: 0.7842 (mtt) cc_final: 0.7591 (mtt) REVERT: R 109 ASP cc_start: 0.6833 (t0) cc_final: 0.6560 (t0) REVERT: R 119 LYS cc_start: 0.6442 (ttpt) cc_final: 0.6036 (tttt) REVERT: R 120 GLU cc_start: 0.6019 (pt0) cc_final: 0.5183 (mm-30) REVERT: R 128 ASP cc_start: 0.6965 (OUTLIER) cc_final: 0.6704 (m-30) REVERT: R 151 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6502 (mt-10) REVERT: R 168 GLU cc_start: 0.4678 (OUTLIER) cc_final: 0.4015 (tt0) REVERT: R 173 ASP cc_start: 0.6651 (m-30) cc_final: 0.6296 (m-30) REVERT: R 184 ASP cc_start: 0.7148 (m-30) cc_final: 0.6853 (m-30) REVERT: R 225 ARG cc_start: 0.6369 (ttp-170) cc_final: 0.6128 (ttm170) REVERT: R 270 THR cc_start: 0.6810 (m) cc_final: 0.5922 (p) REVERT: R 271 GLU cc_start: 0.5650 (tp30) cc_final: 0.5291 (tp30) REVERT: R 282 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6572 (tttm) REVERT: R 365 LYS cc_start: 0.6064 (mmtm) cc_final: 0.5333 (tttm) REVERT: R 409 LYS cc_start: 0.6258 (ttmm) cc_final: 0.5792 (tttt) REVERT: R 418 GLN cc_start: 0.6722 (mm110) cc_final: 0.6469 (mm-40) REVERT: R 428 ASP cc_start: 0.6941 (t70) cc_final: 0.6737 (t70) REVERT: R 436 GLU cc_start: 0.6212 (tp30) cc_final: 0.5116 (pm20) REVERT: R 443 MET cc_start: 0.6845 (tpp) cc_final: 0.6517 (tpp) REVERT: R 445 GLN cc_start: 0.6549 (tt0) cc_final: 0.5760 (tp40) REVERT: S 109 ASP cc_start: 0.6805 (t0) cc_final: 0.6232 (t0) REVERT: S 120 GLU cc_start: 0.6326 (pt0) cc_final: 0.5257 (mm-30) REVERT: S 128 ASP cc_start: 0.7250 (m-30) cc_final: 0.7026 (m-30) REVERT: S 151 GLU cc_start: 0.6613 (mt-10) cc_final: 0.5738 (mm-30) REVERT: S 155 ASP cc_start: 0.6483 (t0) cc_final: 0.5992 (t70) REVERT: S 168 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.4147 (tt0) REVERT: S 169 ASN cc_start: 0.5730 (OUTLIER) cc_final: 0.4561 (m-40) REVERT: S 225 ARG cc_start: 0.6187 (ttt180) cc_final: 0.5888 (ttm170) REVERT: S 226 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6590 (tttt) REVERT: S 266 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5557 (mp0) REVERT: S 271 GLU cc_start: 0.5881 (tp30) cc_final: 0.5664 (tp30) REVERT: S 365 LYS cc_start: 0.6437 (mmtm) cc_final: 0.5669 (tttm) REVERT: S 409 LYS cc_start: 0.6272 (ttmm) cc_final: 0.5871 (tttt) REVERT: S 421 ASN cc_start: 0.6339 (m-40) cc_final: 0.4961 (t0) REVERT: S 445 GLN cc_start: 0.6850 (tt0) cc_final: 0.6649 (tt0) REVERT: T 13 LYS cc_start: 0.6006 (ttmm) cc_final: 0.5373 (tttp) REVERT: T 16 GLU cc_start: 0.6702 (tp30) cc_final: 0.6326 (tm-30) REVERT: T 21 ARG cc_start: 0.6343 (mmm-85) cc_final: 0.5826 (mmm160) REVERT: T 53 MET cc_start: 0.7382 (mtm) cc_final: 0.6907 (mtp) REVERT: T 119 LYS cc_start: 0.6109 (tptp) cc_final: 0.5601 (tttt) REVERT: T 120 GLU cc_start: 0.6066 (pt0) cc_final: 0.5257 (mm-30) REVERT: T 121 MET cc_start: 0.6516 (ttp) cc_final: 0.6286 (ttp) REVERT: T 122 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6414 (mt-10) REVERT: T 128 ASP cc_start: 0.7172 (m-30) cc_final: 0.6960 (m-30) REVERT: T 151 GLU cc_start: 0.6624 (mt-10) cc_final: 0.5754 (mm-30) REVERT: T 155 ASP cc_start: 0.6618 (t0) cc_final: 0.6171 (t70) REVERT: T 201 PHE cc_start: 0.7374 (m-80) cc_final: 0.7138 (m-80) REVERT: T 225 ARG cc_start: 0.6355 (ttt180) cc_final: 0.6031 (ttm170) REVERT: T 266 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.5533 (mp0) REVERT: T 270 THR cc_start: 0.6856 (m) cc_final: 0.6237 (p) REVERT: T 271 GLU cc_start: 0.5632 (tp30) cc_final: 0.5314 (tp30) REVERT: T 354 GLU cc_start: 0.7130 (tp30) cc_final: 0.6875 (mm-30) REVERT: T 365 LYS cc_start: 0.6346 (tppt) cc_final: 0.5449 (tttm) REVERT: T 388 GLN cc_start: 0.6611 (mt0) cc_final: 0.6192 (mm-40) REVERT: T 408 LYS cc_start: 0.6738 (tttt) cc_final: 0.6444 (ttpp) REVERT: T 409 LYS cc_start: 0.6547 (ttmm) cc_final: 0.6023 (ttpt) REVERT: T 421 ASN cc_start: 0.6071 (m-40) cc_final: 0.4771 (t0) REVERT: T 436 GLU cc_start: 0.6159 (tp30) cc_final: 0.4930 (pm20) REVERT: T 445 GLN cc_start: 0.6630 (tt0) cc_final: 0.5743 (tp40) REVERT: U 4 ARG cc_start: 0.5974 (tmt170) cc_final: 0.5622 (tpt90) outliers start: 148 outliers final: 50 residues processed: 864 average time/residue: 1.6648 time to fit residues: 1735.2850 Evaluate side-chains 813 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 730 time to evaluate : 4.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain G residue 226 LYS Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain G residue 443 MET Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 169 ASN Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 436 GLU Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain N residue 226 LYS Chi-restraints excluded: chain N residue 366 VAL Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 169 ASN Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 366 VAL Chi-restraints excluded: chain O residue 385 VAL Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 282 LYS Chi-restraints excluded: chain R residue 366 VAL Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 226 LYS Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 366 VAL Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 169 ASN Chi-restraints excluded: chain T residue 266 GLU Chi-restraints excluded: chain T residue 277 THR Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain T residue 385 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 6.9990 chunk 361 optimal weight: 0.9990 chunk 249 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 322 optimal weight: 10.0000 chunk 482 optimal weight: 6.9990 chunk 510 optimal weight: 7.9990 chunk 251 optimal weight: 9.9990 chunk 456 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 421 ASN B 36 ASN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN C 36 ASN C 413 ASN F 36 ASN ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 ASN G 36 ASN G 228 ASN G 413 ASN H 36 ASN H 413 ASN L 36 ASN L 169 ASN L 421 ASN N 36 ASN N 228 ASN N 413 ASN O 36 ASN O 413 ASN R 36 ASN R 169 ASN R 421 ASN S 36 ASN S 413 ASN T 36 ASN T 228 ASN T 413 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 44100 Z= 0.318 Angle : 0.618 6.598 59700 Z= 0.337 Chirality : 0.047 0.172 6444 Planarity : 0.005 0.046 7860 Dihedral : 6.641 59.624 5888 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.24 % Allowed : 12.52 % Favored : 84.24 % 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: 0.03 (0.11), residues: 5316 helix: 1.09 (0.11), residues: 2280 sheet: -1.74 (0.15), residues: 744 loop : -0.33 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 427 HIS 0.006 0.002 HIS O 197 PHE 0.022 0.002 PHE L 287 TYR 0.038 0.003 TYR G 298 ARG 0.005 0.001 ARG X 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 731 time to evaluate : 4.979 Fit side-chains REVERT: A 16 GLU cc_start: 0.6734 (tp30) cc_final: 0.6180 (tm-30) REVERT: A 52 MET cc_start: 0.7335 (mmm) cc_final: 0.6801 (mmm) REVERT: A 109 ASP cc_start: 0.6793 (t0) cc_final: 0.6529 (t0) REVERT: A 119 LYS cc_start: 0.6492 (ttpt) cc_final: 0.6085 (tttt) REVERT: A 120 GLU cc_start: 0.6150 (pt0) cc_final: 0.5203 (mm-30) REVERT: A 128 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6711 (m-30) REVERT: A 151 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6483 (mt-10) REVERT: A 168 GLU cc_start: 0.4582 (OUTLIER) cc_final: 0.3984 (pp20) REVERT: A 184 ASP cc_start: 0.7160 (m-30) cc_final: 0.6863 (m-30) REVERT: A 225 ARG cc_start: 0.6359 (ttp-170) cc_final: 0.6086 (ttm170) REVERT: A 266 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5891 (tm-30) REVERT: A 271 GLU cc_start: 0.5579 (tp30) cc_final: 0.5318 (tp30) REVERT: A 365 LYS cc_start: 0.6091 (mmtm) cc_final: 0.5359 (tttm) REVERT: A 385 VAL cc_start: 0.6594 (OUTLIER) cc_final: 0.6379 (p) REVERT: A 409 LYS cc_start: 0.6169 (ttmm) cc_final: 0.5745 (tttt) REVERT: A 418 GLN cc_start: 0.6706 (mm110) cc_final: 0.6474 (mm-40) REVERT: A 436 GLU cc_start: 0.5735 (OUTLIER) cc_final: 0.5403 (pm20) REVERT: A 443 MET cc_start: 0.6814 (tpp) cc_final: 0.6367 (tpp) REVERT: A 445 GLN cc_start: 0.6488 (tt0) cc_final: 0.5720 (tp40) REVERT: B 16 GLU cc_start: 0.6399 (tp30) cc_final: 0.5922 (tm-30) REVERT: B 109 ASP cc_start: 0.6804 (t0) cc_final: 0.6229 (t0) REVERT: B 120 GLU cc_start: 0.6290 (pt0) cc_final: 0.5228 (mm-30) REVERT: B 151 GLU cc_start: 0.6509 (mt-10) cc_final: 0.5717 (mm-30) REVERT: B 155 ASP cc_start: 0.6436 (t0) cc_final: 0.5929 (t70) REVERT: B 168 GLU cc_start: 0.5107 (OUTLIER) cc_final: 0.4674 (tt0) REVERT: B 201 PHE cc_start: 0.7055 (m-80) cc_final: 0.6121 (m-80) REVERT: B 226 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6526 (tttt) REVERT: B 365 LYS cc_start: 0.6435 (mmtm) cc_final: 0.5665 (tttm) REVERT: B 409 LYS cc_start: 0.6209 (ttmm) cc_final: 0.5800 (tttt) REVERT: B 421 ASN cc_start: 0.6312 (m-40) cc_final: 0.4947 (t0) REVERT: B 428 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6729 (t70) REVERT: B 436 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.5272 (pm20) REVERT: B 445 GLN cc_start: 0.6775 (tt0) cc_final: 0.6543 (tt0) REVERT: C 13 LYS cc_start: 0.6006 (ttmm) cc_final: 0.5341 (tttp) REVERT: C 16 GLU cc_start: 0.6677 (tp30) cc_final: 0.6378 (tm-30) REVERT: C 53 MET cc_start: 0.7370 (mtm) cc_final: 0.6914 (mtp) REVERT: C 119 LYS cc_start: 0.6063 (tptp) cc_final: 0.5562 (tttt) REVERT: C 120 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.5363 (mm-30) REVERT: C 122 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6383 (mt-10) REVERT: C 128 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6857 (m-30) REVERT: C 151 GLU cc_start: 0.6629 (mt-10) cc_final: 0.5715 (mm-30) REVERT: C 155 ASP cc_start: 0.6669 (t0) cc_final: 0.6167 (t70) REVERT: C 225 ARG cc_start: 0.6351 (ttt180) cc_final: 0.6005 (ttt180) REVERT: C 266 GLU cc_start: 0.6087 (OUTLIER) cc_final: 0.5629 (mp0) REVERT: C 270 THR cc_start: 0.6824 (m) cc_final: 0.6224 (p) REVERT: C 271 GLU cc_start: 0.5674 (tp30) cc_final: 0.5202 (tp30) REVERT: C 354 GLU cc_start: 0.7159 (tp30) cc_final: 0.6912 (mm-30) REVERT: C 365 LYS cc_start: 0.6344 (tppt) cc_final: 0.5437 (tttm) REVERT: C 388 GLN cc_start: 0.6548 (mt0) cc_final: 0.6032 (mm-40) REVERT: C 408 LYS cc_start: 0.6750 (tttt) cc_final: 0.6460 (ttpp) REVERT: C 409 LYS cc_start: 0.6547 (ttmm) cc_final: 0.5979 (ttpt) REVERT: C 421 ASN cc_start: 0.6034 (m-40) cc_final: 0.4747 (t0) REVERT: C 436 GLU cc_start: 0.5845 (OUTLIER) cc_final: 0.5216 (pm20) REVERT: C 445 GLN cc_start: 0.6590 (tt0) cc_final: 0.5747 (tp40) REVERT: F 16 GLU cc_start: 0.6734 (tp30) cc_final: 0.6182 (tm-30) REVERT: F 21 ARG cc_start: 0.6703 (mtp85) cc_final: 0.6337 (mmp-170) REVERT: F 52 MET cc_start: 0.7338 (mmm) cc_final: 0.6797 (mmm) REVERT: F 109 ASP cc_start: 0.6793 (t0) cc_final: 0.6527 (t0) REVERT: F 119 LYS cc_start: 0.6446 (ttpt) cc_final: 0.6056 (tttt) REVERT: F 120 GLU cc_start: 0.6144 (pt0) cc_final: 0.5195 (mm-30) REVERT: F 128 ASP cc_start: 0.6944 (OUTLIER) cc_final: 0.6655 (m-30) REVERT: F 151 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6351 (mt-10) REVERT: F 168 GLU cc_start: 0.4532 (OUTLIER) cc_final: 0.4094 (tt0) REVERT: F 173 ASP cc_start: 0.6691 (m-30) cc_final: 0.6341 (m-30) REVERT: F 184 ASP cc_start: 0.7148 (m-30) cc_final: 0.6840 (m-30) REVERT: F 225 ARG cc_start: 0.6381 (ttp-170) cc_final: 0.6164 (ttm170) REVERT: F 266 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5773 (tm-30) REVERT: F 270 THR cc_start: 0.6804 (m) cc_final: 0.5913 (p) REVERT: F 271 GLU cc_start: 0.5686 (tp30) cc_final: 0.5339 (tp30) REVERT: F 365 LYS cc_start: 0.6088 (mmtm) cc_final: 0.5359 (tttm) REVERT: F 385 VAL cc_start: 0.6607 (OUTLIER) cc_final: 0.6393 (p) REVERT: F 409 LYS cc_start: 0.6162 (ttmm) cc_final: 0.5737 (tttt) REVERT: F 418 GLN cc_start: 0.6697 (mm110) cc_final: 0.6464 (mm-40) REVERT: F 436 GLU cc_start: 0.5694 (OUTLIER) cc_final: 0.5261 (pm20) REVERT: F 443 MET cc_start: 0.6832 (tpp) cc_final: 0.6373 (tpp) REVERT: F 445 GLN cc_start: 0.6523 (tt0) cc_final: 0.5743 (tp40) REVERT: G 16 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6192 (tm-30) REVERT: G 109 ASP cc_start: 0.6807 (t0) cc_final: 0.6231 (t0) REVERT: G 120 GLU cc_start: 0.6180 (pt0) cc_final: 0.5116 (mm-30) REVERT: G 122 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6272 (mt-10) REVERT: G 151 GLU cc_start: 0.6509 (mt-10) cc_final: 0.5716 (mm-30) REVERT: G 155 ASP cc_start: 0.6424 (t0) cc_final: 0.5915 (t70) REVERT: G 168 GLU cc_start: 0.4996 (OUTLIER) cc_final: 0.4512 (tt0) REVERT: G 201 PHE cc_start: 0.7031 (m-80) cc_final: 0.6135 (m-80) REVERT: G 226 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.6521 (tttt) REVERT: G 266 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5667 (mp0) REVERT: G 365 LYS cc_start: 0.6429 (mmtm) cc_final: 0.5667 (tttm) REVERT: G 409 LYS cc_start: 0.6234 (ttmm) cc_final: 0.5824 (tttt) REVERT: G 421 ASN cc_start: 0.6322 (m-40) cc_final: 0.4956 (t0) REVERT: G 436 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5333 (pm20) REVERT: G 443 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.6180 (tpp) REVERT: H 13 LYS cc_start: 0.6016 (ttmm) cc_final: 0.5350 (tttp) REVERT: H 16 GLU cc_start: 0.6697 (tp30) cc_final: 0.6391 (tm-30) REVERT: H 119 LYS cc_start: 0.6047 (tptp) cc_final: 0.5541 (tttt) REVERT: H 120 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5396 (mm-30) REVERT: H 128 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6859 (m-30) REVERT: H 151 GLU cc_start: 0.6713 (mt-10) cc_final: 0.5766 (mm-30) REVERT: H 155 ASP cc_start: 0.6642 (t0) cc_final: 0.6127 (t70) REVERT: H 168 GLU cc_start: 0.4748 (OUTLIER) cc_final: 0.4188 (tm-30) REVERT: H 225 ARG cc_start: 0.6343 (ttt180) cc_final: 0.5997 (ttt180) REVERT: H 270 THR cc_start: 0.6766 (m) cc_final: 0.6165 (p) REVERT: H 271 GLU cc_start: 0.5669 (tp30) cc_final: 0.5171 (tp30) REVERT: H 354 GLU cc_start: 0.7160 (tp30) cc_final: 0.6894 (mm-30) REVERT: H 365 LYS cc_start: 0.6345 (tppt) cc_final: 0.5437 (tttm) REVERT: H 388 GLN cc_start: 0.6462 (mt0) cc_final: 0.6066 (mm-40) REVERT: H 408 LYS cc_start: 0.6751 (tttt) cc_final: 0.6462 (ttpp) REVERT: H 409 LYS cc_start: 0.6548 (ttmm) cc_final: 0.5982 (ttpt) REVERT: H 421 ASN cc_start: 0.6022 (m-40) cc_final: 0.4725 (t0) REVERT: H 436 GLU cc_start: 0.5846 (OUTLIER) cc_final: 0.5220 (pm20) REVERT: H 445 GLN cc_start: 0.6557 (tt0) cc_final: 0.5682 (tp40) REVERT: L 16 GLU cc_start: 0.6721 (tp30) cc_final: 0.6247 (tm-30) REVERT: L 52 MET cc_start: 0.7249 (mmm) cc_final: 0.6714 (mmm) REVERT: L 109 ASP cc_start: 0.6785 (t0) cc_final: 0.6525 (t0) REVERT: L 119 LYS cc_start: 0.6401 (ttpt) cc_final: 0.6012 (tttt) REVERT: L 120 GLU cc_start: 0.6157 (pt0) cc_final: 0.5181 (mm-30) REVERT: L 128 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6631 (m-30) REVERT: L 151 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6345 (mt-10) REVERT: L 168 GLU cc_start: 0.4517 (OUTLIER) cc_final: 0.4077 (tt0) REVERT: L 173 ASP cc_start: 0.6723 (m-30) cc_final: 0.6409 (m-30) REVERT: L 184 ASP cc_start: 0.7101 (m-30) cc_final: 0.6779 (m-30) REVERT: L 225 ARG cc_start: 0.6424 (ttp-170) cc_final: 0.6030 (ttm170) REVERT: L 266 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5884 (tm-30) REVERT: L 270 THR cc_start: 0.6799 (m) cc_final: 0.5907 (p) REVERT: L 271 GLU cc_start: 0.5573 (tp30) cc_final: 0.5256 (tp30) REVERT: L 365 LYS cc_start: 0.6088 (mmtm) cc_final: 0.5357 (tttm) REVERT: L 385 VAL cc_start: 0.6621 (OUTLIER) cc_final: 0.6403 (p) REVERT: L 409 LYS cc_start: 0.6264 (ttmm) cc_final: 0.5837 (tttt) REVERT: L 418 GLN cc_start: 0.6687 (mm110) cc_final: 0.6455 (mm-40) REVERT: L 436 GLU cc_start: 0.6222 (tp30) cc_final: 0.5107 (pm20) REVERT: L 443 MET cc_start: 0.6860 (tpp) cc_final: 0.6391 (tpp) REVERT: L 445 GLN cc_start: 0.6531 (tt0) cc_final: 0.5742 (tp40) REVERT: N 16 GLU cc_start: 0.6395 (tp30) cc_final: 0.5919 (tm-30) REVERT: N 109 ASP cc_start: 0.6803 (t0) cc_final: 0.6230 (t0) REVERT: N 120 GLU cc_start: 0.6076 (pt0) cc_final: 0.5023 (mm-30) REVERT: N 122 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6260 (mt-10) REVERT: N 151 GLU cc_start: 0.6512 (mt-10) cc_final: 0.5720 (mm-30) REVERT: N 155 ASP cc_start: 0.6450 (t0) cc_final: 0.6017 (t70) REVERT: N 168 GLU cc_start: 0.5014 (OUTLIER) cc_final: 0.4376 (tt0) REVERT: N 201 PHE cc_start: 0.6977 (m-80) cc_final: 0.6087 (m-80) REVERT: N 226 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6532 (tttt) REVERT: N 365 LYS cc_start: 0.6421 (mmtm) cc_final: 0.5664 (tttm) REVERT: N 409 LYS cc_start: 0.6220 (ttmm) cc_final: 0.5811 (tttt) REVERT: N 421 ASN cc_start: 0.6306 (m-40) cc_final: 0.4941 (t0) REVERT: N 428 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6716 (t70) REVERT: O 13 LYS cc_start: 0.5974 (ttmm) cc_final: 0.5332 (tttp) REVERT: O 16 GLU cc_start: 0.6704 (tp30) cc_final: 0.6393 (tm-30) REVERT: O 53 MET cc_start: 0.7370 (mtm) cc_final: 0.6916 (mtp) REVERT: O 119 LYS cc_start: 0.6074 (tptp) cc_final: 0.5572 (tttt) REVERT: O 120 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5387 (mm-30) REVERT: O 122 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6402 (mt-10) REVERT: O 128 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6853 (m-30) REVERT: O 151 GLU cc_start: 0.6618 (mt-10) cc_final: 0.5708 (mm-30) REVERT: O 155 ASP cc_start: 0.6635 (t0) cc_final: 0.6128 (t70) REVERT: O 168 GLU cc_start: 0.4757 (OUTLIER) cc_final: 0.4196 (tm-30) REVERT: O 225 ARG cc_start: 0.6355 (ttt180) cc_final: 0.5755 (ttt180) REVERT: O 270 THR cc_start: 0.6761 (m) cc_final: 0.6160 (p) REVERT: O 271 GLU cc_start: 0.5665 (tp30) cc_final: 0.5167 (tp30) REVERT: O 354 GLU cc_start: 0.7154 (tp30) cc_final: 0.6907 (mm-30) REVERT: O 365 LYS cc_start: 0.6345 (tppt) cc_final: 0.5433 (tttm) REVERT: O 388 GLN cc_start: 0.6468 (mt0) cc_final: 0.6074 (mm-40) REVERT: O 408 LYS cc_start: 0.6744 (tttt) cc_final: 0.6455 (ttpp) REVERT: O 409 LYS cc_start: 0.6540 (ttmm) cc_final: 0.5973 (ttpt) REVERT: O 421 ASN cc_start: 0.6030 (m-40) cc_final: 0.4743 (t0) REVERT: O 436 GLU cc_start: 0.6148 (tp30) cc_final: 0.5687 (tp30) REVERT: O 445 GLN cc_start: 0.6563 (tt0) cc_final: 0.5691 (tp40) REVERT: P 4 ARG cc_start: 0.6044 (tmt170) cc_final: 0.5604 (tpt90) REVERT: R 16 GLU cc_start: 0.6731 (tp30) cc_final: 0.6174 (tm-30) REVERT: R 52 MET cc_start: 0.7299 (mmm) cc_final: 0.6649 (mmm) REVERT: R 70 MET cc_start: 0.7925 (mtt) cc_final: 0.7691 (mtt) REVERT: R 109 ASP cc_start: 0.6793 (t0) cc_final: 0.6531 (t0) REVERT: R 119 LYS cc_start: 0.6433 (ttpt) cc_final: 0.6055 (tttt) REVERT: R 120 GLU cc_start: 0.6031 (pt0) cc_final: 0.5160 (mm-30) REVERT: R 128 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6761 (m-30) REVERT: R 151 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6489 (mt-10) REVERT: R 173 ASP cc_start: 0.6688 (m-30) cc_final: 0.6325 (m-30) REVERT: R 184 ASP cc_start: 0.7151 (m-30) cc_final: 0.6843 (m-30) REVERT: R 225 ARG cc_start: 0.6394 (ttp-170) cc_final: 0.6146 (ttm170) REVERT: R 266 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5908 (tm-30) REVERT: R 270 THR cc_start: 0.6803 (m) cc_final: 0.5906 (p) REVERT: R 271 GLU cc_start: 0.5631 (tp30) cc_final: 0.5293 (tp30) REVERT: R 282 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6639 (tttm) REVERT: R 365 LYS cc_start: 0.6114 (mmtm) cc_final: 0.5365 (tttm) REVERT: R 385 VAL cc_start: 0.6614 (OUTLIER) cc_final: 0.6389 (p) REVERT: R 409 LYS cc_start: 0.6259 (ttmm) cc_final: 0.5832 (tttt) REVERT: R 418 GLN cc_start: 0.6697 (mm110) cc_final: 0.6465 (mm-40) REVERT: R 428 ASP cc_start: 0.6879 (t70) cc_final: 0.6488 (t0) REVERT: R 436 GLU cc_start: 0.6232 (tp30) cc_final: 0.5109 (pm20) REVERT: R 445 GLN cc_start: 0.6503 (tt0) cc_final: 0.5736 (tp40) REVERT: S 109 ASP cc_start: 0.6797 (t0) cc_final: 0.6225 (t0) REVERT: S 120 GLU cc_start: 0.6319 (pt0) cc_final: 0.5259 (mm-30) REVERT: S 128 ASP cc_start: 0.7100 (m-30) cc_final: 0.6858 (m-30) REVERT: S 151 GLU cc_start: 0.6657 (mt-10) cc_final: 0.5764 (mm-30) REVERT: S 155 ASP cc_start: 0.6417 (t0) cc_final: 0.5938 (t70) REVERT: S 168 GLU cc_start: 0.5109 (OUTLIER) cc_final: 0.4766 (tt0) REVERT: S 225 ARG cc_start: 0.6104 (ttt180) cc_final: 0.5805 (ttm170) REVERT: S 226 LYS cc_start: 0.6805 (OUTLIER) cc_final: 0.6496 (tttt) REVERT: S 365 LYS cc_start: 0.6454 (mmtm) cc_final: 0.5681 (tttm) REVERT: S 409 LYS cc_start: 0.6190 (ttmm) cc_final: 0.5776 (tttt) REVERT: S 421 ASN cc_start: 0.6316 (m-40) cc_final: 0.4951 (t0) REVERT: S 428 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6714 (t70) REVERT: T 13 LYS cc_start: 0.5985 (ttmm) cc_final: 0.5342 (tttp) REVERT: T 16 GLU cc_start: 0.6687 (tp30) cc_final: 0.6366 (tm-30) REVERT: T 21 ARG cc_start: 0.6294 (mmm-85) cc_final: 0.5626 (mmp-170) REVERT: T 53 MET cc_start: 0.7366 (mtm) cc_final: 0.6910 (mtp) REVERT: T 119 LYS cc_start: 0.6062 (tptp) cc_final: 0.5562 (tttt) REVERT: T 120 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5393 (mm-30) REVERT: T 122 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6376 (mt-10) REVERT: T 128 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6848 (m-30) REVERT: T 151 GLU cc_start: 0.6620 (mt-10) cc_final: 0.5711 (mm-30) REVERT: T 155 ASP cc_start: 0.6631 (t0) cc_final: 0.6126 (t70) REVERT: T 168 GLU cc_start: 0.4301 (OUTLIER) cc_final: 0.3944 (tt0) REVERT: T 225 ARG cc_start: 0.6294 (ttt180) cc_final: 0.5994 (ttm170) REVERT: T 266 GLU cc_start: 0.6076 (OUTLIER) cc_final: 0.5581 (mp0) REVERT: T 270 THR cc_start: 0.6805 (m) cc_final: 0.6203 (p) REVERT: T 271 GLU cc_start: 0.5669 (tp30) cc_final: 0.5190 (tp30) REVERT: T 354 GLU cc_start: 0.7155 (tp30) cc_final: 0.6907 (mm-30) REVERT: T 365 LYS cc_start: 0.6348 (tppt) cc_final: 0.5442 (tttm) REVERT: T 388 GLN cc_start: 0.6458 (mt0) cc_final: 0.6038 (mm-40) REVERT: T 408 LYS cc_start: 0.6750 (tttt) cc_final: 0.6461 (ttpp) REVERT: T 409 LYS cc_start: 0.6550 (ttmm) cc_final: 0.5983 (ttpt) REVERT: T 421 ASN cc_start: 0.6025 (m-40) cc_final: 0.4738 (t0) REVERT: T 436 GLU cc_start: 0.6152 (tp30) cc_final: 0.5691 (tp30) REVERT: T 445 GLN cc_start: 0.6564 (tt0) cc_final: 0.5699 (tp40) REVERT: U 4 ARG cc_start: 0.6009 (tmt170) cc_final: 0.5656 (tpt90) outliers start: 150 outliers final: 53 residues processed: 826 average time/residue: 1.6480 time to fit residues: 1648.0517 Evaluate side-chains 821 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 719 time to evaluate : 4.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 226 LYS Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 282 LYS Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain G residue 443 MET Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 169 ASN Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 436 GLU Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain L residue 266 GLU Chi-restraints excluded: chain L residue 282 LYS Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain L residue 385 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain N residue 226 LYS Chi-restraints excluded: chain N residue 282 LYS Chi-restraints excluded: chain N residue 366 VAL Chi-restraints excluded: chain N residue 428 ASP Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 169 ASN Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 366 VAL Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 169 ASN Chi-restraints excluded: chain R residue 266 GLU Chi-restraints excluded: chain R residue 282 LYS Chi-restraints excluded: chain R residue 366 VAL Chi-restraints excluded: chain R residue 385 VAL Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain S residue 226 LYS Chi-restraints excluded: chain S residue 366 VAL Chi-restraints excluded: chain S residue 428 ASP Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 120 GLU Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain T residue 168 GLU Chi-restraints excluded: chain T residue 169 ASN Chi-restraints excluded: chain T residue 266 GLU Chi-restraints excluded: chain T residue 277 THR Chi-restraints excluded: chain T residue 366 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 380 optimal weight: 6.9990 chunk 210 optimal weight: 0.4980 chunk 435 optimal weight: 0.4980 chunk 352 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 260 optimal weight: 10.0000 chunk 458 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 421 ASN B 36 ASN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN C 228 ASN F 36 ASN F 169 ASN F 421 ASN G 36 ASN G 169 ASN G 413 ASN H 36 ASN H 228 ASN L 36 ASN ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 421 ASN N 36 ASN ** N 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 413 ASN O 36 ASN O 228 ASN R 36 ASN ** R 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 421 ASN S 36 ASN S 169 ASN S 228 ASN S 413 ASN T 36 ASN T 228 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 44100 Z= 0.150 Angle : 0.465 5.345 59700 Z= 0.251 Chirality : 0.040 0.145 6444 Planarity : 0.003 0.033 7860 Dihedral : 6.082 56.925 5888 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.40 % Allowed : 13.95 % Favored : 83.66 % 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: 0.46 (0.11), residues: 5316 helix: 1.54 (0.11), residues: 2280 sheet: -1.63 (0.15), residues: 744 loop : -0.16 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 427 HIS 0.004 0.001 HIS H 197 PHE 0.011 0.001 PHE A 287 TYR 0.027 0.002 TYR S 298 ARG 0.003 0.000 ARG W 4 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 760 time to evaluate : 4.667 Fit side-chains REVERT: A 16 GLU cc_start: 0.6692 (tp30) cc_final: 0.6132 (tm-30) REVERT: A 52 MET cc_start: 0.7344 (mmm) cc_final: 0.6790 (mmm) REVERT: A 53 MET cc_start: 0.7282 (mtm) cc_final: 0.6903 (mtp) REVERT: A 119 LYS cc_start: 0.6499 (ttpt) cc_final: 0.6061 (tttt) REVERT: A 120 GLU cc_start: 0.6095 (pt0) cc_final: 0.5193 (mm-30) REVERT: A 122 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6415 (mt-10) REVERT: A 128 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6595 (m-30) REVERT: A 151 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6473 (mt-10) REVERT: A 168 GLU cc_start: 0.4424 (OUTLIER) cc_final: 0.3960 (pp20) REVERT: A 184 ASP cc_start: 0.7192 (m-30) cc_final: 0.6902 (m-30) REVERT: A 225 ARG cc_start: 0.6457 (ttp-170) cc_final: 0.6185 (ttm170) REVERT: A 266 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5891 (tm-30) REVERT: A 271 GLU cc_start: 0.5568 (tp30) cc_final: 0.5275 (tp30) REVERT: A 365 LYS cc_start: 0.6102 (mmtm) cc_final: 0.5352 (tttm) REVERT: A 409 LYS cc_start: 0.6141 (ttmm) cc_final: 0.5716 (tttt) REVERT: A 418 GLN cc_start: 0.6702 (mm110) cc_final: 0.6482 (mm110) REVERT: A 443 MET cc_start: 0.6648 (tpp) cc_final: 0.6234 (tpp) REVERT: A 445 GLN cc_start: 0.6475 (tt0) cc_final: 0.5725 (tp40) REVERT: B 16 GLU cc_start: 0.6365 (tp30) cc_final: 0.5830 (tm-30) REVERT: B 120 GLU cc_start: 0.6290 (pt0) cc_final: 0.5257 (mm-30) REVERT: B 151 GLU cc_start: 0.6485 (mt-10) cc_final: 0.5686 (mm-30) REVERT: B 155 ASP cc_start: 0.6450 (t0) cc_final: 0.5927 (t70) REVERT: B 201 PHE cc_start: 0.7050 (m-80) cc_final: 0.6138 (m-80) REVERT: B 365 LYS cc_start: 0.6413 (mmtm) cc_final: 0.5647 (tttm) REVERT: B 409 LYS cc_start: 0.6231 (ttmm) cc_final: 0.5846 (tttt) REVERT: B 421 ASN cc_start: 0.6240 (m-40) cc_final: 0.4905 (t0) REVERT: B 428 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6650 (t0) REVERT: B 436 GLU cc_start: 0.5661 (OUTLIER) cc_final: 0.4974 (pm20) REVERT: B 445 GLN cc_start: 0.6748 (tt0) cc_final: 0.6499 (tt0) REVERT: C 13 LYS cc_start: 0.6107 (ttmm) cc_final: 0.5428 (tttp) REVERT: C 16 GLU cc_start: 0.6652 (tp30) cc_final: 0.6271 (tm-30) REVERT: C 53 MET cc_start: 0.7272 (mtm) cc_final: 0.6882 (mtp) REVERT: C 119 LYS cc_start: 0.6068 (tptp) cc_final: 0.5586 (tttt) REVERT: C 120 GLU cc_start: 0.6164 (pt0) cc_final: 0.5429 (mm-30) REVERT: C 122 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6389 (mt-10) REVERT: C 128 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6865 (m-30) REVERT: C 151 GLU cc_start: 0.6663 (mt-10) cc_final: 0.5768 (mm-30) REVERT: C 155 ASP cc_start: 0.6606 (t0) cc_final: 0.6094 (t70) REVERT: C 168 GLU cc_start: 0.4837 (OUTLIER) cc_final: 0.3958 (tm-30) REVERT: C 225 ARG cc_start: 0.6272 (ttt180) cc_final: 0.5878 (ttt180) REVERT: C 270 THR cc_start: 0.6654 (m) cc_final: 0.6059 (p) REVERT: C 271 GLU cc_start: 0.5608 (tp30) cc_final: 0.5185 (tp30) REVERT: C 327 SER cc_start: 0.6898 (m) cc_final: 0.6627 (t) REVERT: C 354 GLU cc_start: 0.7128 (tp30) cc_final: 0.6907 (mm-30) REVERT: C 365 LYS cc_start: 0.6346 (tppt) cc_final: 0.5384 (tttm) REVERT: C 388 GLN cc_start: 0.6562 (mt0) cc_final: 0.6033 (mm-40) REVERT: C 408 LYS cc_start: 0.6551 (tttt) cc_final: 0.6342 (ttpp) REVERT: C 409 LYS cc_start: 0.6511 (ttmm) cc_final: 0.5914 (ttmt) REVERT: C 421 ASN cc_start: 0.5985 (m-40) cc_final: 0.4700 (t0) REVERT: C 436 GLU cc_start: 0.5556 (OUTLIER) cc_final: 0.5112 (pm20) REVERT: C 445 GLN cc_start: 0.6457 (tt0) cc_final: 0.5637 (tp40) REVERT: F 16 GLU cc_start: 0.6697 (tp30) cc_final: 0.6140 (tm-30) REVERT: F 21 ARG cc_start: 0.6610 (mtp85) cc_final: 0.6292 (mmp-170) REVERT: F 52 MET cc_start: 0.7363 (mmm) cc_final: 0.6819 (mmm) REVERT: F 53 MET cc_start: 0.7271 (mtm) cc_final: 0.6863 (mtp) REVERT: F 119 LYS cc_start: 0.6484 (ttpt) cc_final: 0.6043 (tttt) REVERT: F 120 GLU cc_start: 0.6070 (pt0) cc_final: 0.5173 (mm-30) REVERT: F 122 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6403 (mt-10) REVERT: F 128 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6563 (m-30) REVERT: F 151 GLU cc_start: 0.6630 (mt-10) cc_final: 0.6311 (mt-10) REVERT: F 168 GLU cc_start: 0.4613 (OUTLIER) cc_final: 0.4212 (tt0) REVERT: F 184 ASP cc_start: 0.7195 (m-30) cc_final: 0.6895 (m-30) REVERT: F 225 ARG cc_start: 0.6392 (ttp-170) cc_final: 0.6158 (ttm170) REVERT: F 266 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5824 (tm-30) REVERT: F 270 THR cc_start: 0.6664 (m) cc_final: 0.5751 (p) REVERT: F 271 GLU cc_start: 0.5621 (tp30) cc_final: 0.5296 (tp30) REVERT: F 365 LYS cc_start: 0.6085 (mmtm) cc_final: 0.5331 (tttm) REVERT: F 409 LYS cc_start: 0.6135 (ttmm) cc_final: 0.5709 (tttt) REVERT: F 418 GLN cc_start: 0.6692 (mm110) cc_final: 0.6464 (mm-40) REVERT: F 436 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.4923 (pm20) REVERT: F 443 MET cc_start: 0.6656 (tpp) cc_final: 0.6231 (tpp) REVERT: F 445 GLN cc_start: 0.6518 (tt0) cc_final: 0.5767 (tp40) REVERT: G 120 GLU cc_start: 0.6234 (pt0) cc_final: 0.5222 (mm-30) REVERT: G 122 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6243 (mt-10) REVERT: G 151 GLU cc_start: 