Starting phenix.real_space_refine on Sat Oct 31 09:39:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tf6_25863/10_2026/7tf6_25863.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf6_25863/10_2026/7tf6_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7tf6_25863/10_2026/7tf6_25863.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tf6_25863/10_2026/7tf6_25863.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tf6_25863/10_2026/7tf6_25863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf6_25863/10_2026/7tf6_25863.map" model { file = "/net/cci-nas-00/data/ceres_data/7tf6_25863/10_2026/7tf6_25863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf6_25863/10_2026/7tf6_25863.cif" } resolution = 2.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.112 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. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/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: 10.12, per 1000 atoms: 0.23 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.9 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: 1.31 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: 8.92 Time building geometry restraints manager: 4.70 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: 0.00 - 1.15: 57827 1.15 - 2.30: 1535 2.30 - 3.45: 508 3.45 - 4.61: 63 4.61 - 5.76: 31 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 2.450 nonbonded pdb=" O GLY O 243 " pdb=" H1 GLN O 503 " model vdw 1.687 2.450 nonbonded pdb=" O GLY N 243 " pdb=" H1 GLN N 503 " model vdw 1.687 2.450 nonbonded pdb=" O GLY S 243 " pdb=" H1 GLN S 503 " model vdw 1.692 2.450 nonbonded pdb=" O GLY B 243 " pdb=" H1 GLN B 503 " model vdw 1.694 2.450 ... (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 Time spend for trying shortcut: 0.01 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: 6.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.130 Process input model: 39.480 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 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= 0.115 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (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 ARG 0.007 0.000 ARG W 4 TYR 0.018 0.001 TYR O 203 PHE 0.011 0.001 PHE B 287 TRP 0.009 0.001 TRP L 427 HIS 0.002 0.001 HIS S 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (44100) covalent geometry : angle 0.50517 / 0.28 (59700) hydrogen bonds : bond 0.14194 / 9.43 ( 1545) hydrogen bonds : angle 5.37894 / 3.82 ( 4413) *********************** 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 to be fit. rotamer outliers: 62 poor density : 923 time to evaluate : 1.702 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: 0.7183 (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: 0.6349 (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: 0.6535 (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: 0.6746 (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: 0.5941 (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: 0.5903 (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: 0.5841 (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: 0.6322 (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: 0.6188 (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: 0.6415 (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: 0.7660 time to fit residues: 897.8621 Evaluate side-chains 830 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 789 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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: [394, 430, 41, 265, 523, 497, 414, 310, 488, 366, 223] chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 7.9990 chunk 223 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 189 HIS A 421 ASN A 445 GLN B 36 ASN B 189 HIS C 189 HIS ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 ASN C 445 GLN F 36 ASN F 189 HIS F 421 ASN F 445 GLN G 36 ASN G 189 HIS G 413 ASN G 418 GLN H 189 HIS ** H 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN H 445 GLN L 36 ASN L 189 HIS L 421 ASN N 36 ASN N 169 ASN N 189 HIS N 418 GLN O 189 HIS ** O 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 228 ASN O 445 GLN R 36 ASN R 189 HIS R 421 ASN R 445 GLN S 36 ASN S 189 HIS S 413 ASN T 189 HIS T 228 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.153725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133721 restraints weight = 39235.622| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 0.99 r_work: 0.3430 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 44100 Z= 0.196 Angle : 0.581 6.233 59700 Z= 0.316 Chirality : 0.046 0.170 6444 Planarity : 0.005 0.044 7860 Dihedral : 6.968 65.069 5933 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.39 % Allowed : 11.83 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.11), residues: 5316 helix: 1.21 (0.11), residues: 2304 sheet: -1.40 (0.15), residues: 840 loop : -0.31 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 4 TYR 0.032 0.002 TYR S 298 PHE 0.021 0.002 PHE B 287 TRP 0.016 0.002 TRP G 427 HIS 0.006 0.002 HIS H 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (44100) covalent geometry : angle 0.58100 / 0.32 (59700) hydrogen bonds : bond 0.06035 / 3.98 ( 1545) hydrogen bonds : angle 4.88449 / 3.47 ( 4413) *********************** 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 963 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 806 time to evaluate : 1.586 Fit side-chains REVERT: A 16 GLU cc_start: 0.7835 (tp30) cc_final: 0.7549 (tm-30) REVERT: A 52 MET cc_start: 0.8707 (mmm) cc_final: 0.8253 (mmm) REVERT: A 119 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7702 (tttt) REVERT: A 120 GLU cc_start: 0.7065 (pt0) cc_final: 0.6756 (mm-30) REVERT: A 225 ARG cc_start: 0.8141 (ttp-170) cc_final: 0.7902 (ttm170) REVERT: A 246 MET cc_start: 0.8344 (ttp) cc_final: 0.8076 (ttp) REVERT: A 277 THR cc_start: 0.8406 (t) cc_final: 0.8120 (m) REVERT: A 365 LYS cc_start: 0.7565 (mmtm) cc_final: 0.7106 (tttm) REVERT: A 401 MET cc_start: 0.9094 (ttt) cc_final: 0.8841 (ttt) REVERT: A 436 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: A 443 MET cc_start: 0.7669 (tpp) cc_final: 0.7444 (tpp) REVERT: B 16 GLU cc_start: 0.7703 (tp30) cc_final: 0.7359 (tm-30) REVERT: B 120 GLU cc_start: 0.7180 (pt0) cc_final: 0.6902 (mm-30) REVERT: B 122 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7619 (mt-10) REVERT: B 151 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8090 (mm-30) REVERT: B 168 GLU cc_start: 0.5318 (OUTLIER) cc_final: 0.4116 (tt0) REVERT: B 169 ASN cc_start: 0.7035 (OUTLIER) cc_final: 0.5536 (m-40) REVERT: B 225 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.7998 (ttm170) REVERT: B 226 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8048 (tttt) REVERT: B 270 THR cc_start: 0.8229 (m) cc_final: 0.7969 (p) REVERT: B 365 LYS cc_start: 0.7844 (mmtm) cc_final: 0.7433 (tttm) REVERT: B 399 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8075 (ttpt) REVERT: B 421 ASN cc_start: 0.8522 (m-40) cc_final: 0.7943 (t0) REVERT: B 436 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: C 13 LYS cc_start: 0.7912 (ttmm) cc_final: 0.7395 (tttp) REVERT: C 16 GLU cc_start: 0.7813 (tp30) cc_final: 0.7593 (tm-30) REVERT: C 53 MET cc_start: 0.8324 (mtm) cc_final: 0.8121 (mtp) REVERT: C 119 LYS cc_start: 0.7787 (tptp) cc_final: 0.7437 (tttt) REVERT: C 120 GLU cc_start: 0.7160 (pt0) cc_final: 0.6818 (mm-30) REVERT: C 155 ASP cc_start: 0.8079 (t0) cc_final: 0.7850 (t70) REVERT: C 168 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.5164 (tt0) REVERT: C 266 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: C 270 THR cc_start: 0.8367 (m) cc_final: 0.8129 (p) REVERT: C 365 LYS cc_start: 0.7659 (tppt) cc_final: 0.7181 (tttm) REVERT: C 388 GLN cc_start: 0.8085 (mt0) cc_final: 0.7814 (mm110) REVERT: C 405 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7179 (tm-30) REVERT: C 409 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8246 (ttmt) REVERT: C 421 ASN cc_start: 0.8460 (m-40) cc_final: 0.7956 (t0) REVERT: C 436 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7289 (pm20) REVERT: F 16 GLU cc_start: 0.7766 (tp30) cc_final: 0.7499 (tm-30) REVERT: F 52 MET cc_start: 0.8706 (mmm) cc_final: 0.8245 (mmm) REVERT: F 119 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7696 (tttt) REVERT: F 120 GLU cc_start: 0.7066 (pt0) cc_final: 0.6745 (mm-30) REVERT: F 168 GLU cc_start: 0.5476 (OUTLIER) cc_final: 0.5129 (pp20) REVERT: F 225 ARG cc_start: 0.8107 (ttp-170) cc_final: 0.7886 (ttm170) REVERT: F 246 MET cc_start: 0.8338 (ttp) cc_final: 0.8072 (ttp) REVERT: F 270 THR cc_start: 0.8278 (m) cc_final: 0.7937 (p) REVERT: F 277 THR cc_start: 0.8405 (t) cc_final: 0.8112 (m) REVERT: F 365 LYS cc_start: 0.7583 (mmtm) cc_final: 0.7126 (tttm) REVERT: F 436 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: G 16 GLU cc_start: 0.7738 (tp30) cc_final: 0.7416 (tm-30) REVERT: G 120 GLU cc_start: 0.7198 (pt0) cc_final: 0.6901 (mm-30) REVERT: G 151 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8096 (mm-30) REVERT: G 168 GLU cc_start: 0.5473 (OUTLIER) cc_final: 0.4249 (tt0) REVERT: G 169 ASN cc_start: 0.7049 (OUTLIER) cc_final: 0.5538 (m-40) REVERT: G 225 ARG cc_start: 0.8258 (ttp-170) cc_final: 0.8004 (ttm170) REVERT: G 226 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8051 (tttt) REVERT: G 266 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6434 (tp30) REVERT: G 270 THR cc_start: 0.8265 (m) cc_final: 0.7996 (p) REVERT: G 271 GLU cc_start: 0.7425 (tp30) cc_final: 0.7215 (tp30) REVERT: G 365 LYS cc_start: 0.7879 (mmtm) cc_final: 0.7450 (tttm) REVERT: G 399 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8074 (ttpt) REVERT: G 421 ASN cc_start: 0.8525 (m-40) cc_final: 0.7960 (t0) REVERT: G 436 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: H 13 LYS cc_start: 0.7920 (ttmm) cc_final: 0.7400 (tttp) REVERT: H 16 GLU cc_start: 0.7825 (tp30) cc_final: 0.7586 (tm-30) REVERT: H 53 MET cc_start: 0.8354 (mtm) cc_final: 0.8108 (mtp) REVERT: H 119 LYS cc_start: 0.7779 (tptp) cc_final: 0.7426 (tttt) REVERT: H 120 GLU cc_start: 0.7145 (pt0) cc_final: 0.6816 (mm-30) REVERT: H 122 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7742 (mt-10) REVERT: H 151 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8074 (mm-30) REVERT: H 155 ASP cc_start: 0.8075 (t0) cc_final: 0.7847 (t70) REVERT: H 168 GLU cc_start: 0.5844 (OUTLIER) cc_final: 0.5106 (tt0) REVERT: H 270 THR cc_start: 0.8361 (m) cc_final: 0.8131 (p) REVERT: H 271 GLU cc_start: 0.7285 (tp30) cc_final: 0.6957 (tp30) REVERT: H 365 LYS cc_start: 0.7665 (tppt) cc_final: 0.7180 (tttm) REVERT: H 388 GLN cc_start: 0.8091 (mt0) cc_final: 0.7820 (mm110) REVERT: H 405 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7281 (tm-30) REVERT: H 421 ASN cc_start: 0.8462 (m-40) cc_final: 0.7956 (t0) REVERT: H 436 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: H 445 GLN cc_start: 0.8089 (tt0) cc_final: 0.7825 (tp40) REVERT: L 16 GLU cc_start: 0.7905 (tp30) cc_final: 0.7600 (tm-30) REVERT: L 119 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7690 (tttt) REVERT: L 120 GLU cc_start: 0.7111 (pt0) cc_final: 0.6861 (mm-30) REVERT: L 168 GLU cc_start: 0.5542 (OUTLIER) cc_final: 0.5178 (pp20) REVERT: L 225 ARG cc_start: 0.8169 (ttp-170) cc_final: 0.7923 (ttm170) REVERT: L 270 THR cc_start: 0.8268 (m) cc_final: 0.7920 (p) REVERT: L 277 THR cc_start: 0.8405 (t) cc_final: 0.8112 (m) REVERT: L 365 LYS cc_start: 0.7592 (mmtm) cc_final: 0.7126 (tttm) REVERT: N 16 GLU cc_start: 0.7714 (tp30) cc_final: 0.7369 (tm-30) REVERT: N 120 GLU cc_start: 0.7106 (pt0) cc_final: 0.6821 (mm-30) REVERT: N 151 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8084 (mm-30) REVERT: N 155 ASP cc_start: 0.7986 (t0) cc_final: 0.7784 (t70) REVERT: N 168 GLU cc_start: 0.5491 (OUTLIER) cc_final: 0.4818 (tm-30) REVERT: N 225 ARG cc_start: 0.8252 (ttp-170) cc_final: 0.8009 (ttm170) REVERT: N 226 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8051 (tttt) REVERT: N 270 THR cc_start: 0.8220 (m) cc_final: 0.7959 (p) REVERT: N 365 LYS cc_start: 0.7860 (mmtm) cc_final: 0.7457 (tttm) REVERT: N 399 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8049 (ttpt) REVERT: N 421 ASN cc_start: 0.8520 (m-40) cc_final: 0.7950 (t0) REVERT: O 13 LYS cc_start: 0.7900 (ttmm) cc_final: 0.7376 (tttp) REVERT: O 16 GLU cc_start: 0.7859 (tp30) cc_final: 0.7622 (tm-30) REVERT: O 53 MET cc_start: 0.8286 (mtm) cc_final: 0.8068 (mtp) REVERT: O 119 LYS cc_start: 0.7795 (tptp) cc_final: 0.7438 (tttt) REVERT: O 120 GLU cc_start: 0.7135 (pt0) cc_final: 0.6816 (mm-30) REVERT: O 151 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8046 (mm-30) REVERT: O 155 ASP cc_start: 0.8085 (t0) cc_final: 0.7851 (t70) REVERT: O 168 GLU cc_start: 0.5943 (OUTLIER) cc_final: 0.5205 (tt0) REVERT: O 270 THR cc_start: 0.8363 (m) cc_final: 0.8137 (p) REVERT: O 271 GLU cc_start: 0.7297 (tp30) cc_final: 0.6966 (tp30) REVERT: O 365 LYS cc_start: 0.7646 (tppt) cc_final: 0.7179 (tttm) REVERT: O 388 GLN cc_start: 0.8085 (mt0) cc_final: 0.7821 (mm110) REVERT: O 405 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7318 (tm-30) REVERT: O 421 ASN cc_start: 0.8453 (m-40) cc_final: 0.7950 (t0) REVERT: O 445 GLN cc_start: 0.8075 (tt0) cc_final: 0.7810 (tp40) REVERT: R 16 GLU cc_start: 0.7851 (tp30) cc_final: 0.7544 (tm-30) REVERT: R 52 MET cc_start: 0.8535 (mmm) cc_final: 0.8266 (mmm) REVERT: R 119 LYS cc_start: 0.7977 (ttpt) cc_final: 0.7711 (tttt) REVERT: R 168 GLU cc_start: 0.5826 (OUTLIER) cc_final: 0.4847 (tt0) REVERT: R 201 PHE cc_start: 0.7735 (m-80) cc_final: 0.7449 (m-80) REVERT: R 225 ARG cc_start: 0.8137 (ttp-170) cc_final: 0.7924 (ttm170) REVERT: R 246 MET cc_start: 0.8337 (ttp) cc_final: 0.8064 (ttp) REVERT: R 270 THR cc_start: 0.8265 (m) cc_final: 0.7914 (p) REVERT: R 277 THR cc_start: 0.8406 (t) cc_final: 0.8110 (m) REVERT: R 365 LYS cc_start: 0.7585 (mmtm) cc_final: 0.7116 (tttm) REVERT: R 401 MET cc_start: 0.9089 (ttt) cc_final: 0.8772 (ttt) REVERT: S 16 GLU cc_start: 0.7706 (tp30) cc_final: 0.7367 (tm-30) REVERT: S 120 GLU cc_start: 0.7199 (pt0) cc_final: 0.6900 (mm-30) REVERT: S 151 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8109 (mm-30) REVERT: S 168 GLU cc_start: 0.5572 (OUTLIER) cc_final: 0.4730 (tt0) REVERT: S 169 ASN cc_start: 0.7088 (OUTLIER) cc_final: 0.5725 (m-40) REVERT: S 225 ARG cc_start: 0.8220 (ttt180) cc_final: 0.7987 (ttm170) REVERT: S 226 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8051 (tttt) REVERT: S 270 THR cc_start: 0.8260 (m) cc_final: 0.7999 (p) REVERT: S 271 GLU cc_start: 0.7451 (tp30) cc_final: 0.7194 (tp30) REVERT: S 365 LYS cc_start: 0.7838 (mmtm) cc_final: 0.7443 (tttm) REVERT: S 399 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8070 (ttpt) REVERT: S 421 ASN cc_start: 0.8524 (m-40) cc_final: 0.7951 (t0) REVERT: T 13 LYS cc_start: 0.7905 (ttmm) cc_final: 0.7384 (tttp) REVERT: T 16 GLU cc_start: 0.7833 (tp30) cc_final: 0.7609 (tm-30) REVERT: T 119 LYS cc_start: 0.7797 (tptp) cc_final: 0.7440 (tttt) REVERT: T 120 GLU cc_start: 0.7130 (pt0) cc_final: 0.6806 (mm-30) REVERT: T 151 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8048 (mm-30) REVERT: T 155 ASP cc_start: 0.8078 (t0) cc_final: 0.7831 (t70) REVERT: T 266 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6228 (mp0) REVERT: T 270 THR cc_start: 0.8363 (m) cc_final: 0.8133 (p) REVERT: T 365 LYS cc_start: 0.7659 (tppt) cc_final: 0.7180 (tttm) REVERT: T 388 GLN cc_start: 0.8113 (mt0) cc_final: 0.7890 (mm-40) REVERT: T 409 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8245 (ttmt) REVERT: T 421 ASN cc_start: 0.8447 (m-40) cc_final: 0.7926 (t0) REVERT: T 445 GLN cc_start: 0.8124 (tt0) cc_final: 0.7837 (tp40) outliers start: 157 outliers final: 37 residues processed: 896 average time/residue: 0.7672 time to fit residues: 834.8395 Evaluate side-chains 813 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 746 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 366 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 169 ASN Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 436 GLU 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 436 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 436 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 399 LYS Chi-restraints excluded: chain G residue 436 GLU 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 436 GLU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain L residue 366 VAL 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 N residue 399 LYS 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 R residue 39 VAL Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 169 ASN Chi-restraints excluded: chain R residue 366 VAL 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 399 LYS 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 V residue 2 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: [118, 299, 195, 71, 363, 245, 381, 399, 282, 99, 314] chunk 118 optimal weight: 10.0000 chunk 299 optimal weight: 0.5980 chunk 195 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 363 optimal weight: 0.3980 chunk 245 optimal weight: 0.5980 chunk 381 optimal weight: 2.9990 chunk 399 optimal weight: 7.9990 chunk 282 optimal weight: 3.9990 chunk 99 optimal weight: 0.0370 chunk 314 optimal weight: 3.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 421 ASN B 36 ASN B 228 ASN C 36 ASN C 228 ASN F 36 ASN F 421 ASN G 36 ASN G 228 ASN G 413 ASN H 36 ASN L 36 ASN L 421 ASN N 36 ASN ** N 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 228 ASN O 36 ASN O 228 ASN R 36 ASN R 421 ASN S 36 ASN S 228 ASN S 413 ASN S 445 GLN T 36 ASN T 228 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.157709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.137845 restraints weight = 39191.999| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.02 r_work: 0.3479 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1747 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= 0.085 Angle : 0.420 4.963 59700 Z= 0.225 Chirality : 0.039 0.141 6444 Planarity : 0.003 0.031 7860 Dihedral : 6.071 59.302 5904 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.88 % Allowed : 14.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.11), residues: 5316 helix: 1.69 (0.11), residues: 2304 sheet: -1.56 (0.16), residues: 744 loop : -0.09 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 4 TYR 0.021 0.001 TYR H 298 PHE 0.008 0.001 PHE L 287 TRP 0.010 0.001 TRP G 427 HIS 0.003 0.001 HIS L 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.08 (44100) covalent geometry : angle 0.41966 / 0.22 (59700) hydrogen bonds : bond 0.03972 / 2.62 ( 1545) hydrogen bonds : angle 4.37887 / 3.12 ( 4413) *********************** 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 851 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 764 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7836 (tp30) cc_final: 0.7477 (tm-30) REVERT: A 52 MET cc_start: 0.8716 (mmm) cc_final: 0.8274 (mmm) REVERT: A 119 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7664 (tttt) REVERT: A 168 GLU cc_start: 0.5207 (OUTLIER) cc_final: 0.3600 (mp0) REVERT: A 277 THR cc_start: 0.8343 (t) cc_final: 0.8113 (m) REVERT: A 365 LYS cc_start: 0.7627 (mmtm) cc_final: 0.7174 (tttm) REVERT: B 16 GLU cc_start: 0.7655 (tp30) cc_final: 0.7265 (tm-30) REVERT: B 120 GLU cc_start: 0.7029 (pt0) cc_final: 0.6825 (mm-30) REVERT: B 122 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7525 (mt-10) REVERT: B 151 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8031 (mm-30) REVERT: B 168 GLU cc_start: 0.5053 (OUTLIER) cc_final: 0.4845 (tm-30) REVERT: B 169 ASN cc_start: 0.6552 (OUTLIER) cc_final: 0.5441 (m-40) REVERT: B 225 ARG cc_start: 0.8098 (ttp-170) cc_final: 0.7846 (ttm170) REVERT: B 365 LYS cc_start: 0.7813 (mmtm) cc_final: 0.7413 (tttm) REVERT: B 399 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8190 (ttpt) REVERT: B 421 ASN cc_start: 0.8464 (m-40) cc_final: 0.7890 (t0) REVERT: B 436 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: C 13 LYS cc_start: 0.7875 (ttmm) cc_final: 0.7378 (tttp) REVERT: C 16 GLU cc_start: 0.7778 (tp30) cc_final: 0.7539 (tm-30) REVERT: C 119 LYS cc_start: 0.7748 (tptp) cc_final: 0.7430 (tttt) REVERT: C 120 GLU cc_start: 0.7107 (pt0) cc_final: 0.6837 (mm-30) REVERT: C 155 ASP cc_start: 0.8085 (t0) cc_final: 0.7848 (t70) REVERT: C 168 GLU cc_start: 0.5603 (OUTLIER) cc_final: 0.5095 (tt0) REVERT: C 270 THR cc_start: 0.8161 (m) cc_final: 0.7944 (p) REVERT: C 365 LYS cc_start: 0.7682 (tppt) cc_final: 0.7199 (tttm) REVERT: C 388 GLN cc_start: 0.8117 (mt0) cc_final: 0.7837 (mm110) REVERT: C 409 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8188 (ttpt) REVERT: C 421 ASN cc_start: 0.8361 (m-40) cc_final: 0.7880 (t0) REVERT: F 16 GLU cc_start: 0.7832 (tp30) cc_final: 0.7488 (tm-30) REVERT: F 52 MET cc_start: 0.8710 (mmm) cc_final: 0.8365 (mmm) REVERT: F 119 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7682 (tttt) REVERT: F 168 GLU cc_start: 0.4922 (OUTLIER) cc_final: 0.4629 (tt0) REVERT: F 225 ARG cc_start: 0.8078 (ttp-170) cc_final: 0.7867 (ttt180) REVERT: F 270 THR cc_start: 0.8166 (m) cc_final: 0.7840 (p) REVERT: F 277 THR cc_start: 0.8334 (t) cc_final: 0.8108 (m) REVERT: F 365 LYS cc_start: 0.7625 (mmtm) cc_final: 0.7163 (tttm) REVERT: F 436 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7431 (pm20) REVERT: G 16 GLU cc_start: 0.7689 (tp30) cc_final: 0.7335 (tm-30) REVERT: G 151 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8045 (mm-30) REVERT: G 168 GLU cc_start: 0.5171 (OUTLIER) cc_final: 0.4647 (tt0) REVERT: G 169 ASN cc_start: 0.6581 (OUTLIER) cc_final: 0.6119 (m-40) REVERT: G 225 ARG cc_start: 0.8111 (ttp-170) cc_final: 0.7855 (ttm170) REVERT: G 365 LYS cc_start: 