0.6484 (mt-10) cc_final: 0.5685 (mm-30) REVERT: G 155 ASP cc_start: 0.6440 (t0) cc_final: 0.5917 (t70) REVERT: G 168 GLU cc_start: 0.4788 (OUTLIER) cc_final: 0.4166 (tt0) REVERT: G 169 ASN cc_start: 0.5578 (OUTLIER) cc_final: 0.4320 (m-40) REVERT: G 201 PHE cc_start: 0.7047 (m-80) cc_final: 0.6161 (m-80) REVERT: G 365 LYS cc_start: 0.6422 (mmtm) cc_final: 0.5655 (tttm) REVERT: G 409 LYS cc_start: 0.6241 (ttmm) cc_final: 0.5856 (tttt) REVERT: G 421 ASN cc_start: 0.6316 (m-40) cc_final: 0.4959 (t0) REVERT: G 428 ASP cc_start: 0.7224 (t70) cc_final: 0.6627 (t0) REVERT: G 436 GLU cc_start: 0.5699 (OUTLIER) cc_final: 0.5022 (pm20) REVERT: H 13 LYS cc_start: 0.6120 (ttmm) cc_final: 0.5439 (tttp) REVERT: H 16 GLU cc_start: 0.6690 (tp30) cc_final: 0.6282 (tm-30) REVERT: H 119 LYS cc_start: 0.5998 (tptp) cc_final: 0.5559 (tttt) REVERT: H 120 GLU cc_start: 0.6220 (pt0) cc_final: 0.5392 (mm-30) REVERT: H 128 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6865 (m-30) REVERT: H 151 GLU cc_start: 0.6739 (mt-10) cc_final: 0.5794 (mm-30) REVERT: H 155 ASP cc_start: 0.6553 (t0) cc_final: 0.6028 (t70) REVERT: H 168 GLU cc_start: 0.4781 (OUTLIER) cc_final: 0.3873 (tm-30) REVERT: H 225 ARG cc_start: 0.6230 (ttt180) cc_final: 0.5916 (ttt180) REVERT: H 270 THR cc_start: 0.6637 (m) cc_final: 0.6049 (p) REVERT: H 271 GLU cc_start: 0.5608 (tp30) cc_final: 0.5175 (tp30) REVERT: H 327 SER cc_start: 0.6889 (m) cc_final: 0.6615 (t) REVERT: H 354 GLU cc_start: 0.7125 (tp30) cc_final: 0.6902 (mm-30) REVERT: H 365 LYS cc_start: 0.6348 (tppt) cc_final: 0.5385 (tttm) REVERT: H 388 GLN cc_start: 0.6489 (mt0) cc_final: 0.6044 (mm-40) REVERT: H 408 LYS cc_start: 0.6552 (tttt) cc_final: 0.6343 (ttpp) REVERT: H 409 LYS cc_start: 0.6515 (ttmm) cc_final: 0.5919 (ttmt) REVERT: H 421 ASN cc_start: 0.5994 (m-40) cc_final: 0.4712 (t0) REVERT: H 428 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6984 (t70) REVERT: H 436 GLU cc_start: 0.5603 (OUTLIER) cc_final: 0.5109 (pm20) REVERT: H 445 GLN cc_start: 0.6481 (tt0) cc_final: 0.5656 (tp40) REVERT: L 16 GLU cc_start: 0.6691 (tp30) cc_final: 0.6129 (tm-30) REVERT: L 52 MET cc_start: 0.7313 (mmm) cc_final: 0.6817 (mmm) REVERT: L 53 MET cc_start: 0.7304 (mtm) cc_final: 0.6917 (mtp) REVERT: L 119 LYS cc_start: 0.6458 (ttpt) cc_final: 0.6014 (tttt) REVERT: L 120 GLU cc_start: 0.6137 (pt0) cc_final: 0.5208 (mm-30) REVERT: L 122 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6466 (mt-10) REVERT: L 128 ASP cc_start: 0.6883 (m-30) cc_final: 0.6611 (m-30) REVERT: L 151 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6358 (mt-10) REVERT: L 184 ASP cc_start: 0.7097 (m-30) cc_final: 0.6783 (m-30) REVERT: L 225 ARG cc_start: 0.6514 (ttp-170) cc_final: 0.6169 (ttt180) REVERT: L 266 GLU cc_start: 0.6235 (OUTLIER) cc_final: 0.5925 (tm-30) REVERT: L 270 THR cc_start: 0.6647 (m) cc_final: 0.5736 (p) REVERT: L 271 GLU cc_start: 0.5629 (tp30) cc_final: 0.5316 (tp30) REVERT: L 365 LYS cc_start: 0.6089 (mmtm) cc_final: 0.5331 (tttm) REVERT: L 409 LYS cc_start: 0.6146 (ttmm) cc_final: 0.5720 (tttt) REVERT: L 418 GLN cc_start: 0.6683 (mm110) cc_final: 0.6462 (mm110) REVERT: L 443 MET cc_start: 0.6661 (tpp) cc_final: 0.6213 (tpp) REVERT: L 445 GLN cc_start: 0.6479 (tt0) cc_final: 0.5724 (tp40) REVERT: N 16 GLU cc_start: 0.6366 (tp30) cc_final: 0.5837 (tm-30) REVERT: N 120 GLU cc_start: 0.6201 (pt0) cc_final: 0.5192 (mm-30) REVERT: N 122 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6228 (mt-10) REVERT: N 151 GLU cc_start: 0.6486 (mt-10) cc_final: 0.5690 (mm-30) REVERT: N 155 ASP cc_start: 0.6446 (t0) cc_final: 0.6020 (t70) REVERT: N 201 PHE cc_start: 0.7045 (m-80) cc_final: 0.6161 (m-80) REVERT: N 270 THR cc_start: 0.6660 (m) cc_final: 0.5854 (p) REVERT: N 365 LYS cc_start: 0.6413 (mmtm) cc_final: 0.5650 (tttm) REVERT: N 409 LYS cc_start: 0.6254 (ttmm) cc_final: 0.5870 (tttt) REVERT: N 421 ASN cc_start: 0.6302 (m-40) cc_final: 0.4943 (t0) REVERT: N 428 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6637 (t0) REVERT: O 13 LYS cc_start: 0.6099 (ttmm) cc_final: 0.5419 (tttp) REVERT: O 16 GLU cc_start: 0.6674 (tp30) cc_final: 0.6261 (tm-30) REVERT: O 53 MET cc_start: 0.7330 (mtm) cc_final: 0.6910 (mtp) REVERT: O 119 LYS cc_start: 0.6077 (tptp) cc_final: 0.5594 (tttt) REVERT: O 120 GLU cc_start: 0.6185 (pt0) cc_final: 0.5452 (mm-30) REVERT: O 122 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6402 (mt-10) REVERT: O 128 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6858 (m-30) REVERT: O 151 GLU cc_start: 0.6660 (mt-10) cc_final: 0.5778 (mm-30) REVERT: O 155 ASP cc_start: 0.6547 (t0) cc_final: 0.6057 (t70) REVERT: O 168 GLU cc_start: 0.4786 (OUTLIER) cc_final: 0.3911 (tm-30) REVERT: O 225 ARG cc_start: 0.6285 (ttt180) cc_final: 0.5928 (ttt180) REVERT: O 270 THR cc_start: 0.6635 (m) cc_final: 0.6046 (p) REVERT: O 271 GLU cc_start: 0.5603 (tp30) cc_final: 0.5171 (tp30) REVERT: O 327 SER cc_start: 0.6880 (m) cc_final: 0.6605 (t) REVERT: O 354 GLU cc_start: 0.7141 (tp30) cc_final: 0.6913 (mm-30) REVERT: O 365 LYS cc_start: 0.6319 (tppt) cc_final: 0.5375 (tttm) REVERT: O 388 GLN cc_start: 0.6492 (mt0) cc_final: 0.6048 (mm-40) REVERT: O 408 LYS cc_start: 0.6545 (tttt) cc_final: 0.6336 (ttpp) REVERT: O 409 LYS cc_start: 0.6505 (ttmm) cc_final: 0.5909 (ttmt) REVERT: O 421 ASN cc_start: 0.5982 (m-40) cc_final: 0.4697 (t0) REVERT: O 436 GLU cc_start: 0.6181 (tp30) cc_final: 0.5700 (tp30) REVERT: O 445 GLN cc_start: 0.6483 (tt0) cc_final: 0.5658 (tp40) REVERT: P 4 ARG cc_start: 0.6038 (tmt170) cc_final: 0.5610 (tpt90) REVERT: R 16 GLU cc_start: 0.6690 (tp30) cc_final: 0.6126 (tm-30) REVERT: R 52 MET cc_start: 0.7325 (mmm) cc_final: 0.6704 (mmm) REVERT: R 53 MET cc_start: 0.7254 (mtm) cc_final: 0.6858 (mtp) REVERT: R 70 MET cc_start: 0.7934 (mtt) cc_final: 0.7631 (mtt) REVERT: R 119 LYS cc_start: 0.6452 (ttpt) cc_final: 0.6005 (tttt) REVERT: R 120 GLU cc_start: 0.6027 (pt0) cc_final: 0.5124 (mm-30) REVERT: R 122 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6352 (mt-10) REVERT: R 128 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6676 (m-30) REVERT: R 151 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6468 (mt-10) REVERT: R 184 ASP cc_start: 0.7199 (m-30) cc_final: 0.6898 (m-30) REVERT: R 225 ARG cc_start: 0.6540 (ttp-170) cc_final: 0.6313 (ttm170) REVERT: R 266 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5913 (tm-30) REVERT: R 270 THR cc_start: 0.6631 (m) cc_final: 0.5729 (p) REVERT: R 271 GLU cc_start: 0.5612 (tp30) cc_final: 0.5289 (tp30) REVERT: R 365 LYS cc_start: 0.6098 (mmtm) cc_final: 0.5342 (tttm) REVERT: R 409 LYS cc_start: 0.6141 (ttmm) cc_final: 0.5714 (tttt) REVERT: R 418 GLN cc_start: 0.6691 (mm110) cc_final: 0.6471 (mm110) REVERT: R 428 ASP cc_start: 0.6874 (t70) cc_final: 0.6507 (t0) REVERT: R 445 GLN cc_start: 0.6550 (tt0) cc_final: 0.5780 (tp40) REVERT: S 120 GLU cc_start: 0.6271 (pt0) cc_final: 0.5231 (mm-30) REVERT: S 128 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6914 (m-30) REVERT: S 151 GLU cc_start: 0.6633 (mt-10) cc_final: 0.5741 (mm-30) REVERT: S 155 ASP cc_start: 0.6451 (t0) cc_final: 0.5954 (t70) REVERT: S 168 GLU cc_start: 0.4812 (OUTLIER) cc_final: 0.4276 (tt0) REVERT: S 225 ARG cc_start: 0.6211 (ttt180) cc_final: 0.5904 (ttt180) REVERT: S 266 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5717 (mp0) REVERT: S 365 LYS cc_start: 0.6439 (mmtm) cc_final: 0.5665 (tttm) REVERT: S 409 LYS cc_start: 0.6201 (ttmm) cc_final: 0.5815 (tttt) REVERT: S 421 ASN cc_start: 0.6243 (m-40) cc_final: 0.4911 (t0) REVERT: S 428 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6635 (t0) REVERT: T 13 LYS cc_start: 0.6103 (ttmm) cc_final: 0.5417 (tttp) REVERT: T 16 GLU cc_start: 0.6646 (tp30) cc_final: 0.6245 (tm-30) REVERT: T 21 ARG cc_start: 0.6274 (mmm-85) cc_final: 0.5780 (mmm160) REVERT: T 53 MET cc_start: 0.7318 (mtm) cc_final: 0.6898 (mtp) REVERT: T 119 LYS cc_start: 0.6063 (tptp) cc_final: 0.5581 (tttt) REVERT: T 120 GLU cc_start: 0.6170 (pt0) cc_final: 0.5442 (mm-30) REVERT: T 122 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6395 (mt-10) REVERT: T 128 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6855 (m-30) REVERT: T 151 GLU cc_start: 0.6670 (mt-10) cc_final: 0.5783 (mm-30) REVERT: T 155 ASP cc_start: 0.6542 (t0) cc_final: 0.6020 (t70) REVERT: T 225 ARG cc_start: 0.6241 (ttt180) cc_final: 0.5951 (ttt180) REVERT: T 270 THR cc_start: 0.6633 (m) cc_final: 0.6036 (p) REVERT: T 271 GLU cc_start: 0.5630 (tp30) cc_final: 0.5182 (tp30) REVERT: T 327 SER cc_start: 0.6886 (m) cc_final: 0.6610 (t) REVERT: T 354 GLU cc_start: 0.7121 (tp30) cc_final: 0.6906 (mm-30) REVERT: T 365 LYS cc_start: 0.6323 (tppt) cc_final: 0.5379 (tttm) REVERT: T 388 GLN cc_start: 0.6496 (mt0) cc_final: 0.6040 (mm-40) REVERT: T 408 LYS cc_start: 0.6551 (tttt) cc_final: 0.6343 (ttpp) REVERT: T 409 LYS cc_start: 0.6517 (ttmm) cc_final: 0.5920 (ttmt) REVERT: T 421 ASN cc_start: 0.5977 (m-40) cc_final: 0.4692 (t0) REVERT: T 436 GLU cc_start: 0.6194 (tp30) cc_final: 0.5695 (tp30) REVERT: T 445 GLN cc_start: 0.6485 (tt0) cc_final: 0.5665 (tp40) REVERT: U 4 ARG cc_start: 0.5966 (tmt170) cc_final: 0.5641 (tpt90) outliers start: 111 outliers final: 49 residues processed: 829 average time/residue: 1.6340 time to fit residues: 1643.0748 Evaluate side-chains 819 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 740 time to evaluate : 4.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 169 ASN Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 428 ASP Chi-restraints excluded: chain H residue 436 GLU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 266 GLU Chi-restraints excluded: chain L residue 282 LYS Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 366 VAL Chi-restraints excluded: chain N residue 428 ASP Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 169 ASN Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 366 VAL Chi-restraints excluded: chain O residue 385 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 266 GLU Chi-restraints excluded: chain R residue 282 LYS Chi-restraints excluded: chain R residue 366 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 53 MET Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 428 ASP Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain T residue 169 ASN Chi-restraints excluded: chain T residue 277 THR Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain T residue 385 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 6.9990 chunk 459 optimal weight: 5.9990 chunk 100 optimal weight: 0.2980 chunk 299 optimal weight: 0.3980 chunk 125 optimal weight: 8.9990 chunk 510 optimal weight: 0.9980 chunk 424 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 268 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 36 ASN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN F 36 ASN ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** G 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 413 ASN H 36 ASN L 36 ASN ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN ** N 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 413 ASN O 36 ASN R 36 ASN ** R 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 ASN ** S 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 413 ASN T 36 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.032 44100 Z= 0.095 Angle : 0.391 4.994 59700 Z= 0.207 Chirality : 0.038 0.133 6444 Planarity : 0.002 0.029 7860 Dihedral : 5.268 58.004 5888 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.42 % Allowed : 15.31 % Favored : 83.27 % 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: 0.99 (0.12), residues: 5316 helix: 1.96 (0.11), residues: 2304 sheet: -0.97 (0.15), residues: 876 loop : 0.04 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 427 HIS 0.002 0.000 HIS C 197 PHE 0.005 0.001 PHE A 253 TYR 0.019 0.001 TYR R 203 ARG 0.004 0.000 ARG F 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 776 time to evaluate : 4.954 Fit side-chains REVERT: A 16 GLU cc_start: 0.6694 (tp30) cc_final: 0.6094 (tm-30) REVERT: A 52 MET cc_start: 0.7361 (mmm) cc_final: 0.6795 (mmm) REVERT: A 53 MET cc_start: 0.7249 (mtm) cc_final: 0.6885 (mtp) REVERT: A 119 LYS cc_start: 0.6510 (ttpt) cc_final: 0.6089 (tttt) REVERT: A 120 GLU cc_start: 0.6112 (pt0) cc_final: 0.5350 (mm-30) REVERT: A 128 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6575 (m-30) REVERT: A 151 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6431 (mt-10) REVERT: A 168 GLU cc_start: 0.4260 (OUTLIER) cc_final: 0.3967 (pp20) REVERT: A 184 ASP cc_start: 0.7174 (m-30) cc_final: 0.6881 (m-30) REVERT: A 225 ARG cc_start: 0.6356 (ttp-170) cc_final: 0.5910 (ttt180) REVERT: A 271 GLU cc_start: 0.5843 (tp30) cc_final: 0.5393 (tp30) REVERT: A 365 LYS cc_start: 0.6126 (mmtm) cc_final: 0.5337 (tttm) REVERT: A 409 LYS cc_start: 0.6097 (ttmm) cc_final: 0.5690 (tttt) REVERT: A 418 GLN cc_start: 0.6706 (mm110) cc_final: 0.6486 (mm110) REVERT: A 428 ASP cc_start: 0.7254 (t70) cc_final: 0.6656 (m-30) REVERT: A 445 GLN cc_start: 0.6502 (tt0) cc_final: 0.5728 (tp40) REVERT: B 16 GLU cc_start: 0.6369 (tp30) cc_final: 0.5825 (tm-30) REVERT: B 120 GLU cc_start: 0.5936 (pt0) cc_final: 0.5139 (mm-30) REVERT: B 151 GLU cc_start: 0.6492 (mt-10) cc_final: 0.5682 (mm-30) REVERT: B 155 ASP cc_start: 0.6510 (t0) cc_final: 0.5980 (t70) REVERT: B 201 PHE cc_start: 0.7063 (m-80) cc_final: 0.6164 (m-80) REVERT: B 365 LYS cc_start: 0.6333 (mmtm) cc_final: 0.5558 (tttm) REVERT: B 409 LYS cc_start: 0.6216 (ttmm) cc_final: 0.5802 (tttt) REVERT: B 421 ASN cc_start: 0.6249 (m-40) cc_final: 0.4862 (t0) REVERT: B 428 ASP cc_start: 0.7157 (t70) cc_final: 0.6636 (t0) REVERT: B 445 GLN cc_start: 0.6736 (tt0) cc_final: 0.6477 (tt0) REVERT: C 13 LYS cc_start: 0.5790 (ttmm) cc_final: 0.5175 (tttp) REVERT: C 16 GLU cc_start: 0.6551 (tp30) cc_final: 0.6168 (tm-30) REVERT: C 53 MET cc_start: 0.7286 (mtm) cc_final: 0.6910 (mtp) REVERT: C 119 LYS cc_start: 0.6050 (tptp) cc_final: 0.5596 (tttt) REVERT: C 120 GLU cc_start: 0.6053 (OUTLIER) cc_final: 0.5697 (mt-10) REVERT: C 122 GLU cc_start: 0.6524 (mt-10) cc_final: 0.6252 (mt-10) REVERT: C 128 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6945 (m-30) REVERT: C 151 GLU cc_start: 0.6683 (mt-10) cc_final: 0.5770 (mm-30) REVERT: C 155 ASP cc_start: 0.6596 (t0) cc_final: 0.6053 (t70) REVERT: C 225 ARG cc_start: 0.6135 (ttt180) cc_final: 0.5803 (ttt180) REVERT: C 270 THR cc_start: 0.6553 (m) cc_final: 0.5978 (p) REVERT: C 271 GLU cc_start: 0.5618 (tp30) cc_final: 0.5192 (tp30) REVERT: C 365 LYS cc_start: 0.6323 (tppt) cc_final: 0.5337 (tttm) REVERT: C 388 GLN cc_start: 0.6545 (mt0) cc_final: 0.5964 (mm-40) REVERT: C 408 LYS cc_start: 0.6437 (tttt) cc_final: 0.6220 (ttpp) REVERT: C 409 LYS cc_start: 0.6394 (ttmm) cc_final: 0.5815 (ttmt) REVERT: C 421 ASN cc_start: 0.5930 (m-40) cc_final: 0.4674 (t0) REVERT: C 428 ASP cc_start: 0.7232 (t70) cc_final: 0.6628 (m-30) REVERT: C 436 GLU cc_start: 0.5550 (pm20) cc_final: 0.5025 (pm20) REVERT: C 445 GLN cc_start: 0.6464 (tt0) cc_final: 0.5619 (tp40) REVERT: F 16 GLU cc_start: 0.6700 (tp30) cc_final: 0.6102 (tm-30) REVERT: F 21 ARG cc_start: 0.6606 (mtp85) cc_final: 0.6309 (mmp-170) REVERT: F 52 MET