0.7847 (mmtm) cc_final: 0.7424 (tttm) REVERT: G 399 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8177 (ttpt) REVERT: G 421 ASN cc_start: 0.8476 (m-40) cc_final: 0.7932 (t0) REVERT: H 13 LYS cc_start: 0.7860 (ttmm) cc_final: 0.7353 (tttp) REVERT: H 16 GLU cc_start: 0.7740 (tp30) cc_final: 0.7482 (tm-30) REVERT: H 53 MET cc_start: 0.8327 (mtm) cc_final: 0.8118 (mtp) REVERT: H 119 LYS cc_start: 0.7749 (tptp) cc_final: 0.7407 (tttt) REVERT: H 120 GLU cc_start: 0.7094 (pt0) cc_final: 0.6830 (mm-30) REVERT: H 122 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7697 (mt-10) REVERT: H 151 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8096 (mm-30) REVERT: H 155 ASP cc_start: 0.8085 (t0) cc_final: 0.7830 (t70) REVERT: H 168 GLU cc_start: 0.5546 (OUTLIER) cc_final: 0.5140 (tt0) REVERT: H 270 THR cc_start: 0.8165 (m) cc_final: 0.7951 (p) REVERT: H 271 GLU cc_start: 0.7226 (tp30) cc_final: 0.6889 (tp30) REVERT: H 365 LYS cc_start: 0.7664 (tppt) cc_final: 0.7187 (tttm) REVERT: H 388 GLN cc_start: 0.8116 (mt0) cc_final: 0.7832 (mm110) REVERT: H 421 ASN cc_start: 0.8356 (m-40) cc_final: 0.7868 (t0) REVERT: H 445 GLN cc_start: 0.7924 (tt0) cc_final: 0.7705 (tp40) REVERT: L 16 GLU cc_start: 0.7854 (tp30) cc_final: 0.7503 (tm-30) REVERT: L 119 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7681 (tttt) REVERT: L 168 GLU cc_start: 0.5091 (OUTLIER) cc_final: 0.4618 (tt0) REVERT: L 270 THR cc_start: 0.8135 (m) cc_final: 0.7810 (p) REVERT: L 277 THR cc_start: 0.8340 (t) cc_final: 0.8111 (m) REVERT: L 365 LYS cc_start: 0.7607 (mmtm) cc_final: 0.7152 (tttm) REVERT: N 16 GLU cc_start: 0.7650 (tp30) cc_final: 0.7250 (tm-30) REVERT: N 120 GLU cc_start: 0.7019 (pt0) cc_final: 0.6791 (mm-30) REVERT: N 151 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8057 (mm-30) REVERT: N 225 ARG cc_start: 0.8062 (ttp-170) cc_final: 0.7824 (ttm170) REVERT: N 365 LYS cc_start: 0.7863 (mmtm) cc_final: 0.7458 (tttm) REVERT: N 399 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8179 (ttpt) REVERT: N 421 ASN cc_start: 0.8461 (m-40) cc_final: 0.7907 (t0) REVERT: O 13 LYS cc_start: 0.7880 (ttmm) cc_final: 0.7366 (tttp) REVERT: O 16 GLU cc_start: 0.7740 (tp30) cc_final: 0.7484 (tm-30) REVERT: O 119 LYS cc_start: 0.7743 (tptp) cc_final: 0.7418 (tttt) REVERT: O 120 GLU cc_start: 0.7096 (pt0) cc_final: 0.6832 (mm-30) REVERT: O 151 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8059 (mm-30) REVERT: O 155 ASP cc_start: 0.8094 (t0) cc_final: 0.7838 (t70) REVERT: O 168 GLU cc_start: 0.5567 (OUTLIER) cc_final: 0.5170 (tt0) REVERT: O 270 THR cc_start: 0.8171 (m) cc_final: 0.7962 (p) REVERT: O 271 GLU cc_start: 0.7257 (tp30) cc_final: 0.6915 (tp30) REVERT: O 365 LYS cc_start: 0.7673 (tppt) cc_final: 0.7195 (tttm) REVERT: O 388 GLN cc_start: 0.8106 (mt0) cc_final: 0.7829 (mm110) REVERT: O 421 ASN cc_start: 0.8348 (m-40) cc_final: 0.7862 (t0) REVERT: O 445 GLN cc_start: 0.7928 (tt0) cc_final: 0.7700 (tp40) REVERT: R 16 GLU cc_start: 0.7830 (tp30) cc_final: 0.7480 (tm-30) REVERT: R 52 MET cc_start: 0.8535 (mmm) cc_final: 0.8326 (mmm) REVERT: R 119 LYS cc_start: 0.7973 (ttpt) cc_final: 0.7684 (tttt) REVERT: R 168 GLU cc_start: 0.5411 (OUTLIER) cc_final: 0.4704 (tt0) REVERT: R 201 PHE cc_start: 0.7716 (m-80) cc_final: 0.7406 (m-80) REVERT: R 270 THR cc_start: 0.8170 (m) cc_final: 0.7822 (p) REVERT: R 277 THR cc_start: 0.8339 (t) cc_final: 0.8107 (m) REVERT: R 365 LYS cc_start: 0.7619 (mmtm) cc_final: 0.7155 (tttm) REVERT: S 16 GLU cc_start: 0.7659 (tp30) cc_final: 0.7263 (tm-30) REVERT: S 151 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8034 (mm-30) REVERT: S 168 GLU cc_start: 0.5222 (OUTLIER) cc_final: 0.4992 (tt0) REVERT: S 169 ASN cc_start: 0.6704 (OUTLIER) cc_final: 0.6209 (m-40) REVERT: S 365 LYS cc_start: 0.7840 (mmtm) cc_final: 0.7435 (tttm) REVERT: S 399 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8165 (ttpt) REVERT: S 421 ASN cc_start: 0.8467 (m-40) cc_final: 0.7913 (t0) REVERT: T 13 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7396 (tttp) REVERT: T 16 GLU cc_start: 0.7789 (tp30) cc_final: 0.7552 (tm-30) REVERT: T 119 LYS cc_start: 0.7748 (tptp) cc_final: 0.7430 (tttt) REVERT: T 120 GLU cc_start: 0.7114 (pt0) cc_final: 0.6844 (mm-30) REVERT: T 151 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8069 (mm-30) REVERT: T 155 ASP cc_start: 0.8024 (t0) cc_final: 0.7776 (t70) REVERT: T 270 THR cc_start: 0.8163 (m) cc_final: 0.7939 (p) REVERT: T 365 LYS cc_start: 0.7671 (tppt) cc_final: 0.7179 (tttm) REVERT: T 388 GLN cc_start: 0.8135 (mt0) cc_final: 0.7897 (mm-40) REVERT: T 421 ASN cc_start: 0.8364 (m-40) cc_final: 0.7869 (t0) REVERT: T 445 GLN cc_start: 0.7985 (tt0) cc_final: 0.7719 (tp40) outliers start: 87 outliers final: 31 residues processed: 815 average time/residue: 0.7350 time to fit residues: 733.9210 Evaluate side-chains 804 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 754 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 436 GLU 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 F residue 39 VAL Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 436 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 399 LYS 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 L residue 39 VAL Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 399 LYS 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 R residue 39 VAL Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 169 ASN 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 330 LEU Chi-restraints excluded: chain S residue 366 VAL Chi-restraints excluded: chain S residue 399 LYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: [437, 97, 348, 142, 266, 493, 366, 95, 171, 28, 325] chunk 437 optimal weight: 8.9990 chunk 97 optimal weight: 0.0070 chunk 348 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 266 optimal weight: 0.0020 chunk 493 optimal weight: 3.9990 chunk 366 optimal weight: 9.9990 chunk 95 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.5441 > 50:) chunk 171 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 325 optimal weight: 10.0000 overall best weight: 3.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 36 ASN B 418 GLN C 36 ASN F 36 ASN G 36 ASN G 413 ASN H 36 ASN H 228 ASN L 36 ASN N 36 ASN ** N 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN R 36 ASN S 36 ASN S 413 ASN T 36 ASN T 445 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133800 restraints weight = 38819.560| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.01 r_work: 0.3426 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2036 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= 0.174 Angle : 0.545 6.431 59700 Z= 0.296 Chirality : 0.044 0.159 6444 Planarity : 0.004 0.040 7860 Dihedral : 6.631 64.694 5903 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.46 % Allowed : 13.77 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.11), residues: 5316 helix: 1.40 (0.11), residues: 2304 sheet: -1.66 (0.15), residues: 744 loop : -0.13 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 4 TYR 0.032 0.002 TYR S 298 PHE 0.020 0.002 PHE L 287 TRP 0.016 0.002 TRP F 427 HIS 0.006 0.002 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (44100) covalent geometry : angle 0.54531 / 0.30 (59700) hydrogen bonds : bond 0.05610 / 3.70 ( 1545) hydrogen bonds : angle 4.73010 / 3.36 ( 4413) *********************** 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 845 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 731 time to evaluate : 1.674 Fit side-chains REVERT: A 16 GLU cc_start: 0.7939 (tp30) cc_final: 0.7565 (tm-30) REVERT: A 52 MET cc_start: 0.8713 (mmm) cc_final: 0.8268 (mmm) REVERT: A 119 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7692 (tttt) REVERT: A 168 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.3620 (mt-10) REVERT: A 277 THR cc_start: 0.8383 (t) cc_final: 0.8127 (m) REVERT: A 365 LYS cc_start: 0.7573 (mmtm) cc_final: 0.7125 (tttm) REVERT: A 401 MET cc_start: 0.9091 (ttt) cc_final: 0.8846 (ttt) REVERT: A 436 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7379 (pm20) REVERT: A 443 MET cc_start: 0.7821 (tpp) cc_final: 0.7508 (tpp) REVERT: B 16 GLU cc_start: 0.7703 (tp30) cc_final: 0.7359 (tm-30) REVERT: B 120 GLU cc_start: 0.7153 (pt0) cc_final: 0.6896 (mm-30) REVERT: B 122 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7544 (mt-10) REVERT: B 151 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8059 (mm-30) REVERT: B 155 ASP cc_start: 0.8031 (t0) cc_final: 0.7808 (t70) REVERT: B 168 GLU cc_start: 0.5429 (OUTLIER) cc_final: 0.4708 (tt0) REVERT: B 169 ASN cc_start: 0.6980 (OUTLIER) cc_final: 0.5611 (m-40) REVERT: B 226 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8029 (tttt) REVERT: B 365 LYS cc_start: 0.7795 (mmtm) cc_final: 0.7402 (tttm) REVERT: B 399 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8169 (ttpt) REVERT: B 421 ASN cc_start: 0.8551 (m-40) cc_final: 0.7951 (t0) REVERT: B 436 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: C 13 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7479 (tttp) REVERT: C 16 GLU cc_start: 0.7890 (tp30) cc_final: 0.7633 (tm-30) REVERT: C 119 LYS cc_start: 0.7789 (tptp) cc_final: 0.7455 (tttt) REVERT: C 120 GLU cc_start: 0.7261 (pt0) cc_final: 0.6982 (mm-30) REVERT: C 155 ASP cc_start: 0.8164 (t0) cc_final: 0.7928 (t70) REVERT: C 168 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5159 (tt0) REVERT: C 270 THR cc_start: 0.8309 (m) cc_final: 0.8104 (p) REVERT: C 365 LYS cc_start: 0.7643 (tppt) cc_final: 0.7194 (tttm) REVERT: C 388 GLN cc_start: 0.8153 (mt0) cc_final: 0.7845 (mm-40) REVERT: C 409 LYS cc_start: 0.8438 (ttmm) cc_final: 0.8178 (ttpt) REVERT: C 421 ASN cc_start: 0.8465 (m-40) cc_final: 0.7960 (t0) REVERT: C 436 GLU cc_start: 0.7244 (pm20) cc_final: 0.7004 (pm20) REVERT: F 16 GLU cc_start: 0.7920 (tp30) cc_final: 0.7559 (tm-30) REVERT: F 52 MET cc_start: 0.8714 (mmm) cc_final: 0.8267 (mmm) REVERT: F 119 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7693 (tttt) REVERT: F 168 GLU cc_start: 0.5277 (OUTLIER) cc_final: 0.4325 (tt0) REVERT: F 270 THR cc_start: 0.8254 (m) cc_final: 0.7903 (p) REVERT: F 277 THR cc_start: 0.8384 (t) cc_final: 0.8125 (m) REVERT: F 365 LYS cc_start: 0.7582 (mmtm) cc_final: 0.7108 (tttm) REVERT: F 401 MET cc_start: 0.9076 (ttt) cc_final: 0.8747 (ttt) REVERT: F 436 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7649 (pm20) REVERT: G 16 GLU cc_start: 0.7799 (tp30) cc_final: 0.7503 (tm-30) REVERT: G 151 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8062 (mm-30) REVERT: G 155 ASP cc_start: 0.7998 (t0) cc_final: 0.7780 (t70) REVERT: G 168 GLU cc_start: 0.5533 (OUTLIER) cc_final: 0.4590 (tt0) REVERT: G 169 ASN cc_start: 0.6995 (OUTLIER) cc_final: 0.5613 (m-40) REVERT: G 226 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7998 (tttt) REVERT: G 266 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6221 (mp0) REVERT: G 365 LYS cc_start: 0.7833 (mmtm) cc_final: 0.7427 (tttm) REVERT: G 399 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8167 (ttpt) REVERT: G 421 ASN cc_start: 0.8526 (m-40) cc_final: 0.7961 (t0) REVERT: G 436 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7305 (pm20) REVERT: H 13 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7456 (tttp) REVERT: H 16 GLU cc_start: 0.7870 (tp30) cc_final: 0.7607 (tm-30) REVERT: H 53 MET cc_start: 0.8353 (mtm) cc_final: 0.8121 (mtp) REVERT: H 119 LYS cc_start: 0.7793 (tptp) cc_final: 0.7427 (tttt) REVERT: H 120 GLU cc_start: 0.7239 (pt0) cc_final: 0.6963 (mm-30) REVERT: H 122 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7694 (mt-10) REVERT: H 151 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8088 (mm-30) REVERT: H 155 ASP cc_start: 0.8129 (t0) cc_final: 0.7869 (t70) REVERT: H 168 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5136 (tt0) REVERT: H 270 THR cc_start: 0.8306 (m) cc_final: 0.8099 (p) REVERT: H 271 GLU cc_start: 0.7283 (tp30) cc_final: 0.6967 (tp30) REVERT: H 365 LYS cc_start: 0.7655 (tppt) cc_final: 0.7204 (tttm) REVERT: H 388 GLN cc_start: 0.8151 (mt0) cc_final: 0.7879 (mm-40) REVERT: H 421 ASN cc_start: 0.8458 (m-40) cc_final: 0.7954 (t0) REVERT: L 16 GLU cc_start: 0.7933 (tp30) cc_final: 0.7563 (tm-30) REVERT: L 119 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7699 (tttt) REVERT: L 168 GLU cc_start: 0.5329 (OUTLIER) cc_final: 0.4314 (tt0) REVERT: L 266 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6348 (tm-30) REVERT: L 270 THR cc_start: 0.8255 (m) cc_final: 0.7902 (p) REVERT: L 277 THR cc_start: 0.8385 (t) cc_final: 0.8127 (m) REVERT: L 365 LYS cc_start: 0.7569 (mmtm) cc_final: 0.7106 (tttm) REVERT: L 436 GLU cc_start: 0.8220 (pt0) cc_final: 0.7998 (tp30) REVERT: L 443 MET cc_start: 0.7771 (tpp) cc_final: 0.7508 (tpp) REVERT: N 16 GLU cc_start: 0.7681 (tp30) cc_final: 0.7335 (tm-30) REVERT: N 120 GLU cc_start: 0.7109 (pt0) cc_final: 0.6832 (mm-30) REVERT: N 151 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8076 (mm-30) REVERT: N 168 GLU cc_start: 0.6192 (OUTLIER) cc_final: 0.5000 (tm-30) REVERT: N 226 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7968 (tttt) REVERT: N 365 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7405 (tttm) REVERT: N 399 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8162 (ttpt) REVERT: N 421 ASN cc_start: 0.8530 (m-40) cc_final: 0.7959 (t0) REVERT: O 13 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7478 (tttp) REVERT: O 16 GLU cc_start: 0.7853 (tp30) cc_final: 0.7588 (tm-30) REVERT: O 119 LYS cc_start: 0.7786 (tptp) cc_final: 0.7444 (tttt) REVERT: O 120 GLU cc_start: 0.7235 (pt0) cc_final: 0.6980 (mm-30) REVERT: O 151 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8067 (mm-30) REVERT: O 155 ASP cc_start: 0.8115 (t0) cc_final: 0.7871 (t70) REVERT: O 168 GLU cc_start: 0.5945 (OUTLIER) cc_final: 0.5216 (tt0) REVERT: O 270 THR cc_start: 0.8309 (m) cc_final: 0.8104 (p) REVERT: O 271 GLU cc_start: 0.7294 (tp30) cc_final: 0.6970 (tp30) REVERT: O 365 LYS cc_start: 0.7666 (tppt) cc_final: 0.7215 (tttm) REVERT: O 388 GLN cc_start: 0.8145 (mt0) cc_final: 0.7854 (mm110) REVERT: O 421 ASN cc_start: 0.8464 (m-40) cc_final: 0.7953 (t0) REVERT: O 445 GLN cc_start: 0.7954 (tt0) cc_final: 0.7747 (tp40) REVERT: R 16 GLU cc_start: 0.7906 (tp30) cc_final: 0.7541 (tm-30) REVERT: R 52 MET cc_start: 0.8589 (mmm) cc_final: 0.8291 (mmm) REVERT: R 119 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7726 (tttt) REVERT: R 168 GLU cc_start: 0.5724 (OUTLIER) cc_final: 0.4714 (tt0) REVERT: R 266 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6379 (tm-30) REVERT: R 270 THR cc_start: 0.8253 (m) cc_final: 0.7892 (p) REVERT: R 277 THR cc_start: 0.8388 (t) cc_final: 0.8121 (m) REVERT: R 365 LYS cc_start: 0.7572 (mmtm) cc_final: 0.7109 (tttm) REVERT: R 401 MET cc_start: 0.9082 (ttt) cc_final: 0.8850 (ttt) REVERT: R 443 MET cc_start: 0.7834 (tpp) cc_final: 0.7594 (tpp) REVERT: S 16 GLU cc_start: 0.7693 (tp30) cc_final: 0.7352 (tm-30) REVERT: S 151 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8037 (mm-30) REVERT: S 155 ASP cc_start: 0.8027 (t0) cc_final: 0.7820 (t70) REVERT: S 168 GLU cc_start: 0.5555 (OUTLIER) cc_final: 0.4927 (tt0) REVERT: S 169 ASN cc_start: 0.7037 (OUTLIER) cc_final: 0.5697 (m-40) REVERT: S 266 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: S 365 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7422 (tttm) REVERT: S 399 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8151 (ttpt) REVERT: S 421 ASN cc_start: 0.8549 (m-40) cc_final: 0.7959 (t0) REVERT: T 13 LYS cc_start: 0.7996 (ttmm) cc_final: 0.7489 (tttp) REVERT: T 16 GLU cc_start: 0.7872 (tp30) cc_final: 0.7622 (tm-30) REVERT: T 119 LYS cc_start: 0.7793 (tptp) cc_final: 0.7448 (tttt) REVERT: T 120 GLU cc_start: 0.7244 (pt0) cc_final: 0.6976 (mm-30) REVERT: T 151 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8104 (mm-30) REVERT: T 155 ASP cc_start: 0.8103 (t0) cc_final: 0.7843 (t70) REVERT: T 270 THR cc_start: 0.8309 (m) cc_final: 0.8103 (p) REVERT: T 365 LYS cc_start: 0.7664 (tppt) cc_final: 0.7212 (tttm) REVERT: T 388 GLN cc_start: 0.8142 (mt0) cc_final: 0.7927 (mm-40) REVERT: T 421 ASN cc_start: 0.8462 (m-40) cc_final: 0.7951 (t0) REVERT: T 445 GLN cc_start: 0.7965 (tt0) cc_final: 0.7725 (tp40) outliers start: 114 outliers final: 43 residues processed: 812 average time/residue: 0.7318 time to fit residues: 728.9081 Evaluate side-chains 792 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 720 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 366 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 169 ASN Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 436 GLU 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 277 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 436 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 330 LEU Chi-restraints excluded: chain G residue 399 LYS Chi-restraints excluded: chain G residue 436 GLU 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 L residue 39 VAL 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 366 VAL 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 330 LEU Chi-restraints excluded: chain N residue 399 LYS 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 R residue 39 VAL Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 169 ASN Chi-restraints excluded: chain R residue 266 GLU Chi-restraints excluded: chain R residue 366 VAL 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 266 GLU Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain S residue 366 VAL Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain S residue 399 LYS Chi-restraints excluded: chain T residue 39 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: [150, 124, 232, 190, 313, 122, 445, 386, 23, 152, 419] chunk 150 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 313 optimal weight: 9.9990 chunk 122 optimal weight: 0.2980 chunk 445 optimal weight: 6.9990 chunk 386 optimal weight: 0.5980 chunk 23 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 419 optimal weight: 9.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 36 ASN B 228 ASN C 36 ASN F 36 ASN G 36 ASN G 228 ASN G 413 ASN H 36 ASN L 36 ASN N 36 ASN ** N 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 228 ASN O 36 ASN R 36 ASN S 36 ASN S 228 ASN S 413 ASN T 36 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133109 restraints weight = 38778.744| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.01 r_work: 0.3417 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 44100 Z= 0.193 Angle : 0.578 6.408 59700 Z= 0.315 Chirality : 0.045 0.163 6444 Planarity : 0.005 0.042 7860 Dihedral : 6.854 67.853 5903 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.63 % Allowed : 13.75 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.11), residues: 5316 helix: 1.24 (0.11), residues: 2304 sheet: -1.74 (0.15), residues: 744 loop : -0.17 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 4 TYR 0.035 0.002 TYR N 298 PHE 0.021 0.002 PHE L 287 TRP 0.018 0.002 TRP A 427 HIS 0.006 0.002 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (44100) covalent geometry : angle 0.57778 / 0.31 (59700) hydrogen bonds : bond 0.05940 / 3.92 ( 1545) hydrogen bonds : angle 4.83343 / 3.43 ( 4413) *********************** 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 842 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 720 time to evaluate : 1.356 Fit side-chains REVERT: A 16 GLU cc_start: 0.7937 (tp30) cc_final: 0.7578 (tm-30) REVERT: A 52 MET cc_start: 0.8719 (mmm) cc_final: 0.8299 (mmm) REVERT: A 119 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7724 (tttt) REVERT: A 168 GLU cc_start: 0.5610 (OUTLIER) cc_final: 0.3623 (mt-10) REVERT: A 266 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6312 (tm-30) REVERT: A 277 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8135 (m) REVERT: A 365 LYS cc_start: 0.7588 (mmtm) cc_final: 0.7141 (tttm) REVERT: A 401 MET cc_start: 0.9092 (ttt) cc_final: 0.8791 (ttt) REVERT: A 436 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: A 443 MET cc_start: 0.7839 (tpp) cc_final: 0.7550 (tpp) REVERT: B 16 GLU cc_start: 0.7693 (tp30) cc_final: 0.7344 (tm-30) REVERT: B 120 GLU cc_start: 0.7234 (pt0) cc_final: 0.6922 (mm-30) REVERT: B 151 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8074 (mm-30) REVERT: B 155 ASP cc_start: 0.8036 (t0) cc_final: 0.7805 (t70) REVERT: B 168 GLU cc_start: 0.5523 (OUTLIER) cc_final: 0.4652 (tt0) REVERT: B 169 ASN cc_start: 0.7038 (OUTLIER) cc_final: 0.5632 (m-40) REVERT: B 365 LYS cc_start: 0.7815 (mmtm) cc_final: 0.7419 (tttm) REVERT: B 399 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8141 (ttpt) REVERT: B 421 ASN cc_start: 0.8543 (m-40) cc_final: 0.7950 (t0) REVERT: B 436 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: C 13 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7480 (tttp) REVERT: C 119 LYS cc_start: 0.7794 (tptp) cc_final: 0.7450 (tttt) REVERT: C 120 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.7027 (mm-30) REVERT: C 155 ASP cc_start: 0.8181 (t0) cc_final: 0.7953 (t70) REVERT: C 168 GLU cc_start: 0.6024 (OUTLIER) cc_final: 0.5257 (tt0) REVERT: C 266 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: C 270 THR cc_start: 0.8361 (m) cc_final: 0.8144 (p) REVERT: C 365 LYS cc_start: 0.7671 (tppt) cc_final: 0.7175 (tttm) REVERT: C 388 GLN cc_start: 0.8144 (mt0) cc_final: 0.7854 (mm-40) REVERT: C 409 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8199 (ttpt) REVERT: C 421 ASN cc_start: 0.8469 (m-40) cc_final: 0.7959 (t0) REVERT: C 436 GLU cc_start: 0.7204 (pm20) cc_final: 0.6943 (pm20) REVERT: F 16 GLU cc_start: 0.7907 (tp30) cc_final: 0.7561 (tm-30) REVERT: F 52 MET cc_start: 0.8722 (mmm) cc_final: 0.8299 (mmm) REVERT: F 119 LYS cc_start: 0.7965 (ttpt) cc_final: 0.7713 (tttt) REVERT: F 168 GLU cc_start: 0.5336 (OUTLIER) cc_final: 0.4341 (tt0) REVERT: F 266 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6314 (tm-30) REVERT: F 270 THR cc_start: 0.8297 (m) cc_final: 0.7955 (p) REVERT: F 277 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8121 (m) REVERT: F 365 LYS cc_start: 0.7591 (mmtm) cc_final: 0.7124 (tttm) REVERT: F 401 MET cc_start: 0.9079 (ttt) cc_final: 0.8785 (ttt) REVERT: F 436 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: G 16 GLU cc_start: 0.7807 (tp30) cc_final: 0.7493 (tm-30) REVERT: G 151 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8073 (mm-30) REVERT: G 155 ASP cc_start: 0.8026 (t0) cc_final: 0.7792 (t70) REVERT: G 168 GLU cc_start: 0.5668 (OUTLIER) cc_final: 0.4596 (tt0) REVERT: G 169 ASN cc_start: 0.7030 (OUTLIER) cc_final: 0.5586 (m-40) REVERT: G 266 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: G 365 LYS cc_start: 0.7822 (mmtm) cc_final: 0.7428 (tttm) REVERT: G 399 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8125 (ttpt) REVERT: G 421 ASN cc_start: 0.8542 (m-40) cc_final: 0.7960 (t0) REVERT: G 436 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: H 13 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7479 (tttp) REVERT: H 16 GLU cc_start: 0.7877 (tp30) cc_final: 0.7609 (tm-30) REVERT: H 53 MET cc_start: 0.8363 (mtm) cc_final: 0.8134 (mtp) REVERT: H 119 LYS cc_start: 0.7806 (tptp) cc_final: 0.7426 (tttt) REVERT: H 120 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.7015 (mm-30) REVERT: H 151 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8139 (mm-30) REVERT: H 155 ASP cc_start: 0.8149 (t0) cc_final: 0.7875 (t70) REVERT: H 168 GLU cc_start: 0.5972 (OUTLIER) cc_final: 0.5288 (tt0) REVERT: H 270 THR cc_start: 0.8325 (m) cc_final: 0.8114 (p) REVERT: H 271 GLU cc_start: 0.7313 (tp30) cc_final: 0.6996 (tp30) REVERT: H 365 LYS cc_start: 0.7680 (tppt) cc_final: 0.7172 (tttm) REVERT: H 388 GLN cc_start: 0.8128 (mt0) cc_final: 0.7882 (mm-40) REVERT: H 421 ASN cc_start: 0.8470 (m-40) cc_final: 0.7958 (t0) REVERT: L 16 GLU cc_start: 0.7910 (tp30) cc_final: 0.7620 (tm-30) REVERT: L 119 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7721 (tttt) REVERT: L 168 GLU cc_start: 0.5429 (OUTLIER) cc_final: 0.4455 (tt0) REVERT: L 266 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6312 (tm-30) REVERT: L 270 THR cc_start: 0.8307 (m) cc_final: 0.7956 (p) REVERT: L 277 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8125 (m) REVERT: L 365 LYS cc_start: 0.7560 (mmtm) cc_final: 0.7090 (tttm) REVERT: L 443 MET cc_start: 0.7842 (tpp) cc_final: 0.7539 (tpp) REVERT: N 16 GLU cc_start: 0.7712 (tp30) cc_final: 0.7365 (tm-30) REVERT: N 120 GLU cc_start: 0.7123 (pt0) cc_final: 0.6808 (mm-30) REVERT: N 151 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8079 (mm-30) REVERT: N 168 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5306 (tm-30) REVERT: N 365 LYS cc_start: 0.7813 (mmtm) cc_final: 0.7415 (tttm) REVERT: N 399 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8115 (ttpt) REVERT: N 421 ASN cc_start: 0.8548 (m-40) cc_final: 0.7959 (t0) REVERT: O 13 LYS cc_start: 0.8005 (ttmm) cc_final: 0.7487 (tttp) REVERT: O 16 GLU cc_start: 0.7904 (tp30) cc_final: 0.7637 (tm-30) REVERT: O 119 LYS cc_start: 0.7795 (tptp) cc_final: 0.7437 (tttt) REVERT: O 120 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.7016 (mm-30) REVERT: O 151 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8105 (mm-30) REVERT: O 155 ASP cc_start: 0.8131 (t0) cc_final: 0.7862 (t70) REVERT: O 168 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5336 (tt0) REVERT: O 271 GLU cc_start: 0.7351 (tp30) cc_final: 0.7023 (tp30) REVERT: O 365 LYS cc_start: 0.7669 (tppt) cc_final: 0.7191 (tttm) REVERT: O 388 GLN cc_start: 0.8129 (mt0) cc_final: 0.7873 (mm-40) REVERT: O 421 ASN cc_start: 0.8469 (m-40) cc_final: 0.7954 (t0) REVERT: R 16 GLU cc_start: 0.7897 (tp30) cc_final: 0.7558 (tm-30) REVERT: R 52 MET cc_start: 0.8616 (mmm) cc_final: 0.8310 (mmm) REVERT: R 119 LYS cc_start: 0.7956 (ttpt) cc_final: 0.7727 (tttt) REVERT: R 168 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.5112 (tt0) REVERT: R 266 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6284 (tm-30) REVERT: R 270 THR cc_start: 0.8297 (m) cc_final: 0.7946 (p) REVERT: R 277 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8116 (m) REVERT: R 365 LYS cc_start: 0.7586 (mmtm) cc_final: 0.7123 (tttm) REVERT: R 401 MET cc_start: 0.9082 (ttt) cc_final: 0.8808 (ttt) REVERT: S 16 GLU cc_start: 0.7699 (tp30) cc_final: 0.7347 (tm-30) REVERT: S 151 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8075 (mm-30) REVERT: S 155 ASP cc_start: 0.8057 (t0) cc_final: 0.7826 (t70) REVERT: S 168 GLU cc_start: 0.5678 (OUTLIER) cc_final: 0.4859 (tt0) REVERT: S 226 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7973 (tttt) REVERT: S 266 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: S 365 LYS cc_start: 0.7823 (mmtm) cc_final: 0.7430 (tttm) REVERT: S 421 ASN cc_start: 0.8544 (m-40) cc_final: 0.7955 (t0) REVERT: T 13 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7505 (tttp) REVERT: T 119 LYS cc_start: 0.7807 (tptp) cc_final: 0.7448 (tttt) REVERT: T 120 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7039 (mm-30) REVERT: T 151 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8097 (mm-30) REVERT: T 155 ASP cc_start: 0.8128 (t0) cc_final: 0.7862 (t70) REVERT: T 266 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6367 (mp0) REVERT: T 270 THR cc_start: 0.8364 (m) cc_final: 0.8147 (p) REVERT: T 365 LYS cc_start: 0.7666 (tppt) cc_final: 0.7187 (tttm) REVERT: T 388 GLN cc_start: 0.8130 (mt0) cc_final: 0.7925 (mm-40) REVERT: T 421 ASN cc_start: 0.8472 (m-40) cc_final: 0.7958 (t0) outliers start: 122 outliers final: 50 residues processed: 810 average time/residue: 0.7484 time to fit residues: 740.6983 Evaluate side-chains 793 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 706 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 366 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 169 ASN Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 436 GLU 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 366 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 39 VAL 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 277 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 436 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 169 ASN Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 282 LYS Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 399 LYS Chi-restraints excluded: chain G residue 436 GLU 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 366 VAL Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain L residue 39 VAL 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 277 THR Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 168 GLU Chi-restraints excluded: chain N residue 282 LYS Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 366 VAL Chi-restraints excluded: chain N residue 399 LYS 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 366 VAL Chi-restraints excluded: chain O residue 385 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 169 ASN Chi-restraints excluded: chain R residue 266 GLU Chi-restraints excluded: chain R residue 277 THR Chi-restraints excluded: chain R residue 366 VAL 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 330 LEU Chi-restraints excluded: chain S residue 366 VAL Chi-restraints excluded: chain S residue 374 ILE 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 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: [127, 157, 432, 185, 196, 458, 404, 14, 61, 439, 376] chunk 127 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 432 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 196 optimal weight: 0.5980 chunk 458 optimal weight: 1.9990 chunk 404 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 61 optimal weight: 10.0000 chunk 439 optimal weight: 3.9990 chunk 376 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 421 ASN B 36 ASN C 36 ASN C 228 ASN F 36 ASN F 421 ASN G 36 ASN G 413 ASN H 36 ASN H 228 ASN L 36 ASN L 421 ASN N 36 ASN ** N 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN O 228 ASN R 36 ASN R 421 ASN S 36 ASN S 413 ASN T 36 ASN T 228 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.153779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.133860 restraints weight = 39281.694| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.02 r_work: 0.3420 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2072 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= 0.109 Angle : 0.460 5.239 59700 Z= 0.248 Chirality : 0.040 0.143 6444 Planarity : 0.003 0.034 7860 Dihedral : 6.368 62.655 5903 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.12 % Allowed : 14.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.11), residues: 5316 helix: 1.57 (0.11), residues: 2292 sheet: -1.62 (0.15), residues: 744 loop : -0.12 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 4 TYR 0.026 0.002 TYR S 298 PHE 0.011 0.001 PHE R 287 TRP 0.014 0.001 TRP R 427 HIS 0.004 0.001 HIS C 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (44100) covalent geometry : angle 0.45950 / 0.25 (59700) hydrogen bonds : bond 0.04496 / 2.98 ( 1545) hydrogen bonds : angle 4.49148 / 3.19 ( 4413) *********************** 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 840 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 742 time to evaluate : 1.616 Fit side-chains REVERT: A 16 GLU cc_start: 0.7890 (tp30) cc_final: 0.7509 (tm-30) REVERT: A 52 MET cc_start: 0.8714 (mmm) cc_final: 0.8308 (mmm) REVERT: A 119 LYS cc_start: 0.7941 (ttpt) cc_final: 0.7656 (tttt) REVERT: A 168 GLU cc_start: 0.5456 (OUTLIER) cc_final: 0.4882 (pp20) REVERT: A 246 MET cc_start: 0.8353 (ttp) cc_final: 0.8036 (ttp) REVERT: A 266 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6436 (tm-30) REVERT: A 277 THR cc_start: 0.8352 (t) cc_final: 0.8143 (m) REVERT: A 365 LYS cc_start: 0.7591 (mmtm) cc_final: 0.7151 (tttm) REVERT: A 443 MET cc_start: 0.7612 (tpp) cc_final: 0.7343 (tpp) REVERT: B 16 GLU cc_start: 0.7625 (tp30) cc_final: 0.7249 (tm-30) REVERT: B 120 GLU cc_start: 0.7145 (pt0) cc_final: 0.6869 (mm-30) REVERT: B 151 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7994 (mm-30) REVERT: B 155 ASP cc_start: 0.7989 (t0) cc_final: 0.7742 (t70) REVERT: B 168 GLU cc_start: 0.5243 (OUTLIER) cc_final: 0.4758 (tt0) REVERT: B 169 ASN cc_start: 0.6703 (OUTLIER) cc_final: 0.5450 (m-40) REVERT: B 226 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8075 (tttm) REVERT: B 365 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7332 (tttm) REVERT: B 399 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8115 (ttpt) REVERT: B 421 ASN cc_start: 0.8520 (m-40) cc_final: 0.7899 (t0) REVERT: C 13 