cc_start: 0.7345 (mmm) cc_final: 0.6762 (mmm) REVERT: F 53 MET cc_start: 0.7304 (mtm) cc_final: 0.6935 (mtp) REVERT: F 119 LYS cc_start: 0.6477 (ttpt) cc_final: 0.6060 (tttt) REVERT: F 120 GLU cc_start: 0.6025 (pt0) cc_final: 0.5266 (mm-30) REVERT: F 128 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6595 (m-30) REVERT: F 151 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6371 (mt-10) REVERT: F 184 ASP cc_start: 0.7175 (m-30) cc_final: 0.6863 (m-30) REVERT: F 225 ARG cc_start: 0.6400 (ttp-170) cc_final: 0.5912 (ttt180) REVERT: F 270 THR cc_start: 0.6534 (m) cc_final: 0.5611 (p) REVERT: F 271 GLU cc_start: 0.5665 (tp30) cc_final: 0.5343 (tp30) REVERT: F 365 LYS cc_start: 0.6120 (mmtm) cc_final: 0.5346 (tttm) REVERT: F 409 LYS cc_start: 0.6091 (ttmm) cc_final: 0.5682 (tttt) REVERT: F 418 GLN cc_start: 0.6697 (mm110) cc_final: 0.6476 (mm110) REVERT: F 428 ASP cc_start: 0.7253 (t70) cc_final: 0.6652 (m-30) REVERT: F 445 GLN cc_start: 0.6515 (tt0) cc_final: 0.5738 (tp40) REVERT: G 120 GLU cc_start: 0.5936 (pt0) cc_final: 0.5149 (mm-30) REVERT: G 151 GLU cc_start: 0.6489 (mt-10) cc_final: 0.5679 (mm-30) REVERT: G 155 ASP cc_start: 0.6501 (t0) cc_final: 0.5996 (t70) REVERT: G 168 GLU cc_start: 0.4706 (OUTLIER) cc_final: 0.4394 (tt0) REVERT: G 201 PHE cc_start: 0.7071 (m-80) cc_final: 0.6197 (m-80) REVERT: G 365 LYS cc_start: 0.6343 (mmtm) cc_final: 0.5563 (tttm) REVERT: G 409 LYS cc_start: 0.6211 (ttmm) cc_final: 0.5818 (tttt) REVERT: G 421 ASN cc_start: 0.6261 (m-40) cc_final: 0.4875 (t0) REVERT: G 428 ASP cc_start: 0.7152 (t70) cc_final: 0.6637 (t0) REVERT: G 436 GLU cc_start: 0.5607 (OUTLIER) cc_final: 0.5095 (pm20) REVERT: H 13 LYS cc_start: 0.5808 (ttmm) cc_final: 0.5190 (tttp) REVERT: H 16 GLU cc_start: 0.6557 (tp30) cc_final: 0.6151 (tm-30) REVERT: H 119 LYS cc_start: 0.6013 (tptp) cc_final: 0.5611 (tttt) REVERT: H 120 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5705 (mt-10) REVERT: H 128 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6945 (m-30) REVERT: H 151 GLU cc_start: 0.6719 (mt-10) cc_final: 0.5814 (mm-30) REVERT: H 155 ASP cc_start: 0.6590 (t0) cc_final: 0.6067 (t70) REVERT: H 225 ARG cc_start: 0.6111 (ttt180) cc_final: 0.5792 (ttt180) REVERT: H 270 THR cc_start: 0.6541 (m) cc_final: 0.5969 (p) REVERT: H 271 GLU cc_start: 0.5624 (tp30) cc_final: 0.5170 (tp30) REVERT: H 365 LYS cc_start: 0.6310 (tppt) cc_final: 0.5337 (tttm) REVERT: H 388 GLN cc_start: 0.6542 (mt0) cc_final: 0.6035 (mm-40) REVERT: H 408 LYS cc_start: 0.6438 (tttt) cc_final: 0.6222 (ttpp) REVERT: H 409 LYS cc_start: 0.6396 (ttmm) cc_final: 0.5818 (ttmt) REVERT: H 421 ASN cc_start: 0.5939 (m-40) cc_final: 0.4685 (t0) REVERT: H 428 ASP cc_start: 0.7204 (t70) cc_final: 0.6612 (m-30) REVERT: H 436 GLU cc_start: 0.5552 (pm20) cc_final: 0.5011 (pm20) REVERT: H 445 GLN cc_start: 0.6508 (tt0) cc_final: 0.5658 (tp40) REVERT: L 16 GLU cc_start: 0.6681 (tp30) cc_final: 0.6077 (tm-30) REVERT: L 52 MET cc_start: 0.7352 (mmm) cc_final: 0.6690 (mmm) REVERT: L 53 MET cc_start: 0.7236 (mtm) cc_final: 0.6862 (mtp) REVERT: L 119 LYS cc_start: 0.6502 (ttpt) cc_final: 0.6061 (tttt) REVERT: L 120 GLU cc_start: 0.6075 (pt0) cc_final: 0.5186 (mm-30) REVERT: L 122 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6435 (mt-10) REVERT: L 128 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6643 (m-30) REVERT: L 151 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6350 (mt-10) REVERT: L 184 ASP cc_start: 0.7171 (m-30) cc_final: 0.6872 (m-30) REVERT: L 225 ARG cc_start: 0.6396 (ttp-170) cc_final: 0.6029 (ttt180) REVERT: L 270 THR cc_start: 0.6527 (m) cc_final: 0.5598 (p) REVERT: L 271 GLU cc_start: 0.5678 (tp30) cc_final: 0.5373 (tp30) REVERT: L 365 LYS cc_start: 0.6122 (mmtm) cc_final: 0.5346 (tttm) REVERT: L 409 LYS cc_start: 0.6102 (ttmm) cc_final: 0.5702 (tttt) REVERT: L 418 GLN cc_start: 0.6687 (mm110) cc_final: 0.6466 (mm110) REVERT: L 428 ASP cc_start: 0.7249 (t70) cc_final: 0.6649 (m-30) REVERT: L 445 GLN cc_start: 0.6492 (tt0) cc_final: 0.5701 (tp40) REVERT: N 16 GLU cc_start: 0.6382 (tp30) cc_final: 0.5847 (tm-30) REVERT: N 120 GLU cc_start: 0.6046 (pt0) cc_final: 0.5180 (mm-30) REVERT: N 151 GLU cc_start: 0.6468 (mt-10) cc_final: 0.5667 (mm-30) REVERT: N 201 PHE cc_start: 0.7067 (m-80) cc_final: 0.6195 (m-80) REVERT: N 365 LYS cc_start: 0.6336 (mmtm) cc_final: 0.5563 (tttm) REVERT: N 409 LYS cc_start: 0.6211 (ttmm) cc_final: 0.5819 (tttt) REVERT: N 421 ASN cc_start: 0.6245 (m-40) cc_final: 0.4857 (t0) REVERT: N 428 ASP cc_start: 0.7146 (t70) cc_final: 0.6626 (t0) REVERT: O 13 LYS cc_start: 0.5772 (ttmm) cc_final: 0.5129 (tttp) REVERT: O 16 GLU cc_start: 0.6543 (tp30) cc_final: 0.6133 (tm-30) REVERT: O 53 MET cc_start: 0.7319 (mtm) cc_final: 0.6942 (mtp) REVERT: O 119 LYS cc_start: 0.6082 (tptp) cc_final: 0.5619 (tttt) REVERT: O 120 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5718 (mt-10) REVERT: O 122 GLU cc_start: 0.6552 (mt-10) cc_final: 0.6267 (mt-10) REVERT: O 128 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: O 151 GLU cc_start: 0.6669 (mt-10) cc_final: 0.5762 (mm-30) REVERT: O 155 ASP cc_start: 0.6571 (t0) cc_final: 0.6062 (t70) REVERT: O 225 ARG cc_start: 0.6153 (ttt180) cc_final: 0.5851 (ttt180) REVERT: O 270 THR cc_start: 0.6552 (m) cc_final: 0.5984 (p) REVERT: O 271 GLU cc_start: 0.5618 (tp30) cc_final: 0.5163 (tp30) REVERT: O 365 LYS cc_start: 0.6309 (tppt) cc_final: 0.5338 (tttm) REVERT: O 388 GLN cc_start: 0.6550 (mt0) cc_final: 0.6042 (mm-40) REVERT: O 408 LYS cc_start: 0.6430 (tttt) cc_final: 0.6214 (ttpp) REVERT: O 409 LYS cc_start: 0.6386 (ttmm) cc_final: 0.5808 (ttmt) REVERT: O 421 ASN cc_start: 0.5928 (m-40) cc_final: 0.4672 (t0) REVERT: O 428 ASP cc_start: 0.7224 (t70) cc_final: 0.6623 (m-30) REVERT: O 436 GLU cc_start: 0.6205 (tp30) cc_final: 0.5738 (tp30) REVERT: O 445 GLN cc_start: 0.6511 (tt0) cc_final: 0.5658 (tp40) REVERT: P 4 ARG cc_start: 0.6026 (tmt170) cc_final: 0.5603 (tpt90) REVERT: R 16 GLU cc_start: 0.6693 (tp30) cc_final: 0.6087 (tm-30) REVERT: R 52 MET cc_start: 0.7402 (mmm) cc_final: 0.6732 (mmm) REVERT: R 53 MET cc_start: 0.7250 (mtm) cc_final: 0.6878 (mtp) REVERT: R 70 MET cc_start: 0.8001 (mtt) cc_final: 0.7696 (mtt) REVERT: R 119 LYS cc_start: 0.6454 (ttpt) cc_final: 0.5997 (tttt) REVERT: R 120 GLU cc_start: 0.6007 (pt0) cc_final: 0.5260 (mm-30) REVERT: R 122 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6417 (mt-10) REVERT: R 128 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6730 (m-30) REVERT: R 151 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6424 (mt-10) REVERT: R 184 ASP cc_start: 0.7204 (m-30) cc_final: 0.6898 (m-30) REVERT: R 225 ARG cc_start: 0.6376 (ttp-170) cc_final: 0.5954 (ttt180) REVERT: R 270 THR cc_start: 0.6524 (m) cc_final: 0.5586 (p) REVERT: R 271 GLU cc_start: 0.5654 (tp30) cc_final: 0.5345 (tp30) REVERT: R 365 LYS cc_start: 0.6135 (mmtm) cc_final: 0.5362 (tttm) REVERT: R 409 LYS cc_start: 0.6097 (ttmm) cc_final: 0.5689 (tttt) REVERT: R 418 GLN cc_start: 0.6696 (mm110) cc_final: 0.6475 (mm110) REVERT: R 428 ASP cc_start: 0.7173 (t70) cc_final: 0.6469 (m-30) REVERT: R 445 GLN cc_start: 0.6547 (tt0) cc_final: 0.5765 (tp40) REVERT: S 120 GLU cc_start: 0.5966 (pt0) cc_final: 0.5145 (mm-30) REVERT: S 128 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6957 (m-30) REVERT: S 151 GLU cc_start: 0.6617 (mt-10) cc_final: 0.5720 (mm-30) REVERT: S 155 ASP cc_start: 0.6506 (t0) cc_final: 0.6023 (t70) REVERT: S 201 PHE cc_start: 0.7031 (m-80) cc_final: 0.6183 (m-80) REVERT: S 225 ARG cc_start: 0.6293 (ttt180) cc_final: 0.5993 (ttt180) REVERT: S 365 LYS cc_start: 0.6351 (mmtm) cc_final: 0.5564 (tttm) REVERT: S 409 LYS cc_start: 0.6200 (ttmm) cc_final: 0.5809 (tttt) REVERT: S 421 ASN cc_start: 0.6252 (m-40) cc_final: 0.4867 (t0) REVERT: S 428 ASP cc_start: 0.7142 (t70) cc_final: 0.6622 (t0) REVERT: T 13 LYS cc_start: 0.5780 (ttmm) cc_final: 0.5167 (tttp) REVERT: T 16 GLU cc_start: 0.6595 (tp30) cc_final: 0.6207 (tm-30) REVERT: T 21 ARG cc_start: 0.6361 (mmm-85) cc_final: 0.5767 (mmp-170) REVERT: T 53 MET cc_start: 0.7282 (mtm) cc_final: 0.6906 (mtp) REVERT: T 119 LYS cc_start: 0.6071 (tptp) cc_final: 0.5608 (tttt) REVERT: T 120 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5700 (mt-10) REVERT: T 122 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6259 (mt-10) REVERT: T 128 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6934 (m-30) REVERT: T 151 GLU cc_start: 0.6672 (mt-10) cc_final: 0.5735 (mm-30) REVERT: T 155 ASP cc_start: 0.6567 (t0) cc_final: 0.6063 (t70) REVERT: T 225 ARG cc_start: 0.6176 (ttt180) cc_final: 0.5856 (ttt180) REVERT: T 270 THR cc_start: 0.6534 (m) cc_final: 0.5958 (p) REVERT: T 271 GLU cc_start: 0.5608 (tp30) cc_final: 0.5153 (tp30) REVERT: T 365 LYS cc_start: 0.6313 (tppt) cc_final: 0.5342 (tttm) REVERT: T 388 GLN cc_start: 0.6613 (mt0) cc_final: 0.6128 (mm-40) REVERT: T 408 LYS cc_start: 0.6437 (tttt) cc_final: 0.6221 (ttpp) REVERT: T 409 LYS cc_start: 0.6412 (ttmm) cc_final: 0.5834 (ttmt) REVERT: T 421 ASN cc_start: 0.5923 (m-40) cc_final: 0.4667 (t0) REVERT: T 428 ASP cc_start: 0.7228 (t70) cc_final: 0.6626 (m-30) REVERT: T 436 GLU cc_start: 0.6218 (tp30) cc_final: 0.5720 (tp30) REVERT: T 445 GLN cc_start: 0.6512 (tt0) cc_final: 0.5665 (tp40) REVERT: U 4 ARG cc_start: 0.5981 (tmt170) cc_final: 0.5672 (tpt90) outliers start: 66 outliers final: 25 residues processed: 814 average time/residue: 1.6986 time to fit residues: 1689.1243 Evaluate side-chains 790 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 749 time to evaluate : 5.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 53 MET Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 169 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 282 LYS Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 169 ASN Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 120 GLU Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain T residue 169 ASN Chi-restraints excluded: chain T residue 385 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 291 optimal weight: 8.9990 chunk 373 optimal weight: 9.9990 chunk 289 optimal weight: 5.9990 chunk 430 optimal weight: 5.9990 chunk 285 optimal weight: 0.7980 chunk 508 optimal weight: 9.9990 chunk 318 optimal weight: 0.7980 chunk 310 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 36 ASN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN F 36 ASN G 36 ASN ** G 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 413 ASN H 36 ASN L 36 ASN L 169 ASN N 36 ASN ** N 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 413 ASN O 36 ASN R 36 ASN ** R 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 ASN ** S 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 413 ASN T 36 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 44100 Z= 0.325 Angle : 0.617 6.956 59700 Z= 0.336 Chirality : 0.047 0.173 6444 Planarity : 0.005 0.047 7860 Dihedral : 6.373 59.047 5886 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.78 % Allowed : 13.90 % Favored : 83.31 % 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: 0.29 (0.11), residues: 5316 helix: 1.32 (0.11), residues: 2292 sheet: -1.61 (0.15), residues: 744 loop : -0.20 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 427 HIS 0.007 0.002 HIS C 197 PHE 0.022 0.002 PHE R 287 TYR 0.036 0.003 TYR G 298 ARG 0.006 0.001 ARG X 4 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 741 time to evaluate : 4.882 Fit side-chains REVERT: A 16 GLU cc_start: 0.6760 (tp30) cc_final: 0.6278 (tm-30) REVERT: A 52 MET cc_start: 0.7332 (mmm) cc_final: 0.6809 (mmm) REVERT: A 109 ASP cc_start: 0.6804 (t0) cc_final: 0.6528 (t0) REVERT: A 119 LYS cc_start: 0.6475 (ttpt) cc_final: 0.6039 (tttt) REVERT: A 120 GLU cc_start: 0.6038 (pt0) cc_final: 0.5244 (mm-30) REVERT: A 122 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6400 (mt-10) REVERT: A 128 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6654 (m-30) REVERT: A 151 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6478 (mt-10) REVERT: A 168 GLU cc_start: 0.4634 (OUTLIER) cc_final: 0.4051 (pp20) REVERT: A 184 ASP cc_start: 0.7227 (m-30) cc_final: 0.6889 (m-30) REVERT: A 225 ARG cc_start: 0.6374 (ttp-170) cc_final: 0.5993 (ttm170) REVERT: A 246 MET cc_start: 0.7002 (ttp) cc_final: 0.6672 (ttp) REVERT: A 271 GLU cc_start: 0.5580 (tp30) cc_final: 0.5232 (tp30) REVERT: A 365 LYS cc_start: 0.6068 (mmtm) cc_final: 0.5331 (tttm) REVERT: A 385 VAL cc_start: 0.6565 (OUTLIER) cc_final: 0.6331 (p) REVERT: A 409 LYS cc_start: 0.6297 (ttmm) cc_final: 0.5854 (tttt) REVERT: A 418 GLN cc_start: 0.6651 (mm110) cc_final: 0.6430 (mm-40) REVERT: A 436 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.5416 (pm20) REVERT: A 445 GLN cc_start: 0.6530 (tt0) cc_final: 0.5764 (tp40) REVERT: B 16 GLU cc_start: 0.6394 (tp30) cc_final: 0.5842 (tm-30) REVERT: B 109 ASP cc_start: 0.6818 (t0) cc_final: 0.6248 (t0) REVERT: B 120 GLU cc_start: 0.6145 (pt0) cc_final: 0.5149 (mm-30) REVERT: B 151 GLU cc_start: 0.6527 (mt-10) cc_final: 0.5703 (mm-30) REVERT: B 155 ASP cc_start: 0.6480 (t0) cc_final: 0.5968 (t70) REVERT: B 168 GLU cc_start: 0.5361 (OUTLIER) cc_final: 0.4886 (tt0) REVERT: B 201 PHE cc_start: 0.7037 (m-80) cc_final: 0.6149 (m-80) REVERT: B 365 LYS cc_start: 0.6435 (mmtm) cc_final: 0.5664 (tttm) REVERT: B 409 LYS cc_start: 0.6180 (ttmm) cc_final: 0.5802 (tttt) REVERT: B 421 ASN cc_start: 0.6307 (m-40) cc_final: 0.4951 (t0) REVERT: B 436 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.5171 (pm20) REVERT: B 445 GLN cc_start: 0.6770 (tt0) cc_final: 0.6558 (tt0) REVERT: C 13 LYS cc_start: 0.5842 (ttmm) cc_final: 0.5195 (tttp) REVERT: C 16 GLU cc_start: 0.6694 (tp30) cc_final: 0.6391 (tm-30) REVERT: C 53 MET cc_start: 0.7351 (mtm) cc_final: 0.6913 (mtp) REVERT: C 119 LYS cc_start: 0.6049 (tptp) cc_final: 0.5557 (tttt) REVERT: C 120 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5428 (mm-30) REVERT: C 122 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6429 (mt-10) REVERT: C 128 ASP cc_start: 0.7080 (m-30) cc_final: 0.6858 (m-30) REVERT: C 151 GLU cc_start: 0.6690 (mt-10) cc_final: 0.5753 (mm-30) REVERT: C 155 ASP cc_start: 0.6672 (t0) cc_final: 0.6141 (t70) REVERT: C 168 GLU cc_start: 0.4976 (OUTLIER) cc_final: 0.4123 (tm-30) REVERT: C 225 ARG cc_start: 0.6336 (ttt180) cc_final: 0.5989 (ttt180) REVERT: C 266 GLU cc_start: 0.6076 (OUTLIER) cc_final: 0.5662 (mp0) REVERT: C 270 THR cc_start: 0.6764 (m) cc_final: 0.6175 (p) REVERT: C 271 GLU cc_start: 0.5598 (tp30) cc_final: 0.5186 (tp30) REVERT: C 365 LYS cc_start: 0.6349 (tppt) cc_final: 0.5380 (tttm) REVERT: C 388 GLN cc_start: 0.6469 (mt0) cc_final: 0.5956 (mm-40) REVERT: C 408 LYS cc_start: 0.6729 (tttt) cc_final: 0.6445 (ttpp) REVERT: C 409 LYS cc_start: 0.6507 (ttmm) cc_final: 0.5938 (ttmt) REVERT: C 421 ASN cc_start: 0.6028 (m-40) cc_final: 0.4714 (t0) REVERT: C 436 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5316 (pm20) REVERT: C 445 GLN cc_start: 0.6557 (tt0) cc_final: 0.5723 (tp40) REVERT: F 16 GLU cc_start: 0.6764 (tp30) cc_final: 0.6283 (tm-30) REVERT: F 21 ARG cc_start: 0.6710 (mtp85) cc_final: 0.6385 (mmp-170) REVERT: F 52 MET cc_start: 0.7328 (mmm) cc_final: 0.6800 (mmm) REVERT: F 109 ASP cc_start: 0.6805 (t0) cc_final: 0.6529 (t0) REVERT: F 119 LYS cc_start: 0.6462 (ttpt) cc_final: 0.6031 (tttt) REVERT: F 120 GLU cc_start: 0.6058 (pt0) cc_final: 0.5244 (mm-30) REVERT: F 122 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6424 (mt-10) REVERT: F 128 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6630 (m-30) REVERT: F 151 GLU cc_start: 0.6629 (mt-10) cc_final: 0.6342 (mt-10) REVERT: F 168 GLU cc_start: 0.4842 (OUTLIER) cc_final: 0.3799 (tm-30) REVERT: F 184 ASP cc_start: 0.7212 (m-30) cc_final: 0.6889 (m-30) REVERT: F 225 ARG cc_start: 0.6334 (ttp-170) cc_final: 0.6108 (ttm170) REVERT: F 246 MET cc_start: 0.6997 (ttp) cc_final: 0.6666 (ttp) REVERT: F 270 THR cc_start: 0.6791 (m) cc_final: 0.5895 (p) REVERT: F 271 GLU cc_start: 0.5590 (tp30) cc_final: 0.5275 (tp30) REVERT: F 365 LYS cc_start: 0.6062 (mmtm) cc_final: 0.5323 (tttm) REVERT: F 385 VAL cc_start: 0.6509 (OUTLIER) cc_final: 0.6281 (p) REVERT: F 409 LYS cc_start: 0.6292 (ttmm) cc_final: 0.5846 (tttt) REVERT: F 418 GLN cc_start: 0.6643 (mm110) cc_final: 0.6421 (mm-40) REVERT: F 436 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5372 (pm20) REVERT: F 445 GLN cc_start: 0.6526 (tt0) cc_final: 0.5748 (tp40) REVERT: G 16 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.5603 (tm-30) REVERT: G 109 ASP cc_start: 0.6820 (t0) cc_final: 0.6250 (t0) REVERT: G 120 GLU cc_start: 0.6161 (pt0) cc_final: 0.5181 (mm-30) REVERT: G 122 GLU cc_start: 0.6509 (mt-10) cc_final: 0.6229 (mt-10) REVERT: G 151 GLU cc_start: 0.6528 (mt-10) cc_final: 0.5703 (mm-30) REVERT: G 155 ASP cc_start: 0.6471 (t0) cc_final: 0.5959 (t70) REVERT: G 168 GLU cc_start: 0.5097 (OUTLIER) cc_final: 0.4476 (tt0) REVERT: G 266 GLU cc_start: 0.6034 (OUTLIER) cc_final: 0.5591 (mp0) REVERT: G 365 LYS cc_start: 0.6438 (mmtm) cc_final: 0.5667 (tttm) REVERT: G 409 LYS cc_start: 0.6178 (ttmm) cc_final: 0.5805 (tttt) REVERT: G 421 ASN cc_start: 0.6322 (m-40) cc_final: 0.4976 (t0) REVERT: G 428 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6795 (t70) REVERT: G 436 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5378 (pm20) REVERT: H 13 LYS cc_start: 0.5860 (ttmm) cc_final: 0.5208 (tttp) REVERT: H 16 GLU cc_start: 0.6707 (tp30) cc_final: 0.6399 (tm-30) REVERT: H 119 LYS cc_start: 0.6022 (tptp) cc_final: 0.5557 (tttt) REVERT: H 120 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5422 (mm-30) REVERT: H 128 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6860 (m-30) REVERT: H 151 GLU cc_start: 0.6737 (mt-10) cc_final: 0.5783 (mm-30) REVERT: H 155 ASP cc_start: 0.6572 (t0) cc_final: 0.6063 (t70) REVERT: H 168 GLU cc_start: 0.4976 (OUTLIER) cc_final: 0.4084 (tm-30) REVERT: H 225 ARG cc_start: 0.6354 (ttt180) cc_final: 0.6043 (ttt180) REVERT: H 270 THR cc_start: 0.6743 (m) cc_final: 0.6156 (p) REVERT: H 271 GLU cc_start: 0.5599 (tp30) cc_final: 0.5170 (tp30) REVERT: H 365 LYS cc_start: 0.6351 (tppt) cc_final: 0.5382 (tttm) REVERT: H 388 GLN cc_start: 0.6462 (mt0) cc_final: 0.6050 (mm-40) REVERT: H 408 LYS cc_start: 0.6730 (tttt) cc_final: 0.6446 (ttpp) REVERT: H 409 LYS cc_start: 0.6506 (ttmm) cc_final: 0.5942 (ttmt) REVERT: H 421 ASN cc_start: 0.6062 (m-40) cc_final: 0.4759 (t0) REVERT: H 436 GLU cc_start: 0.5917 (OUTLIER) cc_final: 0.5313 (pm20) REVERT: H 445 GLN cc_start: 0.6536 (tt0) cc_final: 0.5674 (tp40) REVERT: L 16 GLU cc_start: 0.6765 (tp30) cc_final: 0.6278 (tm-30) REVERT: L 52 MET cc_start: 0.7285 (mmm) cc_final: 0.6630 (mmm) REVERT: L 109 ASP cc_start: 0.6796 (t0) cc_final: 0.6524 (t0) REVERT: L 119 LYS cc_start: 0.6413 (ttpt) cc_final: 0.6032 (tttt) REVERT: L 120 GLU cc_start: 0.6020 (pt0) cc_final: 0.5131 (mm-30) REVERT: L 128 ASP cc_start: 0.6910 (OUTLIER) cc_final: 0.6632 (m-30) REVERT: L 151 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6389 (mt-10) REVERT: L 184 ASP cc_start: 0.7133 (m-30) cc_final: 0.6800 (m-30) REVERT: L 225 ARG cc_start: 0.6406 (ttp-170) cc_final: 0.6042 (tmm-80) REVERT: L 246 MET cc_start: 0.6996 (ttp) cc_final: 0.6647 (ttp) REVERT: L 270 THR cc_start: 0.6795 (m) cc_final: 0.5901 (p) REVERT: L 271 GLU cc_start: 0.5561 (tp30) cc_final: 0.5257 (tp30) REVERT: L 365 LYS cc_start: 0.6066 (mmtm) cc_final: 0.5324 (tttm) REVERT: L 409 LYS cc_start: 0.6345 (ttmm) cc_final: 0.5897 (tttt) REVERT: L 418 GLN cc_start: 0.6632 (mm110) cc_final: 0.6410 (mm-40) REVERT: L 436 GLU cc_start: 0.6252 (tp30) cc_final: 0.5106 (pm20) REVERT: L 445 GLN cc_start: 0.6522 (tt0) cc_final: 0.5732 (tp40) REVERT: N 16 GLU cc_start: 0.6384 (tp30) cc_final: 0.5843 (tm-30) REVERT: N 109 ASP cc_start: 0.6815 (t0) cc_final: 0.6248 (t0) REVERT: N 120 GLU cc_start: 0.6206 (pt0) cc_final: 0.5213 (mm-30) REVERT: N 122 GLU cc_start: 0.6549 (mt-10) cc_final: 0.6258 (mt-10) REVERT: N 151 GLU cc_start: 0.6530 (mt-10) cc_final: 0.5707 (mm-30) REVERT: N 155 ASP cc_start: 0.6487 (t0) cc_final: 0.6052 (t70) REVERT: N 168 GLU cc_start: 0.5155 (OUTLIER) cc_final: 0.4107 (tm-30) REVERT: N 365 LYS cc_start: 0.6423 (mmtm) cc_final: 0.5655 (tttm) REVERT: N 409 LYS cc_start: 0.6191 (ttmm) cc_final: 0.5812 (tttt) REVERT: N 421 ASN cc_start: 0.6302 (m-40) cc_final: 0.4945 (t0) REVERT: O 13 LYS cc_start: 0.5980 (ttmm) cc_final: 0.5295 (tttp) REVERT: O 16 GLU cc_start: 0.6690 (tp30) cc_final: 0.6374 (tm-30) REVERT: O 53 MET cc_start: 0.7352 (mtm) cc_final: 0.6911 (mtp) REVERT: O 119 LYS cc_start: 0.6087 (tptp) cc_final: 0.5584 (tttt) REVERT: O 120 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5379 (mm-30) REVERT: O 122 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6443 (mt-10) REVERT: O 128 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6852 (m-30) REVERT: O 151 GLU cc_start: 0.6695 (mt-10) cc_final: 0.5750 (mm-30) REVERT: O 155 ASP cc_start: 0.6563 (t0) cc_final: 0.6058 (t70) REVERT: O 168 GLU cc_start: 0.5022 (OUTLIER) cc_final: 0.4125 (tm-30) REVERT: O 225 ARG cc_start: 0.6322 (ttt180) cc_final: 0.5873 (ttt180) REVERT: O 270 THR cc_start: 0.6722 (m) cc_final: 0.6131 (p) REVERT: O 271 GLU cc_start: 0.5595 (tp30) cc_final: 0.5166 (tp30) REVERT: O 365 LYS cc_start: 0.6350 (tppt) cc_final: 0.5382 (tttm) REVERT: O 388 GLN cc_start: 0.6464 (mt0) cc_final: 0.6053 (mm-40) REVERT: O 408 LYS cc_start: 0.6723 (tttt) cc_final: 0.6439 (ttpp) REVERT: O 409 LYS cc_start: 0.6499 (ttmm) cc_final: 0.5931 (ttmt) REVERT: O 421 ASN cc_start: 0.6024 (m-40) cc_final: 0.4710 (t0) REVERT: O 436 GLU cc_start: 0.6189 (tp30) cc_final: 0.5688 (tp30) REVERT: O 445 GLN cc_start: 0.6537 (tt0) cc_final: 0.5674 (tp40) REVERT: R 16 GLU cc_start: 0.6758 (tp30) cc_final: 0.6274 (tm-30) REVERT: R 52 MET cc_start: 0.7313 (mmm) cc_final: 0.6674 (mmm) REVERT: R 70 MET cc_start: 0.7904 (mtt) cc_final: 0.7655 (mtt) REVERT: R 109 ASP cc_start: 0.6802 (t0) cc_final: 0.6529 (t0) REVERT: R 119 LYS cc_start: 0.6415 (ttpt) cc_final: 0.6041 (tttt) REVERT: R 120 GLU cc_start: 0.6008 (pt0) cc_final: 0.5198 (mm-30) REVERT: R 128 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6663 (m-30) REVERT: R 151 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6516 (mt-10) REVERT: R 168 GLU cc_start: 0.4609 (OUTLIER) cc_final: 0.3979 (tt0) REVERT: R 184 ASP cc_start: 0.7214 (m-30) cc_final: 0.6889 (m-30) REVERT: R 225 ARG cc_start: 0.6340 (ttp-170) cc_final: 0.6072 (ttm170) REVERT: R 246 MET cc_start: 0.6998 (ttp) cc_final: 0.6663 (ttp) REVERT: R 270 THR cc_start: 0.6789 (m) cc_final: 0.5890 (p) REVERT: R 271 GLU cc_start: 0.5640 (tp30) cc_final: 0.5328 (tp30) REVERT: R 365 LYS cc_start: 0.6064 (mmtm) cc_final: 0.5317 (tttm) REVERT: R 409 LYS cc_start: 0.6339 (ttmm) cc_final: 0.5891 (tttt) REVERT: R 418 GLN cc_start: 0.6642 (mm110) cc_final: 0.6420 (mm-40) REVERT: R 428 ASP cc_start: 0.6859 (t70) cc_final: 0.6491 (t0) REVERT: R 445 GLN cc_start: 0.6521 (tt0) cc_final: 0.5749 (tp40) REVERT: S 109 ASP cc_start: 0.6816 (t0) cc_final: 0.6243 (t0) REVERT: S 120 GLU cc_start: 0.6162 (pt0) cc_final: 0.5240 (mm-30) REVERT: S 122 GLU cc_start: 0.6499 (mt-10) cc_final: 0.6237 (mt-10) REVERT: S 128 ASP cc_start: 0.7007 (m-30) cc_final: 0.6777 (m-30) REVERT: S 151 GLU cc_start: 0.6675 (mt-10) cc_final: 0.5766 (mm-30) REVERT: S 155 ASP cc_start: 0.6475 (t0) cc_final: 0.5969 (t70) REVERT: S 168 GLU cc_start: 0.5258 (OUTLIER) cc_final: 0.4127 (tm-30) REVERT: S 225 ARG cc_start: 0.6038 (ttt180) cc_final: 0.5791 (ttm170) REVERT: S 266 GLU cc_start: 0.6004 (OUTLIER) cc_final: 0.5584 (mp0) REVERT: S 365 LYS cc_start: 0.6454 (mmtm) cc_final: 0.5669 (tttm) REVERT: S 409 LYS cc_start: 0.6156 (ttmm) cc_final: 0.5786 (tttt) REVERT: S 421 ASN cc_start: 0.6315 (m-40) cc_final: 0.4971 (t0) REVERT: T 13 LYS cc_start: 0.5834 (ttmm) cc_final: 0.5185 (tttp) REVERT: T 16 GLU cc_start: 0.6714 (tp30) cc_final: 0.6389 (tm-30) REVERT: T 21 ARG cc_start: 0.6305 (mmm-85) cc_final: 0.5665 (mmp-170) REVERT: T 53 MET cc_start: 0.7350 (mtm) cc_final: 0.6911 (mtp) REVERT: T 119 LYS cc_start: 0.6076 (tptp) cc_final: 0.5575 (tttt) REVERT: T 120 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5374 (mm-30) REVERT: T 122 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6436 (mt-10) REVERT: T 128 ASP cc_start: 0.7073 (m-30) cc_final: 0.6850 (m-30) REVERT: T 151 GLU cc_start: 0.6697 (mt-10) cc_final: 0.5754 (mm-30) REVERT: T 155 ASP cc_start: 0.6558 (t0) cc_final: 0.6058 (t70) REVERT: T 225 ARG cc_start: 0.6267 (ttt180) cc_final: 0.5939 (ttt180) REVERT: T 266 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5708 (mp0) REVERT: T 270 THR cc_start: 0.6749 (m) cc_final: 0.6155 (p) REVERT: T 271 GLU cc_start: 0.5602 (tp30) cc_final: 0.5178 (tp30) REVERT: T 365 LYS cc_start: 0.6355 (tppt) cc_final: 0.5386 (tttm) REVERT: T 388 GLN cc_start: 0.6462 (mt0) cc_final: 0.6038 (mm-40) REVERT: T 408 LYS cc_start: 0.6731 (tttt) cc_final: 0.6447 (ttpp) REVERT: T 409 LYS cc_start: 0.6512 (ttmm) cc_final: 0.5942 (ttmt) REVERT: T 421 ASN cc_start: 0.6046 (m-40) cc_final: 0.4749 (t0) REVERT: T 436 GLU cc_start: 0.6181 (tp30) cc_final: 0.5680 (tp30) REVERT: T 445 GLN cc_start: 0.6536 (tt0) cc_final: 0.5678 (tp40) outliers start: 129 outliers final: 53 residues processed: 825 average time/residue: 1.6218 time to fit residues: 1623.2161 Evaluate side-chains 823 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 736 time to evaluate : 5.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 169 ASN Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 436 GLU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 169 ASN Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 330 LEU Chi-restraints excluded: chain O residue 366 VAL Chi-restraints excluded: chain O residue 385 VAL Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 282 LYS Chi-restraints excluded: chain R residue 366 VAL Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 120 GLU Chi-restraints excluded: chain T residue 169 ASN Chi-restraints excluded: chain T residue 266 GLU Chi-restraints excluded: chain T residue 277 THR Chi-restraints excluded: chain T residue 330 LEU Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain T residue 385 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 303 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 323 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 400 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 36 ASN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN C 36 ASN F 36 ASN G 36 ASN ** G 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN G 413 ASN H 36 ASN L 36 ASN L 169 ASN N 36 ASN ** N 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 228 ASN N 413 ASN O 36 ASN R 36 ASN ** R 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 ASN ** S 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 228 ASN S 413 ASN T 36 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 44100 Z= 0.250 Angle : 0.556 6.215 59700 Z= 0.302 Chirality : 0.044 0.156 6444 Planarity : 0.004 0.038 7860 Dihedral : 6.314 57.933 5886 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.16 % Allowed : 14.44 % Favored : 83.40 % 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: 0.26 (0.11), residues: 5316 helix: 1.27 (0.11), residues: 2316 sheet: -1.64 (0.15), residues: 744 loop : -0.21 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 427 HIS 0.006 0.001 HIS H 197 PHE 0.019 0.002 PHE F 287 TYR 0.034 0.002 TYR G 298 ARG 0.004 0.001 ARG W 4 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 727 time to evaluate : 5.669 Fit side-chains REVERT: A 16 GLU cc_start: 0.6745 (tp30) cc_final: 0.6186 (tm-30) REVERT: A 52 MET cc_start: 0.7332 (mmm) cc_final: 0.6808 (mmm) REVERT: A 53 MET cc_start: 0.7272 (mtm) cc_final: 0.6880 (mtp) REVERT: A 119 LYS cc_start: 0.6438 (ttpt) cc_final: 0.6005 (tttt) REVERT: A 120 GLU cc_start: 0.6066 (pt0) cc_final: 0.5243 (mm-30) REVERT: A 122 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6368 (mt-10) REVERT: A 128 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6637 (m-30) REVERT: A 151 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6479 (mt-10) REVERT: A 168 GLU cc_start: 0.4626 (OUTLIER) cc_final: 0.4182 (pp20) REVERT: A 184 ASP cc_start: 0.7238 (m-30) cc_final: 0.6913 (m-30) REVERT: A 225 ARG cc_start: 0.6440 (ttp-170) cc_final: 0.6077 (ttm170) REVERT: A 271 GLU cc_start: 0.5571 (tp30) cc_final: 0.5226 (tp30) REVERT: A 365 LYS cc_start: 0.6095 (mmtm) cc_final: 0.5355 (tttm) REVERT: A 409 LYS cc_start: 0.6236 (ttmm) cc_final: 0.5778 (tttt) REVERT: A 418 GLN cc_start: 0.6641 (mm110) cc_final: 0.6425 (mm-40) REVERT: A 436 GLU cc_start: 0.5622 (OUTLIER) cc_final: 0.5339 (pm20) REVERT: A 445 GLN cc_start: 0.6528 (tt0) cc_final: 0.5788 (tp40) REVERT: B 16 GLU cc_start: 0.6392 (tp30) cc_final: 0.5835 (tm-30) REVERT: B 109 ASP cc_start: 0.6784 (t0) cc_final: 0.6242 (t0) REVERT: B 120 GLU cc_start: 0.6162 (pt0) cc_final: 0.5176 (mm-30) REVERT: B 151 GLU cc_start: 0.6526 (mt-10) cc_final: 0.5706 (mm-30) REVERT: B 155 ASP cc_start: 0.6477 (t0) cc_final: 0.5965 (t70) REVERT: B 365 LYS cc_start: 0.6441 (mmtm) cc_final: 0.5666 (tttm) REVERT: B 409 LYS cc_start: 0.6252 (ttmm) cc_final: 0.5872 (tttt) REVERT: B 421 ASN cc_start: 0.6302 (m-40) cc_final: 0.4947 (t0) REVERT: B 436 GLU cc_start: 0.5858 (OUTLIER) cc_final: 0.5161 (pm20) REVERT: B 445 GLN cc_start: 0.6729 (tt0) cc_final: 0.6504 (tt0) REVERT: C 13 LYS cc_start: 0.6018 (ttmm) cc_final: 0.5338 (tttp) REVERT: C 16 GLU cc_start: 0.6713 (tp30) cc_final: 0.6419 (tm-30) REVERT: C 53 MET cc_start: 0.7355 (mtm) cc_final: 0.6917 (mtp) REVERT: C 119 LYS cc_start: 0.6055 (tptp) cc_final: 0.5558 (tttt) REVERT: C 120 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.5430 (mm-30) REVERT: C 122 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6419 (mt-10) REVERT: C 128 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6851 (m-30) REVERT: C 151 GLU cc_start: 0.6706 (mt-10) cc_final: 0.5762 (mm-30) REVERT: C 155 ASP cc_start: 0.6669 (t0) cc_final: 0.6155 (t70) REVERT: C 225 ARG cc_start: 0.6366 (ttt180) cc_final: 0.6031 (ttt180) REVERT: C 266 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5661 (mp0) REVERT: C 270 THR cc_start: 0.6741 (m) cc_final: 0.6154 (p) REVERT: C 271 GLU cc_start: 0.5574 (tp30) cc_final: 0.5190 (tp30) REVERT: C 327 SER cc_start: 0.6879 (m) cc_final: 0.6665 (t) REVERT: C 365 LYS cc_start: 0.6341 (tppt) cc_final: 0.5385 (tttm) REVERT: C 388 GLN cc_start: 0.6484 (mt0) cc_final: 0.5971 (mm-40) REVERT: C 408 LYS cc_start: 0.6711 (tttt) cc_final: 0.6426 (ttpp) REVERT: C 409 LYS cc_start: 0.6462 (ttmm) cc_final: 0.5827 (ttmm) REVERT: C 421 ASN cc_start: 0.6013 (m-40) cc_final: 0.4723 (t0) REVERT: C 436 GLU cc_start: 0.5799 (OUTLIER) cc_final: 0.5188 (pm20) REVERT: C 445 GLN cc_start: 0.6456 (tt0) cc_final: 0.5636 (tp40) REVERT: F 16 GLU cc_start: 0.6729 (tp30) cc_final: 0.6172 (tm-30) REVERT: F 21 ARG cc_start: 0.6688 (mtp85) cc_final: 0.6389 (mmp-170) REVERT: F 52 MET cc_start: 0.7330 (mmm) cc_final: 0.6806 (mmm) REVERT: F 119 LYS cc_start: 0.6473 (ttpt) cc_final: 0.6047 (tttt) REVERT: F 120 GLU cc_start: 0.6077 (pt0) cc_final: 0.5248 (mm-30) REVERT: F 122 GLU cc_start: 0.6695 (mt-10) cc_final: 0.6406 (mt-10) REVERT: F 128 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6607 (m-30) REVERT: F 151 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6338 (mt-10) REVERT: F 168 GLU cc_start: 0.4565 (OUTLIER) cc_final: 0.3507 (tm-30) REVERT: F 184 ASP cc_start: 0.7200 (m-30) cc_final: 0.6883 (m-30) REVERT: F 225 ARG cc_start: 0.6371 (ttp-170) cc_final: 0.6136 (ttm170) REVERT: F 270 THR cc_start: 0.6771 (m) cc_final: 0.5872 (p) REVERT: F 271 GLU cc_start: 0.5579 (tp30) cc_final: 0.5270 (tp30) REVERT: F 365 LYS cc_start: 0.6090 (mmtm) cc_final: 0.5348 (tttm) REVERT: F 385 VAL cc_start: 0.6583 (OUTLIER) cc_final: 0.6358 (p) REVERT: F 409 LYS cc_start: 0.6223 (ttmm) cc_final: 0.5769 (tttt) REVERT: F 418 GLN cc_start: 0.6633 (mm110) cc_final: 0.6416 (mm-40) REVERT: F 436 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.5344 (pm20) REVERT: F 445 GLN cc_start: 0.6523 (tt0) cc_final: 0.5774 (tp40) REVERT: G 109 ASP cc_start: 0.6788 (t0) cc_final: 0.6247 (t0) REVERT: G 120 GLU cc_start: 0.6207 (pt0) cc_final: 0.5210 (mm-30) REVERT: G 122 GLU cc_start: 0.6571 (mt-10) cc_final: 0.6265 (mt-10) REVERT: G 151 GLU cc_start: 0.6527 (mt-10) cc_final: 0.5704 (mm-30) REVERT: G 155 ASP cc_start: 0.6494 (t0) cc_final: 0.5980 (t70) REVERT: G 168 GLU cc_start: 0.5052 (OUTLIER) cc_final: 0.4470 (tt0) REVERT: G 266 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5601 (mp0) REVERT: G 365 LYS cc_start: 0.6445 (mmtm) cc_final: 0.5670 (tttm) REVERT: G 409 LYS cc_start: 0.6260 (ttmm) cc_final: 0.5880 (tttt) REVERT: G 421 ASN cc_start: 0.6311 (m-40) cc_final: 0.4956 (t0) REVERT: G 436 GLU cc_start: 0.5854 (OUTLIER) cc_final: 0.5252 (pm20) REVERT: H 13 LYS cc_start: 0.6029 (ttmm) cc_final: 0.5352 (tttp) REVERT: H 16 GLU cc_start: 0.6701 (tp30) cc_final: 0.6399 (tm-30) REVERT: H 119 LYS cc_start: 0.6012 (tptp) cc_final: 0.5568 (tttt) REVERT: H 120 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5458 (mm-30) REVERT: H 128 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6858 (m-30) REVERT: H 151 GLU cc_start: 0.6742 (mt-10) cc_final: 0.5788 (mm-30) REVERT: H 155 ASP cc_start: 0.6568 (t0) cc_final: 0.6056 (t70) REVERT: H 225 ARG cc_start: 0.6320 (ttt180) cc_final: 0.6020 (ttt180) REVERT: H 270 THR cc_start: 0.6721 (m) cc_final: 0.6124 (p) REVERT: H 271 GLU cc_start: 0.5572 (tp30) cc_final: 0.5175 (tp30) REVERT: H 327 SER cc_start: 0.6878 (m) cc_final: 0.6653 (t) REVERT: H 365 LYS cc_start: 0.6327 (tppt) cc_final: 0.5383 (tttm) REVERT: H 388 GLN cc_start: 0.6472 (mt0) cc_final: 0.6055 (mm-40) REVERT: H 408 LYS cc_start: 0.6714 (tttt) cc_final: 0.6429 (ttpp) REVERT: H 409 LYS cc_start: 0.6467 (ttmm) cc_final: 0.5831 (ttmm) REVERT: H 421 ASN cc_start: 0.6023 (m-40) cc_final: 0.4734 (t0) REVERT: H 436 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.5197 (pm20) REVERT: H 445 GLN cc_start: 0.6480 (tt0) cc_final: 0.5676 (tp40) REVERT: L 16 GLU cc_start: 0.6713 (tp30) cc_final: 0.6238 (tm-30) REVERT: L 52 MET cc_start: 0.7310 (mmm) cc_final: 0.6675 (mmm) REVERT: L 119 LYS cc_start: 0.6420 (ttpt) cc_final: 0.6030 (tttt) REVERT: L 120 GLU cc_start: 0.6075 (pt0) cc_final: 0.5112 (mm-30) REVERT: L 128 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6615 (m-30) REVERT: L 151 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6345 (mt-10) REVERT: L 184 ASP cc_start: 0.7110 (m-30) cc_final: 0.6775 (m-30) REVERT: L 225 ARG cc_start: 0.6446 (ttp-170) cc_final: 0.6151 (ttm170) REVERT: L 270 THR cc_start: 0.6772 (m) cc_final: 0.5875 (p) REVERT: L 271 GLU cc_start: 0.5552 (tp30) cc_final: 0.5253 (tp30) REVERT: L 365 LYS cc_start: 0.6092 (mmtm) cc_final: 0.5348 (tttm) REVERT: L 409 LYS cc_start: 0.6240 (ttmm) cc_final: 0.5790 (tttt) REVERT: L 418 GLN cc_start: 0.6623 (mm110) cc_final: 0.6407 (mm-40) REVERT: L 436 GLU cc_start: 0.6223 (tp30) cc_final: 0.5096 (pm20) REVERT: L 445 GLN cc_start: 0.6496 (tt0) cc_final: 0.5744 (tp40) REVERT: N 16 GLU cc_start: 0.6384 (tp30) cc_final: 0.5841 (tm-30) REVERT: N 120 GLU cc_start: 0.6172 (pt0) cc_final: 0.5207 (mm-30) REVERT: N 122 GLU cc_start: 0.6542 (mt-10) cc_final: 0.6234 (mt-10) REVERT: N 151 GLU cc_start: 0.6530 (mt-10) cc_final: 0.5709 (mm-30) REVERT: N 155 ASP cc_start: 0.6485 (t0) cc_final: 0.6049 (t70) REVERT: N 168 GLU cc_start: 0.5361 (OUTLIER) cc_final: 0.4383 (tm-30) REVERT: N 365 LYS cc_start: 0.6443 (mmtm) cc_final: 0.5672 (tttm) REVERT: N 409 LYS cc_start: 0.6264 (ttmm) cc_final: 0.5883 (tttt) REVERT: N 421 ASN cc_start: 0.6297 (m-40) cc_final: 0.4940 (t0) REVERT: O 13 LYS cc_start: 0.5971 (ttmm) cc_final: 0.5288 (tttp) REVERT: O 16 GLU cc_start: 0.6680 (tp30) cc_final: 0.6371 (tm-30) REVERT: O 53 MET cc_start: 0.7353 (mtm) cc_final: 0.6914 (mtp) REVERT: O 119 LYS cc_start: 0.6094 (tptp) cc_final: 0.5587 (tttt) REVERT: O 120 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5452 (mm-30) REVERT: O 122 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6432 (mt-10) REVERT: O 128 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6851 (m-30) REVERT: O 151 GLU cc_start: 0.6718 (mt-10) cc_final: 0.5762 (mm-30) REVERT: O 155 ASP cc_start: 0.6557 (t0) cc_final: 0.6050 (t70) REVERT: O 168 GLU cc_start: 0.5002 (OUTLIER) cc_final: 0.4067 (tm-30) REVERT: O 225 ARG cc_start: 0.6334 (ttt180) cc_final: 0.5902 (ttt180) REVERT: O 270 THR cc_start: 0.6720 (m) cc_final: 0.6123 (p) REVERT: O 271 GLU cc_start: 0.5568 (tp30) cc_final: 0.5170 (tp30) REVERT: O 327 SER cc_start: 0.6861 (m) cc_final: 0.6631 (t) REVERT: O 365 LYS cc_start: 0.6325 (tppt) cc_final: 0.5383 (tttm) REVERT: O 388 GLN cc_start: 0.6476 (mt0) cc_final: 0.6060 (mm-40) REVERT: O 408 LYS cc_start: 0.6706 (tttt) cc_final: 0.6421 (ttpp) REVERT: O 409 LYS cc_start: 0.6457 (ttmm) cc_final: 0.5821 (ttmm) REVERT: O 421 ASN cc_start: 0.5986 (m-40) cc_final: 0.4687 (t0) REVERT: O 436 GLU cc_start: 0.6177 (tp30) cc_final: 0.5678 (tp30) REVERT: O 445 GLN cc_start: 0.6481 (tt0) cc_final: 0.5676 (tp40) REVERT: R 16 GLU cc_start: 0.6744 (tp30) cc_final: 0.6266 (tm-30) REVERT: R 52 MET cc_start: 0.7316 (mmm) cc_final: 0.6688 (mmm) REVERT: R 70 MET cc_start: 0.7928 (mtt) cc_final: 0.7683 (mtt) REVERT: R 119 LYS cc_start: 0.6400 (ttpt) cc_final: 0.6017 (tttt) REVERT: R 120 GLU cc_start: 0.6028 (pt0) cc_final: 0.5195 (mm-30) REVERT: R 128 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6707 (m-30) REVERT: R 151 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6479 (mt-10) REVERT: R 184 ASP cc_start: 0.7200 (m-30) cc_final: 0.6878 (m-30) REVERT: R 225 ARG cc_start: 0.6385 (ttp-170) cc_final: 0.6101 (ttm170) REVERT: R 270 THR cc_start: 0.6744 (m) cc_final: 0.5844 (p) REVERT: R 271 GLU cc_start: 0.5625 (tp30) cc_final: 0.5319 (tp30) REVERT: R 365 LYS cc_start: 0.6098 (mmtm) cc_final: 0.5355 (tttm) REVERT: R 409 LYS cc_start: 0.6243 (ttmm) cc_final: 0.5784 (tttt) REVERT: R 418 GLN cc_start: 0.6632 (mm110) cc_final: 0.6416 (mm-40) REVERT: R 428 ASP cc_start: 0.6811 (t70) cc_final: 0.6457 (t0) REVERT: R 445 GLN cc_start: 0.6541 (tt0) cc_final: 0.5806 (tp40) REVERT: S 109 ASP cc_start: 0.6785 (t0) cc_final: 0.6240 (t0) REVERT: S 120 GLU cc_start: 0.6251 (pt0) cc_final: 0.5281 (mm-30) REVERT: S 122 GLU cc_start: 0.6501 (mt-10) cc_final: 0.6245 (mt-10) REVERT: S 128 ASP cc_start: 0.7001 (m-30) cc_final: 0.6769 (m-30) REVERT: S 151 GLU cc_start: 0.6673 (mt-10) cc_final: 0.5768 (mm-30) REVERT: S 155 ASP cc_start: 0.6471 (t0) cc_final: 0.5968 (t70) REVERT: S 168 GLU cc_start: 0.5206 (OUTLIER) cc_final: 0.4102 (tm-30) REVERT: S 225 ARG cc_start: 0.6011 (ttt180) cc_final: 0.5727 (ttt180) REVERT: S 226 LYS cc_start: 0.6761 (OUTLIER) cc_final: 0.6468 (tttt) REVERT: S 266 GLU cc_start: 0.5985 (OUTLIER) cc_final: 0.5589 (mp0) REVERT: S 365 LYS cc_start: 0.6444 (mmtm) cc_final: 0.5670 (tttm) REVERT: S 409 LYS cc_start: 0.6241 (ttmm) cc_final: 0.5861 (tttt) REVERT: S 421 ASN cc_start: 0.6304 (m-40) cc_final: 0.4950 (t0) REVERT: T 13 LYS cc_start: 0.6004 (ttmm) cc_final: 0.5326 (tttp) REVERT: T 16 GLU cc_start: 0.6708 (tp30) cc_final: 0.6397 (tm-30) REVERT: T 21 ARG cc_start: 0.6304 (mmm-85) cc_final: 0.5675 (mmp-170) REVERT: T 53 MET cc_start: 0.7354 (mtm) cc_final: 0.6914 (mtp) REVERT: T 119 LYS cc_start: 0.6082 (tptp) cc_final: 0.5573 (tttt) REVERT: T 120 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5445 (mm-30) REVERT: T 122 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6406 (mt-10) REVERT: T 128 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6841 (m-30) REVERT: T 151 GLU cc_start: 0.6731 (mt-10) cc_final: 0.5771 (mm-30) REVERT: T 155 ASP cc_start: 0.6553 (t0) cc_final: 0.6047 (t70) REVERT: T 225 ARG cc_start: 0.6282 (ttt180) cc_final: 0.5962 (ttt180) REVERT: T 266 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.5720 (mp0) REVERT: T 270 THR cc_start: 0.6710 (m) cc_final: 0.6119 (p) REVERT: T 271 GLU cc_start: 0.5591 (tp30) cc_final: 0.5186 (tp30) REVERT: T 327 SER cc_start: 0.6865 (m) cc_final: 0.6637 (t) REVERT: T 365 LYS cc_start: 0.6330 (tppt) cc_final: 0.5387 (tttm) REVERT: T 388 GLN cc_start: 0.6473 (mt0) cc_final: 0.6044 (mm-40) REVERT: T 408 LYS cc_start: 0.6712 (tttt) cc_final: 0.6427 (ttpp) REVERT: T 409 LYS cc_start: 0.6468 (ttmm) cc_final: 0.5830 (ttmm) REVERT: T 421 ASN cc_start: 0.6016 (m-40) cc_final: 0.4731 (t0) REVERT: T 436 GLU cc_start: 0.6175 (tp30) cc_final: 0.5677 (tp30) REVERT: T 445 GLN cc_start: 0.6481 (tt0) cc_final: 0.5680 (tp40) outliers start: 100 outliers final: 49 residues processed: 793 average time/residue: 1.6467 time to fit residues: 1585.1493 Evaluate side-chains 803 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 724 time to evaluate : 5.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 169 ASN Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 436 GLU Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain L residue 282 LYS Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 169 ASN Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 366 VAL Chi-restraints excluded: chain O residue 385 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 282 LYS Chi-restraints excluded: chain R residue 366 VAL Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain S residue 226 LYS Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 120 GLU Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain T residue 169 ASN Chi-restraints excluded: chain T residue 266 GLU Chi-restraints excluded: chain T residue 277 THR Chi-restraints excluded: chain T residue 385 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 10.0000 chunk 487 optimal weight: 7.9990 chunk 444 optimal weight: 4.9990 chunk 474 optimal weight: 4.9990 chunk 285 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 372 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 428 optimal weight: 6.9990 chunk 448 optimal weight: 0.9980 chunk 472 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 36 ASN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN F 36 ASN G 36 ASN ** G 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 413 ASN H 36 ASN L 36 ASN N 36 ASN ** N 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 413 ASN O 36 ASN R 36 ASN ** R 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 ASN ** S 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 413 ASN T 36 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 44100 Z= 0.262 Angle : 0.566 6.350 59700 Z= 0.308 Chirality : 0.045 0.157 6444 Planarity : 0.004 0.040 7860 Dihedral : 6.347 57.808 5886 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.44 % Allowed : 14.16 % Favored : 83.40 % 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: 0.23 (0.11), residues: 5316 helix: 1.25 (0.11), residues: 2316 sheet: -1.63 (0.15), residues: 744 loop : -0.23 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 427 HIS 0.006 0.001 HIS C 197 PHE 0.020 0.002 PHE H 287 TYR 0.034 0.002 TYR G 298 ARG 0.004 0.001 ARG X 4 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 725 time to evaluate : 4.791 Fit side-chains REVERT: A 16 GLU cc_start: 0.6747 (tp30) cc_final: 0.6190 (tm-30) REVERT: A 52 MET cc_start: 0.7330 (mmm) cc_final: 0.6810 (mmm) REVERT: A 53 MET cc_start: 0.7272 (mtm) cc_final: 0.6878 (mtp) REVERT: A 119 LYS cc_start: 0.6467 (ttpt) cc_final: 0.6036 (tttt) REVERT: A 120 GLU cc_start: 0.6059 (pt0) cc_final: 0.5243 (mm-30) REVERT: A 122 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6366 (mt-10) REVERT: A 128 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6699 (m-30) REVERT: A 151 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6480 (mt-10) REVERT: A 168 GLU cc_start: 0.4651 (OUTLIER) cc_final: 0.4191 (pp20) REVERT: A 184 ASP cc_start: 0.7216 (m-30) cc_final: 0.6891 (m-30) REVERT: A 225 ARG cc_start: 0.6444 (ttp-170) cc_final: 0.6082 (ttm170) REVERT: A 266 GLU cc_start: 0.6040 (OUTLIER) cc_final: 0.5729 (tm-30) REVERT: A 271 GLU cc_start: 0.5568 (tp30) cc_final: 0.5228 (tp30) REVERT: A 365 LYS cc_start: 0.6113 (mmtm) cc_final: 0.5375 (tttm) REVERT: A 385 VAL cc_start: 0.6543 (OUTLIER) cc_final: 0.6317 (p) REVERT: A 409 LYS cc_start: 0.6240 (ttmm) cc_final: 0.5783 (tttt) REVERT: A 418 GLN cc_start: 0.6640 (mm110) cc_final: 0.6425 (mm-40) REVERT: A 436 GLU cc_start: 0.5631 (OUTLIER) cc_final: 0.5344 (pm20) REVERT: A 445 GLN cc_start: 0.6530 (tt0) cc_final: 0.5793 (tp40) REVERT: B 16 GLU cc_start: 0.6395 (tp30) cc_final: 0.5840 (tm-30) REVERT: B 109 ASP cc_start: 0.6790 (t0) cc_final: 0.6253 (t0) REVERT: B 120 GLU cc_start: 0.6209 (pt0) cc_final: 0.5190 (mm-30) REVERT: B 151 GLU cc_start: 0.6530 (mt-10) cc_final: 0.5707 (mm-30) REVERT: B 155 ASP cc_start: 0.6516 (t0) cc_final: 0.6001 (t70) REVERT: B 365 LYS cc_start: 0.6442 (mmtm) cc_final: 0.5667 (tttm) REVERT: B 409 LYS cc_start: 0.6250 (ttmm) cc_final: 0.5871 (tttt) REVERT: B 421 ASN cc_start: 0.6303 (m-40) cc_final: 0.4946 (t0) REVERT: B 436 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5448 (pm20) REVERT: B 445 GLN cc_start: 0.6730 (tt0) cc_final: 0.6506 (tt0) REVERT: C 13 LYS cc_start: 0.6016 (ttmm) cc_final: 0.5337 (tttp) REVERT: C 16 GLU cc_start: 0.6714 (tp30) cc_final: 0.6420 (tm-30) REVERT: C 53 MET cc_start: 0.7355 (mtm) cc_final: 0.6917 (mtp) REVERT: C 119 LYS cc_start: 0.6060 (tptp) cc_final: 0.5560 (tttt) REVERT: C 120 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.5449 (mm-30) REVERT: C 122 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6407 (mt-10) REVERT: C 128 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6854 (m-30) REVERT: C 151 GLU cc_start: 0.6704 (mt-10) cc_final: 0.5764 (mm-30) REVERT: C 155 ASP cc_start: 0.6666 (t0) cc_final: 0.6150 (t70) REVERT: C 168 GLU cc_start: 0.5015 (OUTLIER) cc_final: 0.4116 (tm-30) REVERT: C 225 ARG cc_start: 0.6369 (ttt180) cc_final: 0.6029 (ttt180) REVERT: C 266 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5647 (mp0) REVERT: C 270 THR cc_start: 0.6750 (m) cc_final: 0.6162 (p) REVERT: C 271 GLU cc_start: 0.5560 (tp30) cc_final: 0.5184 (tp30) REVERT: C 327 SER cc_start: 0.6933 (m) cc_final: 0.6686 (t) REVERT: C 365 LYS cc_start: 0.6370 (tppt) cc_final: 0.5396 (tttm) REVERT: C 388 GLN cc_start: 0.6388 (mt0) cc_final: 0.5882 (mm-40) REVERT: C 408 LYS cc_start: 0.6697 (tttt) cc_final: 0.6409 (ttpp) REVERT: C 409 LYS cc_start: 0.6475 (ttmm) cc_final: 0.5841 (ttmm) REVERT: C 421 ASN cc_start: 0.6025 (m-40) cc_final: 0.4742 (t0) REVERT: C 436 GLU cc_start: 0.5818 (OUTLIER) cc_final: 0.5201 (pm20) REVERT: C 445 GLN cc_start: 0.6483 (tt0) cc_final: 0.5653 (tp40) REVERT: F 16 GLU cc_start: 0.6731 (tp30) cc_final: 0.6175 (tm-30) REVERT: F 21 ARG cc_start: 0.6699 (mtp85) cc_final: 0.6400 (mmp-170) REVERT: F 52 MET cc_start: 0.7328 (mmm) cc_final: 0.6810 (mmm) REVERT: F 119 LYS cc_start: 0.6474 (ttpt) cc_final: 0.6048 (tttt) REVERT: F 120 GLU cc_start: 0.6080 (pt0) cc_final: 0.5247 (mm-30) REVERT: F 122 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6405 (mt-10) REVERT: F 128 ASP cc_start: 0.6951 (OUTLIER) cc_final: 0.6655 (m-30) REVERT: F 151 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6338 (mt-10) REVERT: F 168 GLU cc_start: 0.4605 (OUTLIER) cc_final: 0.3540 (tm-30) REVERT: F 184 ASP cc_start: 0.7200 (m-30) cc_final: 0.6882 (m-30) REVERT: F 225 ARG cc_start: 0.6340 (ttp-170) cc_final: 0.6109 (ttm170) REVERT: F 266 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5765 (tm-30) REVERT: F 270 THR cc_start: 0.6756 (m) cc_final: 0.5857 (p) REVERT: F 271 GLU cc_start: 0.5580 (tp30) cc_final: 0.5274 (tp30) REVERT: F 365 LYS cc_start: 0.6091 (mmtm) cc_final: 0.5348 (tttm) REVERT: F 385 VAL cc_start: 0.6532 (OUTLIER) cc_final: 0.6301 (p) REVERT: F 409 LYS cc_start: 0.6227 (ttmm) cc_final: 0.5773 (tttt) REVERT: F 418 GLN cc_start: 0.6632 (mm110) cc_final: 0.6417 (mm-40) REVERT: F 436 GLU cc_start: 0.5681 (OUTLIER) cc_final: 0.5353 (pm20) REVERT: F 445 GLN cc_start: 0.6521 (tt0) cc_final: 0.5774 (tp40) REVERT: G 109 ASP cc_start: 0.6793 (t0) cc_final: 0.6255 (t0) REVERT: G 120 GLU cc_start: 0.6228 (pt0) cc_final: 0.5203 (mm-30) REVERT: G 122 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6271 (mt-10) REVERT: G 151 GLU cc_start: 0.6528 (mt-10) cc_final: 0.5705 (mm-30) REVERT: G 155 ASP cc_start: 0.6505 (t0) cc_final: 0.5990 (t70) REVERT: G 168 GLU cc_start: 0.4953 (OUTLIER) cc_final: 0.4329 (tt0) REVERT: G 266 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.5600 (mp0) REVERT: G 365 LYS cc_start: 0.6445 (mmtm) cc_final: 0.5671 (tttm) REVERT: G 409 LYS cc_start: 0.6240 (ttmm) cc_final: 0.5861 (tttt) REVERT: G 421 ASN cc_start: 0.6313 (m-40) cc_final: 0.4955 (t0) REVERT: G 436 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.5308 (pm20) REVERT: H 13 LYS cc_start: 0.6032 (ttmm) cc_final: 0.5349 (tttp) REVERT: H 16 GLU cc_start: 0.6702 (tp30) cc_final: 0.6400 (tm-30) REVERT: H 119 LYS cc_start: 0.6024 (tptp) cc_final: 0.5569 (tttt) REVERT: H 120 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5461 (mm-30) REVERT: H 128 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6858 (m-30) REVERT: H 151 GLU cc_start: 0.6761 (mt-10) cc_final: 0.5798 (mm-30) REVERT: H 155 ASP cc_start: 0.6588 (t0) cc_final: 0.6079 (t70) REVERT: H 225 ARG cc_start: 0.6304 (ttt180) cc_final: 0.5992 (ttt180) REVERT: H 270 THR cc_start: 0.6730 (m) cc_final: 0.6132 (p) REVERT: H 271 GLU cc_start: 0.5568 (tp30) cc_final: 0.5179 (tp30) REVERT: H 327 SER cc_start: 0.6896 (m) cc_final: 0.6662 (t) REVERT: H 365 LYS cc_start: 0.6372 (tppt) cc_final: 0.5397 (tttm) REVERT: H 388 GLN cc_start: 0.6470 (mt0) cc_final: 0.6056 (mm-40) REVERT: H 408 LYS cc_start: 0.6700 (tttt) cc_final: 0.6411 (ttpp) REVERT: H 409 LYS cc_start: 0.6476 (ttmm) cc_final: 0.5846 (ttmm) REVERT: H 421 ASN cc_start: 0.6035 (m-40) cc_final: 0.4752 (t0) REVERT: H 436 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5239 (pm20) REVERT: H 445 GLN cc_start: 0.6490 (tt0) cc_final: 0.5693 (tp40) REVERT: L 16 GLU cc_start: 0.6715 (tp30) cc_final: 0.6243 (tm-30) REVERT: L 52 MET cc_start: 0.7313 (mmm) cc_final: 0.6676 (mmm) REVERT: L 119 LYS cc_start: 0.6416 (ttpt) cc_final: 0.6030 (tttt) REVERT: L 120 GLU cc_start: 0.6057 (pt0) cc_final: 0.5175 (mm-30) REVERT: L 128 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6627 (m-30) REVERT: L 151 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6343 (mt-10) REVERT: L 184 ASP cc_start: 0.7145 (m-30) cc_final: 0.6813 (m-30) REVERT: L 225 ARG cc_start: 0.6429 (ttp-170) cc_final: 0.6140 (ttm170) REVERT: L 266 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.5731 (tm-30) REVERT: L 270 THR cc_start: 0.6758 (m) cc_final: 0.5860 (p) REVERT: L 271 GLU cc_start: 0.5553 (tp30) cc_final: 0.5257 (tp30) REVERT: L 365 LYS cc_start: 0.6092 (mmtm) cc_final: 0.5347 (tttm) REVERT: L 385 VAL cc_start: 0.6555 (OUTLIER) cc_final: 0.6319 (p) REVERT: L 409 LYS cc_start: 0.6243 (ttmm) cc_final: 0.5793 (tttt) REVERT: L 418 GLN cc_start: 0.6621 (mm110) cc_final: 0.6406 (mm-40) REVERT: L 436 GLU cc_start: 0.6224 (tp30) cc_final: 0.5106 (pm20) REVERT: L 445 GLN cc_start: 0.6500 (tt0) cc_final: 0.5747 (tp40) REVERT: N 16 GLU cc_start: 0.6392 (tp30) cc_final: 0.5851 (tm-30) REVERT: N 120 GLU cc_start: 0.6172 (pt0) cc_final: 0.5208 (mm-30) REVERT: N 122 GLU cc_start: 0.6553 (mt-10) cc_final: 0.6249 (mt-10) REVERT: N 151 GLU cc_start: 0.6532 (mt-10) cc_final: 0.5710 (mm-30) REVERT: N 155 ASP cc_start: 0.6486 (t0) cc_final: 0.6049 (t70) REVERT: N 168 GLU cc_start: 0.5367 (OUTLIER) cc_final: 0.4374 (tm-30) REVERT: N 365 LYS cc_start: 0.6445 (mmtm) cc_final: 0.5673 (tttm) REVERT: N 409 LYS cc_start: 0.6243 (ttmm) cc_final: 0.5864 (tttt) REVERT: N 421 ASN cc_start: 0.6299 (m-40) cc_final: 0.4940 (t0) REVERT: O 13 LYS cc_start: 0.5971 (ttmm) cc_final: 0.5289 (tttp) REVERT: O 16 GLU cc_start: 0.6682 (tp30) cc_final: 0.6374 (tm-30) REVERT: O 53 MET cc_start: 0.7352 (mtm) cc_final: 0.6913 (mtp) REVERT: O 119 LYS cc_start: 0.6098 (tptp) cc_final: 0.5589 (tttt) REVERT: O 120 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5473 (mm-30) REVERT: O 122 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6421 (mt-10) REVERT: O 128 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6848 (m-30) REVERT: O 151 GLU cc_start: 0.6729 (mt-10) cc_final: 0.5761 (mm-30) REVERT: O 155 ASP cc_start: 0.6605 (t0) cc_final: 0.6092 (t70) REVERT: O 168 GLU cc_start: 0.5010 (OUTLIER) cc_final: 0.4098 (tm-30) REVERT: O 225 ARG cc_start: 0.6335 (ttt180) cc_final: 0.5891 (ttt180) REVERT: O 270 THR cc_start: 0.6728 (m) cc_final: 0.6130 (p) REVERT: O 271 GLU cc_start: 0.5564 (tp30) cc_final: 0.5175 (tp30) REVERT: O 327 SER cc_start: 0.6910 (m) cc_final: 0.6649 (t) REVERT: O 365 LYS cc_start: 0.6370 (tppt) cc_final: 0.5397 (tttm) REVERT: O 388 GLN cc_start: 0.6473 (mt0) cc_final: 0.6060 (mm-40) REVERT: O 408 LYS cc_start: 0.6692 (tttt) cc_final: 0.6403 (ttpp) REVERT: O 409 LYS cc_start: 0.6464 (ttmm) cc_final: 0.5834 (ttmm) REVERT: O 421 ASN cc_start: 0.6022 (m-40) cc_final: 0.4739 (t0) REVERT: O 436 GLU cc_start: 0.6169 (tp30) cc_final: 0.5677 (tp30) REVERT: O 445 GLN cc_start: 0.6490 (tt0) cc_final: 0.5691 (tp40) REVERT: R 16 GLU cc_start: 0.6747 (tp30) cc_final: 0.6189 (tm-30) REVERT: R 52 MET cc_start: 0.7315 (mmm) cc_final: 0.6689 (mmm) REVERT: R 70 MET cc_start: 0.7902 (mtt) cc_final: 0.7661 (mtt) REVERT: R 119 LYS cc_start: 0.6404 (ttpt) cc_final: 0.6010 (tttt) REVERT: R 120 GLU cc_start: 0.6035 (pt0) cc_final: 0.5200 (mm-30) REVERT: R 128 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6689 (m-30) REVERT: R 151 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6479 (mt-10) REVERT: R 168 GLU cc_start: 0.4473 (OUTLIER) cc_final: 0.3992 (tt0) REVERT: R 184 ASP cc_start: 0.7201 (m-30) cc_final: 0.6856 (m-30) REVERT: R 225 ARG cc_start: 0.6406 (ttp-170) cc_final: 0.6128 (ttm170) REVERT: R 266 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.5730 (tm-30) REVERT: R 270 THR cc_start: 0.6748 (m) cc_final: 0.5844 (p) REVERT: R 271 GLU cc_start: 0.5624 (tp30) cc_final: 0.5321 (tp30) REVERT: R 365 LYS cc_start: 0.6098 (mmtm) cc_final: 0.5354 (tttm) REVERT: R 409 LYS cc_start: 0.6233 (ttmm) cc_final: 0.5771 (tttt) REVERT: R 418 GLN cc_start: 0.6631 (mm110) cc_final: 0.6415 (mm-40) REVERT: R 428 ASP cc_start: 0.6839 (t70) cc_final: 0.6481 (t0) REVERT: R 436 GLU cc_start: 0.6235 (tp30) cc_final: 0.5123 (pm20) REVERT: R 445 GLN cc_start: 0.6543 (tt0) cc_final: 0.5811 (tp40) REVERT: S 109 ASP cc_start: 0.6790 (t0) cc_final: 0.6249 (t0) REVERT: S 120 GLU cc_start: 0.6270 (pt0) cc_final: 0.5273 (mm-30) REVERT: S 122 GLU cc_start: 0.6486 (mt-10) cc_final: 0.6232 (mt-10) REVERT: S 128 ASP cc_start: 0.7002 (m-30) cc_final: 0.6770 (m-30) REVERT: S 151 GLU cc_start: 0.6673 (mt-10) cc_final: 0.5768 (mm-30) REVERT: S 155 ASP cc_start: 0.6500 (t0) cc_final: 0.5988 (t70) REVERT: S 168 GLU cc_start: 0.5198 (OUTLIER) cc_final: 0.4117 (tm-30) REVERT: S 225 ARG cc_start: 0.6011 (ttt180) cc_final: 0.5721 (ttt180) REVERT: S 226 LYS cc_start: 0.6765 (OUTLIER) cc_final: 0.6471 (tttt) REVERT: S 266 GLU cc_start: 0.5954 (OUTLIER) cc_final: 0.5576 (mp0) REVERT: S 365 LYS cc_start: 0.6444 (mmtm) cc_final: 0.5669 (tttm) REVERT: S 409 LYS cc_start: 0.6241 (ttmm) cc_final: 0.5862 (tttt) REVERT: S 421 ASN cc_start: 0.6306 (m-40) cc_final: 0.4951 (t0) REVERT: T 13 LYS cc_start: 0.6003 (ttmm) cc_final: 0.5326 (tttp) REVERT: T 16 GLU cc_start: 0.6709 (tp30) cc_final: 0.6396 (tm-30) REVERT: T 21 ARG cc_start: 0.6298 (mmm-85) cc_final: 0.5660 (mmp-170) REVERT: T 53 MET cc_start: 0.7354 (mtm) cc_final: 0.6913 (mtp) REVERT: T 119 LYS cc_start: 0.6086 (tptp) cc_final: 0.5577 (tttt) REVERT: T 120 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5466 (mm-30) REVERT: T 122 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6415 (mt-10) REVERT: T 128 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.6845 (m-30) REVERT: T 151 GLU cc_start: 0.6729 (mt-10) cc_final: 0.5774 (mm-30) REVERT: T 155 ASP cc_start: 0.6598 (t0) cc_final: 0.6087 (t70) REVERT: T 225 ARG cc_start: 0.6297 (ttt180) cc_final: 0.5972 (ttt180) REVERT: T 266 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.5709 (mp0) REVERT: T 270 THR cc_start: 0.6720 (m) cc_final: 0.6126 (p) REVERT: T 271 GLU cc_start: 0.5587 (tp30) cc_final: 0.5191 (tp30) REVERT: T 327 SER cc_start: 0.6914 (m) cc_final: 0.6658 (t) REVERT: T 365 LYS cc_start: 0.6375 (tppt) cc_final: 0.5401 (tttm) REVERT: T 388 GLN cc_start: 0.6469 (mt0) cc_final: 0.6043 (mm-40) REVERT: T 408 LYS cc_start: 0.6699 (tttt) cc_final: 0.6411 (ttpp) REVERT: T 409 LYS cc_start: 0.6480 (ttmm) cc_final: 0.5845 (ttmm) REVERT: T 421 ASN cc_start: 0.5996 (m-40) cc_final: 0.4702 (t0) REVERT: T 436 GLU cc_start: 0.6171 (tp30) cc_final: 0.5675 (tp30) REVERT: T 445 GLN cc_start: 0.6491 (tt0) cc_final: 0.5696 (tp40) outliers start: 113 outliers final: 55 residues processed: 801 average time/residue: 1.6559 time to fit residues: 1610.9534 Evaluate side-chains 818 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 725 time to evaluate : 4.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 169 ASN Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 436 GLU Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 266 GLU Chi-restraints excluded: chain L residue 282 LYS Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain L residue 385 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain O residue 128 ASP Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 169 ASN Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 366 VAL Chi-restraints excluded: chain O residue 385 VAL Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 266 GLU Chi-restraints excluded: chain R residue 282 LYS Chi-restraints excluded: chain R residue 366 VAL Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 168 GLU Chi-restraints excluded: chain S residue 226 LYS Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 120 GLU Chi-restraints excluded: chain T residue 128 ASP Chi-restraints excluded: chain T residue 169 ASN Chi-restraints excluded: chain T residue 266 GLU Chi-restraints excluded: chain T residue 277 THR Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain T residue 385 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 8.9990 chunk 501 optimal weight: 7.9990 chunk 306 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 348 optimal weight: 6.9990 chunk 526 optimal weight: 5.9990 chunk 484 optimal weight: 9.9990 chunk 418 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 323 optimal weight: 2.9990 chunk 256 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 36 ASN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN C 228 ASN F 36 ASN G 36 ASN G 413 ASN H 36 ASN H 228 ASN L 36 ASN N 36 ASN N 413 ASN O 36 ASN O 228 ASN R 36 ASN S 36 ASN S 413 ASN T 36 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 44100 Z= 0.419 Angle : 0.708 8.577 59700 Z= 0.385 Chirality : 0.052 0.235 6444 Planarity : 0.006 0.052 7860 Dihedral : 6.719 58.821 5886 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.46 % Allowed : 14.16 % Favored : 83.38 % 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: -0.07 (0.11), residues: 5316 helix: 0.98 (0.11), residues: 2280 sheet: -1.75 (0.15), residues: 744 loop : -0.37 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 427 HIS 0.007 0.002 HIS H 197 PHE 0.027 0.003 PHE C 287 TYR 0.042 0.004 TYR G 298 ARG 0.008 0.001 ARG W 4 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 715 time to evaluate : 4.713 Fit side-chains REVERT: A 16 GLU cc_start: 0.6692 (tp30) cc_final: 0.6238 (tm-30) REVERT: A 52 MET cc_start: 0.7318 (mmm) cc_final: 0.6814 (mmm) REVERT: A 119 LYS cc_start: 0.6422 (ttpt) cc_final: 0.6040 (tttt) REVERT: A 120 GLU cc_start: 0.6019 (pt0) cc_final: 0.5160 (mm-30) REVERT: A 128 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6700 (m-30) REVERT: A 151 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6493 (mt-10) REVERT: A 168 GLU cc_start: 0.4804 (OUTLIER) cc_final: 0.4125 (pp20) REVERT: A 184 ASP cc_start: 0.7220 (m-30) cc_final: 0.6887 (m-30) REVERT: A 225 ARG cc_start: 0.6384 (ttp-170) cc_final: 0.6137 (ttm170) REVERT: A 266 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.5750 (tm-30) REVERT: A 282 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6573 (tttm) REVERT: A 365 LYS cc_start: 0.6094 (mmtm) cc_final: 0.5351 (tttm) REVERT: A 385 VAL cc_start: 0.6464 (OUTLIER) cc_final: 0.6247 (p) REVERT: A 409 LYS cc_start: 0.6307 (ttmm) cc_final: 0.5884 (tttt) REVERT: A 418 GLN cc_start: 0.6667 (mm110) cc_final: 0.6452 (mm-40) REVERT: A 436 GLU cc_start: 0.5751 (OUTLIER) cc_final: 0.5378 (pm20) REVERT: A 445 GLN cc_start: 0.6513 (tt0) cc_final: 0.5792 (tp40) REVERT: B 16 GLU cc_start: 0.6401 (tp30) cc_final: 0.5865 (tm-30) REVERT: B 109 ASP cc_start: 0.6806 (t0) cc_final: 0.6222 (t0) REVERT: B 120 GLU cc_start: 0.6211 (pt0) cc_final: 0.5170 (mm-30) REVERT: B 151 GLU cc_start: 0.6549 (mt-10) cc_final: 0.5716 (mm-30) REVERT: B 155 ASP cc_start: 0.6518 (t0) cc_final: 0.6012 (t70) REVERT: B 365 LYS cc_start: 0.6467 (mmtm) cc_final: 0.5692 (tttm) REVERT: B 409 LYS cc_start: 0.6232 (ttmm) cc_final: 0.5818 (tttt) REVERT: B 421 ASN cc_start: 0.6324 (m-40) cc_final: 0.5051 (t0) REVERT: B 436 GLU cc_start: 0.5998 (OUTLIER) cc_final: 0.5422 (pm20) REVERT: B 445 GLN cc_start: 0.6733 (tt0) cc_final: 0.6521 (tt0) REVERT: C 13 LYS cc_start: 0.6001 (ttmm) cc_final: 0.5374 (tttp) REVERT: C 16 GLU cc_start: 0.6721 (tp30) cc_final: 0.6417 (tm-30) REVERT: C 119 LYS cc_start: 0.6067 (tptp) cc_final: 0.5547 (tttt) REVERT: C 120 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5372 (mm-30) REVERT: C 122 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6470 (mt-10) REVERT: C 128 ASP cc_start: 0.7109 (m-30) cc_final: 0.6887 (m-30) REVERT: C 151 GLU cc_start: 0.6713 (mt-10) cc_final: 0.5739 (mm-30) REVERT: C 155 ASP cc_start: 0.6663 (t0) cc_final: 0.6141 (t70) REVERT: C 225 ARG cc_start: 0.6447 (ttt180) cc_final: 0.6082 (ttt180) REVERT: C 266 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5691 (mp0) REVERT: C 270 THR cc_start: 0.6809 (m) cc_final: 0.6218 (p) REVERT: C 271 GLU cc_start: 0.5602 (tp30) cc_final: 0.5244 (tp30) REVERT: C 365 LYS cc_start: 0.6375 (tppt) cc_final: 0.5398 (tttm) REVERT: C 388 GLN cc_start: 0.6376 (mt0) cc_final: 0.5891 (mm-40) REVERT: C 408 LYS cc_start: 0.6698 (tttt) cc_final: 0.6403 (ttpp) REVERT: C 409 LYS cc_start: 0.6561 (ttmm) cc_final: 0.5930 (ttmm) REVERT: C 421 ASN cc_start: 0.6058 (m-40) cc_final: 0.4735 (t0) REVERT: C 436 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5410 (pm20) REVERT: C 445 GLN cc_start: 0.6552 (tt0) cc_final: 0.5734 (tp40) REVERT: F 16 GLU cc_start: 0.6695 (tp30) cc_final: 0.6240 (tm-30) REVERT: F 21 ARG cc_start: 0.6723 (mtp85) cc_final: 0.6394 (mmp-170) REVERT: F 52 MET cc_start: 0.7284 (mmm) cc_final: 0.6775 (mmm) REVERT: F 119 LYS cc_start: 0.6422 (ttpt) cc_final: 0.6038 (tttt) REVERT: F 120 GLU cc_start: 0.6123 (pt0) cc_final: 0.5225 (mm-30) REVERT: F 128 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6677 (m-30) REVERT: F 151 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6380 (mt-10) REVERT: F 168 GLU cc_start: 0.4725 (OUTLIER) cc_final: 0.3630 (tm-30) REVERT: F 184 ASP cc_start: 0.7250 (m-30) cc_final: 0.6914 (m-30) REVERT: F 225 ARG cc_start: 0.6313 (ttp-170) cc_final: 0.6057 (ttm170) REVERT: F 266 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.5913 (tm-30) REVERT: F 270 THR cc_start: 0.6839 (m) cc_final: 0.5954 (p) REVERT: F 271 GLU cc_start: 0.5608 (tp30) cc_final: 0.5301 (tp30) REVERT: F 282 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6578 (tttm) REVERT: F 365 LYS cc_start: 0.6088 (mmtm) cc_final: 0.5348 (tttm) REVERT: F 409 LYS cc_start: 0.6300 (ttmm) cc_final: 0.5876 (tttt) REVERT: F 418 GLN cc_start: 0.6659 (mm110) cc_final: 0.6443 (mm-40) REVERT: F 436 GLU cc_start: 0.5768 (OUTLIER) cc_final: 0.5305 (pm20) REVERT: F 445 GLN cc_start: 0.6525 (tt0) cc_final: 0.5800 (tp40) REVERT: G 109 ASP cc_start: 0.6808 (t0) cc_final: 0.6224 (t0) REVERT: G 120 GLU cc_start: 0.6274 (pt0) cc_final: 0.5202 (mm-30) REVERT: G 122 GLU cc_start: 0.6593 (mt-10) cc_final: 0.6316 (mt-10) REVERT: G 151 GLU cc_start: 0.6550 (mt-10) cc_final: 0.5717 (mm-30) REVERT: G 155 ASP cc_start: 0.6507 (t0) cc_final: 0.6001 (t70) REVERT: G 168 GLU cc_start: 0.5191 (OUTLIER) cc_final: 0.4185 (tt0) REVERT: G 266 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5618 (mp0) REVERT: G 365 LYS cc_start: 0.6471 (mmtm) cc_final: 0.5692 (tttm) REVERT: G 409 LYS cc_start: 0.6243 (ttmm) cc_final: 0.5834 (tttt) REVERT: G 421 ASN cc_start: 0.6333 (m-40) cc_final: 0.5059 (t0) REVERT: G 428 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6721 (t70) REVERT: G 436 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5347 (pm20) REVERT: H 13 LYS cc_start: 0.6012 (ttmm) cc_final: 0.5384 (tttp) REVERT: H 16 GLU cc_start: 0.6723 (tp30) cc_final: 0.6414 (tm-30) REVERT: H 119 LYS cc_start: 0.6024 (tptp) cc_final: 0.5533 (tttt) REVERT: H 120 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5319 (mm-30) REVERT: H 128 ASP cc_start: 0.7107 (m-30) cc_final: 0.6888 (m-30) REVERT: H 151 GLU cc_start: 0.6750 (mt-10) cc_final: 0.5800 (mm-30) REVERT: H 155 ASP cc_start: 0.6666 (t0) cc_final: 0.6176 (t70) REVERT: H 168 GLU cc_start: 0.5005 (OUTLIER) cc_final: 0.4424 (tm-30) REVERT: H 225 ARG cc_start: 0.6435 (ttt180) cc_final: 0.6161 (ttt180) REVERT: H 270 THR cc_start: 0.6782 (m) cc_final: 0.6191 (p) REVERT: H 271 GLU cc_start: 0.5562 (tp30) cc_final: 0.5181 (tp30) REVERT: H 365 LYS cc_start: 0.6378 (tppt) cc_final: 0.5401 (tttm) REVERT: H 388 GLN cc_start: 0.6461 (mt0) cc_final: 0.6067 (mm-40) REVERT: H 408 LYS cc_start: 0.6707 (tttt) cc_final: 0.6414 (ttpp) REVERT: H 409 LYS cc_start: 0.6565 (ttmm) cc_final: 0.5934 (ttmm) REVERT: H 421 ASN cc_start: 0.6068 (m-40) cc_final: 0.4745 (t0) REVERT: H 436 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5400 (pm20) REVERT: H 445 GLN cc_start: 0.6562 (tt0) cc_final: 0.5753 (tp40) REVERT: L 16 GLU cc_start: 0.6698 (tp30) cc_final: 0.6249 (tm-30) REVERT: L 52 MET cc_start: 0.7301 (mmm) cc_final: 0.6842 (mmm) REVERT: L 119 LYS cc_start: 0.6422 (ttpt) cc_final: 0.6043 (tttt) REVERT: L 120 GLU cc_start: 0.6046 (pt0) cc_final: 0.5134 (mm-30) REVERT: L 128 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6686 (m-30) REVERT: L 151 GLU cc_start: 0.6687 (mt-10) cc_final: 0.6399 (mt-10) REVERT: L 184 ASP cc_start: 0.7130 (m-30) cc_final: 0.6784 (m-30) REVERT: L 225 ARG cc_start: 0.6388 (ttp-170) cc_final: 0.6018 (ttm170) REVERT: L 266 GLU cc_start: 0.6163 (OUTLIER) cc_final: 0.5824 (tm-30) REVERT: L 270 THR cc_start: 0.6833 (m) cc_final: 0.5950 (p) REVERT: L 271 GLU cc_start: 0.5578 (tp30) cc_final: 0.5318 (tp30) REVERT: L 282 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6599 (tttm) REVERT: L 365 LYS cc_start: 0.6091 (mmtm) cc_final: 0.5347 (tttm) REVERT: L 409 LYS cc_start: 0.6294 (ttmm) cc_final: 0.5872 (tttt) REVERT: L 418 GLN cc_start: 0.6649 (mm110) cc_final: 0.6434 (mm-40) REVERT: L 436 GLU cc_start: 0.6246 (tp30) cc_final: 0.5141 (pm20) REVERT: L 445 GLN cc_start: 0.6502 (tt0) cc_final: 0.5769 (tp40) REVERT: N 16 GLU cc_start: 0.6405 (tp30) cc_final: 0.5880 (tm-30) REVERT: N 109 ASP cc_start: 0.6804 (t0) cc_final: 0.6223 (t0) REVERT: N 120 GLU cc_start: 0.6176 (pt0) cc_final: 0.5176 (mm-30) REVERT: N 122 GLU cc_start: 0.6574 (mt-10) cc_final: 0.6295 (mt-10) REVERT: N 151 GLU cc_start: 0.6552 (mt-10) cc_final: 0.5720 (mm-30) REVERT: N 155 ASP cc_start: 0.6469 (t0) cc_final: 0.6026 (t70) REVERT: N 168 GLU cc_start: 0.5436 (OUTLIER) cc_final: 0.4463 (tm-30) REVERT: N 365 LYS cc_start: 0.6473 (mmtm) cc_final: 0.5698 (tttm) REVERT: N 409 LYS cc_start: 0.6236 (ttmm) cc_final: 0.5831 (tttt) REVERT: N 421 ASN cc_start: 0.6319 (m-40) cc_final: 0.5044 (t0) REVERT: O 13 LYS cc_start: 0.5961 (ttmm) cc_final: 0.5301 (tttp) REVERT: O 16 GLU cc_start: 0.6680 (tp30) cc_final: 0.6372 (tm-30) REVERT: O 119 LYS cc_start: 0.6093 (tptp) cc_final: 0.5575 (tttt) REVERT: O 120 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5346 (mm-30) REVERT: O 122 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6486 (mt-10) REVERT: O 128 ASP cc_start: 0.7100 (m-30) cc_final: 0.6879 (m-30) REVERT: O 151 GLU cc_start: 0.6721 (mt-10) cc_final: 0.5750 (mm-30) REVERT: O 155 ASP cc_start: 0.6657 (t0) cc_final: 0.6170 (t70) REVERT: O 168 GLU cc_start: 0.5114 (OUTLIER) cc_final: 0.4187 (tm-30) REVERT: O 225 ARG cc_start: 0.6447 (ttt180) cc_final: 0.6103 (ttt180) REVERT: O 270 THR cc_start: 0.6781 (m) cc_final: 0.6189 (p) REVERT: O 271 GLU cc_start: 0.5556 (tp30) cc_final: 0.5175 (tp30) REVERT: O 365 LYS cc_start: 0.6377 (tppt) cc_final: 0.5401 (tttm) REVERT: O 388 GLN cc_start: 0.6462 (mt0) cc_final: 0.6070 (mm-40) REVERT: O 408 LYS cc_start: 0.6692 (tttt) cc_final: 0.6397 (ttpp) REVERT: O 409 LYS cc_start: 0.6555 (ttmm) cc_final: 0.5924 (ttmm) REVERT: O 421 ASN cc_start: 0.6055 (m-40) cc_final: 0.4732 (t0) REVERT: O 436 GLU cc_start: 0.6141 (tp30) cc_final: 0.5062 (pm20) REVERT: O 445 GLN cc_start: 0.6560 (tt0) cc_final: 0.5751 (tp40) REVERT: R 16 GLU cc_start: 0.6690 (tp30) cc_final: 0.6236 (tm-30) REVERT: R 52 MET cc_start: 0.7265 (mmm) cc_final: 0.6630 (mmm) REVERT: R 70 MET cc_start: 0.7912 (mtt) cc_final: 0.7682 (mtt) REVERT: R 119 LYS cc_start: 0.6405 (ttpt) cc_final: 0.6018 (tttt) REVERT: R 120 GLU cc_start: 0.5994 (pt0) cc_final: 0.5163 (mm-30) REVERT: R 128 ASP cc_start: 0.7026 (OUTLIER) cc_final: 0.6720 (m-30) REVERT: R 151 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6505 (mt-10) REVERT: R 168 GLU cc_start: 0.4721 (OUTLIER) cc_final: 0.3931 (tt0) REVERT: R 184 ASP cc_start: 0.7249 (m-30) cc_final: 0.6910 (m-30) REVERT: R 225 ARG cc_start: 0.6325 (ttp-170) cc_final: 0.6053 (ttm170) REVERT: R 266 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5809 (tm-30) REVERT: R 270 THR cc_start: 0.6855 (m) cc_final: 0.5964 (p) REVERT: R 271 GLU cc_start: 0.5564 (tp30) cc_final: 0.5260 (tp30) REVERT: R 282 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6627 (tttm) REVERT: R 365 LYS cc_start: 0.6098 (mmtm) cc_final: 0.5356 (tttm) REVERT: R 409 LYS cc_start: 0.6285 (ttmm) cc_final: 0.5860 (tttt) REVERT: R 418 GLN cc_start: 0.6658 (mm110) cc_final: 0.6443 (mm-40) REVERT: R 436 GLU cc_start: 0.6266 (tp30) cc_final: 0.5135 (pm20) REVERT: R 445 GLN cc_start: 0.6527 (tt0) cc_final: 0.5812 (tp40) REVERT: S 109 ASP cc_start: 0.6802 (t0) cc_final: 0.6215 (t0) REVERT: S 120 GLU cc_start: 0.6284 (pt0) cc_final: 0.5249 (mm-30) REVERT: S 122 GLU cc_start: 0.6536 (mt-10) cc_final: 0.6273 (mt-10) REVERT: S 128 ASP cc_start: 0.7029 (m-30) cc_final: 0.6792 (m-30) REVERT: S 151 GLU cc_start: 0.6681 (mt-10) cc_final: 0.5773 (mm-30) REVERT: S 155 ASP cc_start: 0.6500 (t0) cc_final: 0.6003 (t70) REVERT: S 226 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6599 (tttt) REVERT: S 266 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5592 (mp0) REVERT: S 365 LYS cc_start: 0.6467 (mmtm) cc_final: 0.5691 (tttm) REVERT: S 409 LYS cc_start: 0.6209 (ttmm) cc_final: 0.5799 (tttt) REVERT: S 421 ASN cc_start: 0.6327 (m-40) cc_final: 0.5054 (t0) REVERT: S 443 MET cc_start: 0.6752 (tpp) cc_final: 0.6381 (tpp) REVERT: T 13 LYS cc_start: 0.5989 (ttmm) cc_final: 0.5364 (tttp) REVERT: T 16 GLU cc_start: 0.6716 (tp30) cc_final: 0.6407 (tm-30) REVERT: T 21 ARG cc_start: 0.6273 (mmm-85) cc_final: 0.5644 (mmp-170) REVERT: T 119 LYS cc_start: 0.6081 (tptp) cc_final: 0.5564 (tttt) REVERT: T 120 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.5391 (mm-30) REVERT: T 122 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6479 (mt-10) REVERT: T 128 ASP cc_start: 0.7101 (m-30) cc_final: 0.6878 (m-30) REVERT: T 151 GLU cc_start: 0.6719 (mt-10) cc_final: 0.5759 (mm-30) REVERT: T 155 ASP cc_start: 0.6603 (t0) cc_final: 0.6141 (t70) REVERT: T 225 ARG cc_start: 0.6351 (ttt180) cc_final: 0.6126 (ttm170) REVERT: T 266 GLU cc_start: 0.6101 (OUTLIER) cc_final: 0.5682 (mp0) REVERT: T 270 THR cc_start: 0.6774 (m) cc_final: 0.6179 (p) REVERT: T 271 GLU cc_start: 0.5567 (tp30) cc_final: 0.5170 (tp30) REVERT: T 365 LYS cc_start: 0.6381 (tppt) cc_final: 0.5405 (tttm) REVERT: T 388 GLN cc_start: 0.6432 (mt0) cc_final: 0.6024 (mm-40) REVERT: T 408 LYS cc_start: 0.6699 (tttt) cc_final: 0.6404 (ttpp) REVERT: T 409 LYS cc_start: 0.6585 (ttmm) cc_final: 0.5954 (ttmm) REVERT: T 421 ASN cc_start: 0.6050 (m-40) cc_final: 0.4727 (t0) REVERT: T 436 GLU cc_start: 0.6142 (tp30) cc_final: 0.5066 (pm20) REVERT: T 445 GLN cc_start: 0.6561 (tt0) cc_final: 0.5755 (tp40) outliers start: 114 outliers final: 53 residues processed: 793 average time/residue: 1.6403 time to fit residues: 1582.7174 Evaluate side-chains 805 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 716 time to evaluate : 4.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 436 GLU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 428 ASP Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 169 ASN Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 436 GLU Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 128 ASP Chi-restraints excluded: chain L residue 266 GLU Chi-restraints excluded: chain L residue 282 LYS Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 169 ASN Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 282 LYS Chi-restraints excluded: chain O residue 330 LEU Chi-restraints excluded: chain O residue 366 VAL Chi-restraints excluded: chain O residue 385 VAL Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 266 GLU Chi-restraints excluded: chain R residue 282 LYS Chi-restraints excluded: chain R residue 366 VAL Chi-restraints excluded: chain S residue 7 THR Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 226 LYS Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain T residue 7 THR Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 120 GLU Chi-restraints excluded: chain T residue 169 ASN Chi-restraints excluded: chain T residue 266 GLU Chi-restraints excluded: chain T residue 277 THR Chi-restraints excluded: chain T residue 330 LEU Chi-restraints excluded: chain T residue 366 VAL Chi-restraints excluded: chain T residue 385 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 0.0770 chunk 446 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 386 optimal weight: 0.0170 chunk 61 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 419 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 430 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 421 ASN B 36 ASN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN F 36 ASN F 169 ASN F 421 ASN G 36 ASN ** G 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 413 ASN H 36 ASN L 36 ASN ** L 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 421 ASN N 36 ASN ** N 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 413 ASN O 36 ASN R 36 ASN ** R 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 421 ASN S 36 ASN ** S 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 413 ASN T 36 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136583 restraints weight = 39281.901| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.01 r_work: 0.3455 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 44100 Z= 0.107 Angle : 0.416 4.873 59700 Z= 0.222 Chirality : 0.038 0.130 6444 Planarity : 0.003 0.031 7860 Dihedral : 5.642 55.894 5886 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.32 % Allowed : 15.28 % Favored : 83.40 % 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: 0.72 (0.11), residues: 5316 helix: 1.76 (0.11), residues: 2292 sheet: -1.45 (0.15), residues: 744 loop : -0.07 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.003 0.001 HIS T 197 PHE 0.007 0.001 PHE G 287 TYR 0.021 0.001 TYR S 298 ARG 0.002 0.000 ARG T 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22514.43 seconds wall clock time: 395 minutes 49.68 seconds (23749.68 seconds total)