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7425 (tttp) REVERT: C 119 LYS cc_start: 0.7744 (tptp) cc_final: 0.7413 (tttt) REVERT: C 120 GLU cc_start: 0.7257 (pt0) cc_final: 0.7016 (mm-30) REVERT: C 155 ASP cc_start: 0.8166 (t0) cc_final: 0.7922 (t70) REVERT: C 168 GLU cc_start: 0.5649 (OUTLIER) cc_final: 0.5192 (tt0) REVERT: C 266 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: C 270 THR cc_start: 0.8188 (m) cc_final: 0.7971 (p) REVERT: C 365 LYS cc_start: 0.7652 (tppt) cc_final: 0.7137 (tttm) REVERT: C 388 GLN cc_start: 0.8118 (mt0) cc_final: 0.7819 (mm-40) REVERT: C 409 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8145 (ttmt) REVERT: C 421 ASN cc_start: 0.8394 (m-40) cc_final: 0.7869 (t0) REVERT: F 16 GLU cc_start: 0.7897 (tp30) cc_final: 0.7515 (tm-30) REVERT: F 52 MET cc_start: 0.8714 (mmm) cc_final: 0.8305 (mmm) REVERT: F 119 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7654 (tttt) REVERT: F 168 GLU cc_start: 0.5173 (OUTLIER) cc_final: 0.4498 (tt0) REVERT: F 181 MET cc_start: 0.8163 (mtp) cc_final: 0.7938 (mtp) REVERT: F 246 MET cc_start: 0.8351 (ttp) cc_final: 0.8032 (ttp) REVERT: F 266 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6433 (tm-30) REVERT: F 270 THR cc_start: 0.8193 (m) cc_final: 0.7817 (p) REVERT: F 277 THR cc_start: 0.8347 (t) cc_final: 0.8121 (m) REVERT: F 365 LYS cc_start: 0.7606 (mmtm) cc_final: 0.7164 (tttm) REVERT: F 436 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: G 16 GLU cc_start: 0.7675 (tp30) cc_final: 0.7342 (tm-30) REVERT: G 151 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7978 (mm-30) REVERT: G 155 ASP cc_start: 0.7994 (t0) cc_final: 0.7741 (t70) REVERT: G 168 GLU cc_start: 0.5422 (OUTLIER) cc_final: 0.4667 (tt0) REVERT: G 169 ASN cc_start: 0.6710 (OUTLIER) cc_final: 0.5441 (m-40) REVERT: G 365 LYS cc_start: 0.7782 (mmtm) cc_final: 0.7337 (tttm) REVERT: G 399 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8114 (ttpt) REVERT: G 421 ASN cc_start: 0.8516 (m-40) cc_final: 0.7891 (t0) REVERT: G 436 GLU cc_start: 0.7733 (pm20) cc_final: 0.7188 (pm20) REVERT: H 13 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7431 (tttp) REVERT: H 16 GLU cc_start: 0.7829 (tp30) cc_final: 0.7538 (tm-30) REVERT: H 53 MET cc_start: 0.8403 (mtm) cc_final: 0.8171 (mtp) REVERT: H 119 LYS cc_start: 0.7765 (tptp) cc_final: 0.7410 (tttt) REVERT: H 120 GLU cc_start: 0.7251 (pt0) cc_final: 0.7001 (mm-30) REVERT: H 151 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8122 (mm-30) REVERT: H 155 ASP cc_start: 0.8095 (t0) cc_final: 0.7813 (t70) REVERT: H 168 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5154 (tt0) REVERT: H 270 THR cc_start: 0.8173 (m) cc_final: 0.7950 (p) REVERT: H 271 GLU cc_start: 0.7224 (tp30) cc_final: 0.6919 (tp30) REVERT: H 365 LYS cc_start: 0.7635 (tppt) cc_final: 0.7136 (tttm) REVERT: H 388 GLN cc_start: 0.8050 (mt0) cc_final: 0.7761 (mm-40) REVERT: H 421 ASN cc_start: 0.8405 (m-40) cc_final: 0.7877 (t0) REVERT: L 16 GLU cc_start: 0.7875 (tp30) cc_final: 0.7496 (tm-30) REVERT: L 119 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7634 (tttt) REVERT: L 168 GLU cc_start: 0.5203 (OUTLIER) cc_final: 0.4558 (tt0) REVERT: L 246 MET cc_start: 0.8349 (ttp) cc_final: 0.8032 (ttp) REVERT: L 270 THR cc_start: 0.8179 (m) cc_final: 0.7796 (p) REVERT: L 277 THR cc_start: 0.8342 (t) cc_final: 0.8126 (m) REVERT: L 365 LYS cc_start: 0.7562 (mmtm) cc_final: 0.7112 (tttm) REVERT: L 443 MET cc_start: 0.7627 (tpp) cc_final: 0.7336 (tpp) REVERT: N 16 GLU cc_start: 0.7640 (tp30) cc_final: 0.7251 (tm-30) REVERT: N 120 GLU cc_start: 0.7105 (pt0) cc_final: 0.6822 (mm-30) REVERT: N 151 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7983 (mm-30) REVERT: N 168 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.5238 (tm-30) REVERT: N 365 LYS cc_start: 0.7774 (mmtm) cc_final: 0.7329 (tttm) REVERT: N 399 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8105 (ttpt) REVERT: N 421 ASN cc_start: 0.8516 (m-40) cc_final: 0.7889 (t0) REVERT: O 13 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7413 (tttp) REVERT: O 16 GLU cc_start: 0.7826 (tp30) cc_final: 0.7528 (tm-30) REVERT: O 119 LYS cc_start: 0.7749 (tptp) cc_final: 0.7412 (tttt) REVERT: O 120 GLU cc_start: 0.7245 (pt0) cc_final: 0.7016 (mm-30) REVERT: O 151 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8110 (mm-30) REVERT: O 155 ASP cc_start: 0.8106 (t0) cc_final: 0.7826 (t70) REVERT: O 168 GLU cc_start: 0.5666 (OUTLIER) cc_final: 0.5178 (tt0) REVERT: O 271 GLU cc_start: 0.7172 (tp30) cc_final: 0.6932 (tp30) REVERT: O 365 LYS cc_start: 0.7627 (tppt) cc_final: 0.7147 (tttm) REVERT: O 388 GLN cc_start: 0.8094 (mt0) cc_final: 0.7798 (mm-40) REVERT: O 421 ASN cc_start: 0.8402 (m-40) cc_final: 0.7866 (t0) REVERT: R 16 GLU cc_start: 0.7870 (tp30) cc_final: 0.7491 (tm-30) REVERT: R 52 MET cc_start: 0.8586 (mmm) cc_final: 0.8290 (mmm) REVERT: R 119 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7630 (tttt) REVERT: R 168 GLU cc_start: 0.5631 (OUTLIER) cc_final: 0.4802 (tt0) REVERT: R 246 MET cc_start: 0.8352 (ttp) cc_final: 0.8035 (ttp) REVERT: R 270 THR cc_start: 0.8198 (m) cc_final: 0.7817 (p) REVERT: R 277 THR cc_start: 0.8344 (t) cc_final: 0.8125 (m) REVERT: R 365 LYS cc_start: 0.7586 (mmtm) cc_final: 0.7139 (tttm) REVERT: S 16 GLU cc_start: 0.7594 (tp30) cc_final: 0.7229 (tm-30) REVERT: S 151 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8006 (mm-30) REVERT: S 155 ASP cc_start: 0.8033 (t0) cc_final: 0.7773 (t70) REVERT: S 168 GLU cc_start: 0.5323 (OUTLIER) cc_final: 0.5056 (tt0) REVERT: S 226 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7971 (tttm) REVERT: S 266 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6346 (mp0) REVERT: S 365 LYS cc_start: 0.7772 (mmtm) cc_final: 0.7308 (tttm) REVERT: S 421 ASN cc_start: 0.8523 (m-40) cc_final: 0.7900 (t0) REVERT: T 13 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7446 (tttp) REVERT: T 119 LYS cc_start: 0.7755 (tptp) cc_final: 0.7408 (tttt) REVERT: T 120 GLU cc_start: 0.7252 (pt0) cc_final: 0.7009 (mm-30) REVERT: T 151 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8102 (mm-30) REVERT: T 155 ASP cc_start: 0.8095 (t0) cc_final: 0.7823 (t70) REVERT: T 266 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: T 270 THR cc_start: 0.8192 (m) cc_final: 0.7979 (p) REVERT: T 365 LYS cc_start: 0.7627 (tppt) cc_final: 0.7142 (tttm) REVERT: T 388 GLN cc_start: 0.8037 (mt0) cc_final: 0.7825 (mm-40) REVERT: T 421 ASN cc_start: 0.8392 (m-40) cc_final: 0.7871 (t0) outliers start: 98 outliers final: 48 residues processed: 810 average time/residue: 0.7354 time to fit residues: 729.8418 Evaluate side-chains 801 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 729 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 399 LYS 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 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 F residue 39 VAL 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 366 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 436 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 169 ASN Chi-restraints excluded: chain G residue 399 LYS 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 L residue 39 VAL Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain L residue 366 VAL 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 399 LYS 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 168 GLU Chi-restraints excluded: chain R residue 169 ASN Chi-restraints excluded: chain R residue 366 VAL 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 330 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: [408, 84, 474, 348, 365, 240, 480, 440, 324, 238, 366] chunk 408 optimal weight: 0.0980 chunk 84 optimal weight: 10.0000 chunk 474 optimal weight: 8.9990 chunk 348 optimal weight: 7.9990 chunk 365 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 chunk 480 optimal weight: 5.9990 chunk 440 optimal weight: 7.9990 chunk 324 optimal weight: 4.9990 chunk 238 optimal weight: 8.9990 chunk 366 optimal weight: 1.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 36 ASN C 36 ASN F 36 ASN G 36 ASN G 169 ASN G 413 ASN H 36 ASN L 36 ASN N 36 ASN ** N 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN R 36 ASN S 36 ASN S 413 ASN T 36 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130626 restraints weight = 38926.684| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.01 r_work: 0.3379 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 44100 Z= 0.219 Angle : 0.612 6.751 59700 Z= 0.333 Chirality : 0.047 0.167 6444 Planarity : 0.005 0.043 7860 Dihedral : 6.893 67.983 5903 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.68 % Allowed : 14.29 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.11), residues: 5316 helix: 1.20 (0.11), residues: 2292 sheet: -1.71 (0.15), residues: 744 loop : -0.26 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 4 TYR 0.036 0.003 TYR B 298 PHE 0.022 0.002 PHE H 287 TRP 0.019 0.002 TRP F 427 HIS 0.006 0.002 HIS O 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (44100) covalent geometry : angle 0.61207 / 0.33 (59700) hydrogen bonds : bond 0.06232 / 4.12 ( 1545) hydrogen bonds : angle 4.88132 / 3.46 ( 4413) *********************** 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 826 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 702 time to evaluate : 1.609 Fit side-chains REVERT: A 16 GLU cc_start: 0.7958 (tp30) cc_final: 0.7653 (tm-30) REVERT: A 52 MET cc_start: 0.8691 (mmm) cc_final: 0.8285 (mmm) REVERT: A 119 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7682 (tttt) REVERT: A 168 GLU cc_start: 0.5764 (OUTLIER) cc_final: 0.3653 (mt-10) REVERT: A 277 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8143 (m) REVERT: A 365 LYS cc_start: 0.7546 (mmtm) cc_final: 0.7113 (tttm) REVERT: A 436 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7683 (pm20) REVERT: B 16 GLU cc_start: 0.7664 (tp30) cc_final: 0.7303 (tm-30) REVERT: B 120 GLU cc_start: 0.7306 (pt0) cc_final: 0.6903 (mm-30) REVERT: B 151 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8043 (mm-30) REVERT: B 155 ASP cc_start: 0.8052 (t0) cc_final: 0.7799 (t70) REVERT: B 168 GLU cc_start: 0.5602 (OUTLIER) cc_final: 0.4556 (tt0) REVERT: B 169 ASN cc_start: 0.7066 (OUTLIER) cc_final: 0.5658 (m-40) REVERT: B 226 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8139 (tttt) REVERT: B 365 LYS cc_start: 0.7792 (mmtm) cc_final: 0.7349 (tttm) REVERT: B 421 ASN cc_start: 0.8571 (m-40) cc_final: 0.7938 (t0) REVERT: C 13 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7481 (tttp) REVERT: C 119 LYS cc_start: 0.7777 (tptp) cc_final: 0.7421 (tttt) REVERT: C 155 ASP cc_start: 0.8169 (t0) cc_final: 0.7932 (t70) REVERT: C 168 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5216 (tt0) REVERT: C 266 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6370 (mp0) REVERT: C 270 THR cc_start: 0.8336 (m) cc_final: 0.8105 (p) REVERT: C 365 LYS cc_start: 0.7665 (tppt) cc_final: 0.7150 (tttm) REVERT: C 388 GLN cc_start: 0.8094 (mt0) cc_final: 0.7805 (mm-40) REVERT: C 409 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8142 (ttmm) REVERT: C 421 ASN cc_start: 0.8413 (m-40) cc_final: 0.7893 (t0) REVERT: F 16 GLU cc_start: 0.7947 (tp30) cc_final: 0.7641 (tm-30) REVERT: F 52 MET cc_start: 0.8695 (mmm) cc_final: 0.8287 (mmm) REVERT: F 119 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7685 (tttt) REVERT: F 168 GLU cc_start: 0.5411 (OUTLIER) cc_final: 0.4253 (tt0) REVERT: F 270 THR cc_start: 0.8285 (m) cc_final: 0.7934 (p) REVERT: F 277 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8135 (m) REVERT: F 365 LYS cc_start: 0.7556 (mmtm) cc_final: 0.7113 (tttm) REVERT: F 436 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: G 16 GLU cc_start: 0.7729 (tp30) cc_final: 0.7413 (tm-30) REVERT: G 151 GLU cc_start: 0.8235 (mt-10) cc_final: 0.8032 (mm-30) REVERT: G 155 ASP cc_start: 0.8029 (t0) cc_final: 0.7779 (t70) REVERT: G 168 GLU cc_start: 0.5757 (OUTLIER) cc_final: 0.4528 (tt0) REVERT: G 226 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8132 (tttt) REVERT: G 266 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: G 365 LYS cc_start: 0.7773 (mmtm) cc_final: 0.7335 (tttm) REVERT: G 421 ASN cc_start: 0.8572 (m-40) cc_final: 0.7944 (t0) REVERT: G 436 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7217 (pm20) REVERT: H 13 LYS cc_start: 0.8018 (ttmm) cc_final: 0.7489 (tttp) REVERT: H 16 GLU cc_start: 0.7878 (tp30) cc_final: 0.7669 (tm-30) REVERT: H 53 MET cc_start: 0.8368 (mtm) cc_final: 0.8128 (mtp) REVERT: H 119 LYS cc_start: 0.7802 (tptp) cc_final: 0.7436 (tttt) REVERT: H 151 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8110 (mm-30) REVERT: H 155 ASP cc_start: 0.8125 (t0) cc_final: 0.7857 (t70) REVERT: H 168 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5261 (tt0) REVERT: H 270 THR cc_start: 0.8321 (m) cc_final: 0.8085 (p) REVERT: H 271 GLU cc_start: 0.7283 (tp30) cc_final: 0.6957 (tp30) REVERT: H 365 LYS cc_start: 0.7668 (tppt) cc_final: 0.7148 (tttm) REVERT: H 388 GLN cc_start: 0.8090 (mt0) cc_final: 0.7822 (mm-40) REVERT: H 421 ASN cc_start: 0.8424 (m-40) cc_final: 0.7900 (t0) REVERT: L 16 GLU cc_start: 0.7950 (tp30) cc_final: 0.7648 (tm-30) REVERT: L 119 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7681 (tttt) REVERT: L 168 GLU cc_start: 0.5503 (OUTLIER) cc_final: 0.4316 (tt0) REVERT: L 270 THR cc_start: 0.8282 (m) cc_final: 0.7924 (p) REVERT: L 277 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8144 (m) REVERT: L 365 LYS cc_start: 0.7519 (mmtm) cc_final: 0.7078 (tttm) REVERT: N 16 GLU cc_start: 0.7664 (tp30) cc_final: 0.7289 (tm-30) REVERT: N 120 GLU cc_start: 0.7261 (pt0) cc_final: 0.6904 (mm-30) REVERT: N 151 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8031 (mm-30) REVERT: N 168 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.5308 (tm-30) REVERT: N 226 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8119 (tttt) REVERT: N 365 LYS cc_start: 0.7798 (mmtm) cc_final: 0.7342 (tttm) REVERT: N 421 ASN cc_start: 0.8553 (m-40) cc_final: 0.7926 (t0) REVERT: O 13 LYS cc_start: 0.8005 (ttmm) cc_final: 0.7470 (tttp) REVERT: O 16 GLU cc_start: 0.7884 (tp30) cc_final: 0.7668 (tm-30) REVERT: O 119 LYS cc_start: 0.7796 (tptp) cc_final: 0.7426 (tttt) REVERT: O 151 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8076 (mm-30) REVERT: O 155 ASP cc_start: 0.8162 (t0) cc_final: 0.7891 (t70) REVERT: O 168 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5258 (tt0) REVERT: O 271 GLU cc_start: 0.7249 (tp30) cc_final: 0.6997 (tp30) REVERT: O 365 LYS cc_start: 0.7669 (tppt) cc_final: 0.7158 (tttm) REVERT: O 388 GLN cc_start: 0.8090 (mt0) cc_final: 0.7820 (mm-40) REVERT: O 421 ASN cc_start: 0.8416 (m-40) cc_final: 0.7894 (t0) REVERT: R 16 GLU cc_start: 0.7927 (tp30) cc_final: 0.7565 (tm-30) REVERT: R 52 MET cc_start: 0.8601 (mmm) cc_final: 0.8163 (mmm) REVERT: R 119 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7654 (tttt) REVERT: R 168 GLU cc_start: 0.6027 (OUTLIER) cc_final: 0.5160 (tt0) REVERT: R 270 THR cc_start: 0.8294 (m) cc_final: 0.7940 (p) REVERT: R 277 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8144 (m) REVERT: R 365 LYS cc_start: 0.7547 (mmtm) cc_final: 0.7100 (tttm) REVERT: R 401 MET cc_start: 0.9064 (ttt) cc_final: 0.8835 (ttt) REVERT: S 16 GLU cc_start: 0.7634 (tp30) cc_final: 0.7284 (tm-30) REVERT: S 151 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8045 (mm-30) REVERT: S 155 ASP cc_start: 0.8056 (t0) cc_final: 0.7805 (t70) REVERT: S 168 GLU cc_start: 0.5751 (OUTLIER) cc_final: 0.4884 (tt0) REVERT: S 169 ASN cc_start: 0.7122 (OUTLIER) cc_final: 0.5741 (m-40) REVERT: S 226 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8031 (tttt) REVERT: S 266 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6342 (mp0) REVERT: S 365 LYS cc_start: 0.7781 (mmtm) cc_final: 0.7331 (tttm) REVERT: S 421 ASN cc_start: 0.8574 (m-40) cc_final: 0.7938 (t0) REVERT: T 13 LYS cc_start: 0.8030 (ttmm) cc_final: 0.7485 (tttp) REVERT: T 119 LYS cc_start: 0.7799 (tptp) cc_final: 0.7418 (tttt) REVERT: T 120 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7071 (mm-30) REVERT: T 151 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8087 (mm-30) REVERT: T 155 ASP cc_start: 0.8133 (t0) cc_final: 0.7860 (t70) REVERT: T 168 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.4805 (tm-30) REVERT: T 266 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: T 270 THR cc_start: 0.8337 (m) cc_final: 0.8120 (p) REVERT: T 365 LYS cc_start: 0.7654 (tppt) cc_final: 0.7136 (tttm) REVERT: T 421 ASN cc_start: 0.8416 (m-40) cc_final: 0.7891 (t0) outliers start: 124 outliers final: 50 residues processed: 793 average time/residue: 0.7432 time to fit residues: 720.4662 Evaluate side-chains 788 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 708 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 277 THR 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 169 ASN Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 33 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 F residue 39 VAL Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 277 THR 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 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 330 LEU Chi-restraints excluded: chain G residue 436 GLU Chi-restraints excluded: chain H residue 33 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 L residue 39 VAL Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 366 VAL 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 330 LEU Chi-restraints excluded: chain N residue 366 VAL Chi-restraints excluded: chain O residue 33 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 R residue 39 VAL Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 169 ASN Chi-restraints excluded: chain R residue 277 THR Chi-restraints excluded: chain R residue 366 VAL 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 330 LEU Chi-restraints excluded: chain S residue 366 VAL 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 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 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: [333, 491, 246, 418, 460, 194, 255, 134, 467, 28, 322] chunk 333 optimal weight: 1.9990 chunk 491 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 418 optimal weight: 8.9990 chunk 460 optimal weight: 0.0470 chunk 194 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 467 optimal weight: 7.9990 chunk 28 optimal weight: 0.3980 chunk 322 optimal weight: 0.0050 overall best weight: 0.6896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 36 ASN 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 N 36 ASN ** N 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 228 ASN O 36 ASN R 36 ASN S 36 ASN S 228 ASN S 413 ASN T 36 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.156367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.136702 restraints weight = 39340.963| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.02 r_work: 0.3456 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2092 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= 0.079 Angle : 0.416 4.752 59700 Z= 0.223 Chirality : 0.039 0.132 6444 Planarity : 0.003 0.032 7860 Dihedral : 5.944 59.872 5901 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.11), residues: 5316 helix: 1.81 (0.11), residues: 2292 sheet: -1.48 (0.15), residues: 744 loop : -0.02 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 4 TYR 0.022 0.001 TYR S 298 PHE 0.007 0.001 PHE R 287 TRP 0.013 0.001 TRP A 427 HIS 0.003 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00166 / 0.08 (44100) covalent geometry : angle 0.41610 / 0.22 (59700) hydrogen bonds : bond 0.03649 / 2.42 ( 1545) hydrogen bonds : angle 4.24206 / 3.01 ( 4413) *********************** 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 819 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 753 time to evaluate : 1.661 Fit side-chains REVERT: A 16 GLU cc_start: 0.7874 (tp30) cc_final: 0.7485 (tm-30) REVERT: A 52 MET cc_start: 0.8725 (mmm) cc_final: 0.8327 (mmm) REVERT: A 119 LYS cc_start: 0.7913 (ttpt) cc_final: 0.7615 (tttt) REVERT: A 168 GLU cc_start: 0.5319 (OUTLIER) cc_final: 0.4812 (pp20) REVERT: A 246 MET cc_start: 0.8237 (ttp) cc_final: 0.7994 (ttp) REVERT: A 277 THR cc_start: 0.8344 (t) cc_final: 0.8129 (m) REVERT: A 365 LYS cc_start: 0.7606 (mmtm) cc_final: 0.7164 (tttm) REVERT: B 16 GLU cc_start: 0.7590 (tp30) cc_final: 0.7217 (tm-30) REVERT: B 155 ASP cc_start: 0.8054 (t0) cc_final: 0.7779 (t70) REVERT: B 168 GLU cc_start: 0.5128 (OUTLIER) cc_final: 0.4870 (tt0) REVERT: B 365 LYS cc_start: 0.7764 (mmtm) cc_final: 0.7313 (tttm) REVERT: B 421 ASN cc_start: 0.8488 (m-40) cc_final: 0.7872 (t0) REVERT: C 13 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7323 (tttp) REVERT: C 119 LYS cc_start: 0.7717 (tptp) cc_final: 0.7392 (tttt) REVERT: C 155 ASP cc_start: 0.8121 (t0) cc_final: 0.7871 (t70) REVERT: C 365 LYS cc_start: 0.7689 (tppt) cc_final: 0.7113 (tttm) REVERT: C 388 GLN cc_start: 0.8113 (mt0) cc_final: 0.7796 (mm-40) REVERT: C 409 LYS cc_start: 0.8333 (ttmm) cc_final: 0.8089 (ttmt) REVERT: C 421 ASN cc_start: 0.8371 (m-40) cc_final: 0.7853 (t0) REVERT: F 13 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7731 (ttmt) REVERT: F 16 GLU cc_start: 0.7827 (tp30) cc_final: 0.7441 (tm-30) REVERT: F 52 MET cc_start: 0.8723 (mmm) cc_final: 0.8317 (mmm) REVERT: F 119 LYS cc_start: 0.7910 (ttpt) cc_final: 0.7609 (tttt) REVERT: F 168 GLU cc_start: 0.5033 (OUTLIER) cc_final: 0.4782 (tt0) REVERT: F 181 MET cc_start: 0.8105 (mtp) cc_final: 0.7878 (mtp) REVERT: F 246 MET cc_start: 0.8231 (ttp) cc_final: 0.7989 (ttp) REVERT: F 270 THR cc_start: 0.8103 (m) cc_final: 0.7707 (p) REVERT: F 277 THR cc_start: 0.8336 (t) cc_final: 0.8111 (m) REVERT: F 365 LYS cc_start: 0.7600 (mmtm) cc_final: 0.7164 (tttm) REVERT: F 436 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7396 (pm20) REVERT: G 151 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7971 (mm-30) REVERT: G 155 ASP cc_start: 0.8065 (t0) cc_final: 0.7791 (t70) REVERT: G 168 GLU cc_start: 0.5316 (OUTLIER) cc_final: 0.4935 (tt0) REVERT: G 365 LYS cc_start: 0.7712 (mmtm) cc_final: 0.7248 (tttm) REVERT: G 421 ASN cc_start: 0.8479 (m-40) cc_final: 0.7866 (t0) REVERT: H 13 LYS cc_start: 0.7893 (ttmm) cc_final: 0.7329 (tttp) REVERT: H 16 GLU cc_start: 0.7770 (tp30) cc_final: 0.7476 (tm-30) REVERT: H 53 MET cc_start: 0.8332 (mtm) cc_final: 0.8116 (mtp) REVERT: H 119 LYS cc_start: 0.7730 (tptp) cc_final: 0.7391 (tttt) REVERT: H 151 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8117 (mm-30) REVERT: H 155 ASP cc_start: 0.8081 (t0) cc_final: 0.7807 (t70) REVERT: H 271 GLU cc_start: 0.7148 (tp30) cc_final: 0.6851 (tp30) REVERT: H 365 LYS cc_start: 0.7666 (tppt) cc_final: 0.7135 (tttm) REVERT: H 388 GLN cc_start: 0.8086 (mt0) cc_final: 0.7786 (mm-40) REVERT: H 421 ASN cc_start: 0.8386 (m-40) cc_final: 0.7857 (t0) REVERT: L 16 GLU cc_start: 0.7853 (tp30) cc_final: 0.7459 (tm-30) REVERT: L 119 LYS cc_start: 0.7939 (ttpt) cc_final: 0.7668 (tttt) REVERT: L 168 GLU cc_start: 0.4935 (OUTLIER) cc_final: 0.4664 (tt0) REVERT: L 246 MET cc_start: 0.8223 (ttp) cc_final: 0.7982 (ttp) REVERT: L 270 THR cc_start: 0.8120 (m) cc_final: 0.7730 (p) REVERT: L 277 THR cc_start: 0.8335 (t) cc_final: 0.8120 (m) REVERT: L 365 LYS cc_start: 0.7580 (mmtm) cc_final: 0.7139 (tttm) REVERT: L 436 GLU cc_start: 0.6765 (pm20) cc_final: 0.6515 (pt0) REVERT: N 16 GLU cc_start: 0.7647 (tp30) cc_final: 0.7244 (tm-30) REVERT: N 120 GLU cc_start: 0.7147 (pt0) cc_final: 0.6908 (mm-30) REVERT: N 365 LYS cc_start: 0.7773 (mmtm) cc_final: 0.7314 (tttm) REVERT: N 421 ASN cc_start: 0.8489 (m-40) cc_final: 0.7879 (t0) REVERT: O 13 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7307 (tttp) REVERT: O 16 GLU cc_start: 0.7760 (tp30) cc_final: 0.7459 (tm-30) REVERT: O 119 LYS cc_start: 0.7726 (tptp) cc_final: 0.7390 (tttt) REVERT: O 151 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8110 (mm-30) REVERT: O 155 ASP cc_start: 0.8120 (t0) cc_final: 0.7840 (t70) REVERT: O 271 GLU cc_start: 0.7160 (tp30) cc_final: 0.6918 (tp30) REVERT: O 365 LYS cc_start: 0.7655 (tppt) cc_final: 0.7150 (tttm) REVERT: O 388 GLN cc_start: 0.8110 (mt0) cc_final: 0.7813 (mm-40) REVERT: O 421 ASN cc_start: 0.8374 (m-40) cc_final: 0.7840 (t0) REVERT: R 13 LYS cc_start: 0.7996 (ttmm) cc_final: 0.7716 (ttmt) REVERT: R 16 GLU cc_start: 0.7856 (tp30) cc_final: 0.7467 (tm-30) REVERT: R 52 MET cc_start: 0.8606 (mmm) cc_final: 0.8264 (mmm) REVERT: R 119 LYS cc_start: 0.7928 (ttpt) cc_final: 0.7630 (tttt) REVERT: R 246 MET cc_start: 0.8236 (ttp) cc_final: 0.7995 (ttp) REVERT: R 270 THR cc_start: 0.8115 (m) cc_final: 0.7717 (p) REVERT: R 277 THR cc_start: 0.8335 (t) cc_final: 0.8115 (m) REVERT: R 365 LYS cc_start: 0.7582 (mmtm) cc_final: 0.7137 (tttm) REVERT: S 16 GLU cc_start: 0.7621 (tp30) cc_final: 0.7194 (tt0) REVERT: S 151 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8011 (mm-30) REVERT: S 155 ASP cc_start: 0.8036 (t0) cc_final: 0.7765 (t70) REVERT: S 266 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: S 365 LYS cc_start: 0.7766 (mmtm) cc_final: 0.7326 (tttm) REVERT: S 421 ASN cc_start: 0.8496 (m-40) cc_final: 0.7885 (t0) REVERT: T 13 LYS cc_start: 0.7891 (ttmm) cc_final: 0.7325 (tttp) REVERT: T 119 LYS cc_start: 0.7735 (tptp) cc_final: 0.7414 (tttt) REVERT: T 120 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.7008 (mm-30) REVERT: T 151 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8060 (mm-30) REVERT: T 155 ASP cc_start: 0.8090 (t0) cc_final: 0.7827 (t70) REVERT: T 365 LYS cc_start: 0.7639 (tppt) cc_final: 0.7116 (tttm) REVERT: T 421 ASN cc_start: 0.8368 (m-40) cc_final: 0.7846 (t0) outliers start: 66 outliers final: 33 residues processed: 801 average time/residue: 0.7410 time to fit residues: 727.3993 Evaluate side-chains 782 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 741 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 39 VAL 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 168 GLU Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 436 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 169 ASN Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 169 ASN Chi-restraints excluded: chain O residue 385 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 169 ASN Chi-restraints excluded: chain R residue 366 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 330 LEU 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 385 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: [377, 234, 355, 139, 470, 288, 484, 70, 312, 46, 33] chunk 377 optimal weight: 5.9990 chunk 234 optimal weight: 0.0020 chunk 355 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 470 optimal weight: 9.9990 chunk 288 optimal weight: 2.9990 chunk 484 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 312 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 36 ASN 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** O 36 ASN R 36 ASN S 36 ASN S 413 ASN T 36 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131532 restraints weight = 39184.652| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.00 r_work: 0.3393 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2257 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= 0.176 Angle : 0.554 6.383 59700 Z= 0.301 Chirality : 0.045 0.159 6444 Planarity : 0.004 0.042 7860 Dihedral : 6.499 59.540 5898 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.79 % Allowed : 15.03 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.11), residues: 5316 helix: 1.40 (0.11), residues: 2316 sheet: -1.60 (0.15), residues: 744 loop : -0.11 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 4 TYR 0.032 0.002 TYR B 298 PHE 0.019 0.002 PHE A 287 TRP 0.016 0.002 TRP A 427 HIS 0.006 0.002 HIS O 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (44100) covalent geometry : angle 0.55431 / 0.30 (59700) hydrogen bonds : bond 0.05600 / 3.71 ( 1545) hydrogen bonds : angle 4.71333 / 3.34 ( 4413) *********************** 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 800 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 717 time to evaluate : 1.732 Fit side-chains REVERT: A 16 GLU cc_start: 0.7971 (tp30) cc_final: 0.7648 (tm-30) REVERT: A 52 MET cc_start: 0.8699 (mmm) cc_final: 0.8277 (mmm) REVERT: A 119 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7673 (tttt) REVERT: A 168 GLU cc_start: 0.5650 (OUTLIER) cc_final: 0.3471 (mt-10) REVERT: A 277 THR cc_start: 0.8384 (t) cc_final: 0.8142 (m) REVERT: A 365 LYS cc_start: 0.7588 (mmtm) cc_final: 0.7145 (tttm) REVERT: B 16 GLU cc_start: 0.7645 (tp30) cc_final: 0.7273 (tm-30) REVERT: B 155 ASP cc_start: 0.8039 (t0) cc_final: 0.7782 (t70) REVERT: B 168 GLU cc_start: 0.5443 (OUTLIER) cc_final: 0.4749 (tt0) REVERT: B 169 ASN cc_start: 0.6856 (OUTLIER) cc_final: 0.5495 (m-40) REVERT: B 365 LYS cc_start: 0.7799 (mmtm) cc_final: 0.7339 (tttm) REVERT: B 421 ASN cc_start: 0.8559 (m-40) cc_final: 0.7910 (t0) REVERT: B 436 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7350 (pm20) REVERT: C 13 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7464 (tttp) REVERT: C 119 LYS cc_start: 0.7759 (tptp) cc_final: 0.7407 (tttt) REVERT: C 155 ASP cc_start: 0.8150 (t0) cc_final: 0.7903 (t70) REVERT: C 365 LYS cc_start: 0.7680 (tppt) cc_final: 0.7149 (tttm) REVERT: C 388 GLN cc_start: 0.8110 (mt0) cc_final: 0.7820 (mm-40) REVERT: C 409 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8126 (ttmm) REVERT: C 421 ASN cc_start: 0.8393 (m-40) cc_final: 0.7870 (t0) REVERT: F 16 GLU cc_start: 0.7938 (tp30) cc_final: 0.7618 (tm-30) REVERT: F 52 MET cc_start: 0.8693 (mmm) cc_final: 0.8269 (mmm) REVERT: F 119 LYS cc_start: 0.7946 (ttpt) cc_final: 0.7675 (tttt) REVERT: F 168 GLU cc_start: 0.5291 (OUTLIER) cc_final: 0.4278 (tt0) REVERT: F 270 THR cc_start: 0.8256 (m) cc_final: 0.7899 (p) REVERT: F 277 THR cc_start: 0.8386 (t) cc_final: 0.8135 (m) REVERT: F 365 LYS cc_start: 0.7591 (mmtm) cc_final: 0.7146 (tttm) REVERT: F 436 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7474 (pm20) REVERT: G 151 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8025 (mm-30) REVERT: G 155 ASP cc_start: 0.8047 (t0) cc_final: 0.7788 (t70) REVERT: G 168 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.4941 (tt0) REVERT: G 226 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8078 (tttt) REVERT: G 266 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: G 365 LYS cc_start: 0.7783 (mmtm) cc_final: 0.7342 (tttm) REVERT: G 421 ASN cc_start: 0.8563 (m-40) cc_final: 0.7921 (t0) REVERT: G 436 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: H 13 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7475 (tttp) REVERT: H 16 GLU cc_start: 0.7886 (tp30) cc_final: 0.7665 (tm-30) REVERT: H 53 MET cc_start: 0.8400 (mtm) cc_final: 0.8172 (mtp) REVERT: H 119 LYS cc_start: 0.7777 (tptp) cc_final: 0.7420 (tttt) REVERT: H 151 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8103 (mm-30) REVERT: H 155 ASP cc_start: 0.8103 (t0) cc_final: 0.7819 (t70) REVERT: H 168 GLU cc_start: 0.5908 (OUTLIER) cc_final: 0.5189 (tt0) REVERT: H 271 GLU cc_start: 0.7258 (tp30) cc_final: 0.7009 (tp30) REVERT: H 365 LYS cc_start: 0.7645 (tppt) cc_final: 0.7154 (tttm) REVERT: H 388 GLN cc_start: 0.8078 (mt0) cc_final: 0.7795 (mm-40) REVERT: H 421 ASN cc_start: 0.8410 (m-40) cc_final: 0.7869 (t0) REVERT: L 16 GLU cc_start: 0.7933 (tp30) cc_final: 0.7620 (tm-30) REVERT: L 119 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7680 (tttt) REVERT: L 168 GLU cc_start: 0.5342 (OUTLIER) cc_final: 0.4312 (tt0) REVERT: L 270 THR cc_start: 0.8256 (m) cc_final: 0.7891 (p) REVERT: L 277 THR cc_start: 0.8383 (t) cc_final: 0.8145 (m) REVERT: L 365 LYS cc_start: 0.7572 (mmtm) cc_final: 0.7128 (tttm) REVERT: L 436 GLU cc_start: 0.7554 (pm20) cc_final: 0.7239 (tp30) REVERT: N 16 GLU cc_start: 0.7662 (tp30) cc_final: 0.7265 (tm-30) REVERT: N 120 GLU cc_start: 0.7226 (pt0) cc_final: 0.6927 (mm-30) REVERT: N 226 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8066 (tttt) REVERT: N 365 LYS cc_start: 0.7789 (mmtm) cc_final: 0.7325 (tttm) REVERT: N 421 ASN cc_start: 0.8549 (m-40) cc_final: 0.7916 (t0) REVERT: O 13 LYS cc_start: 0.7999 (ttmm) cc_final: 0.7448 (tttp) REVERT: O 16 GLU cc_start: 0.7873 (tp30) cc_final: 0.7648 (tm-30) REVERT: O 119 LYS cc_start: 0.7762 (tptp) cc_final: 0.7405 (tttt) REVERT: O 151 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8071 (mm-30) REVERT: O 155 ASP cc_start: 0.8107 (t0) cc_final: 0.7825 (t70) REVERT: O 168 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5241 (tt0) REVERT: O 271 GLU cc_start: 0.7240 (tp30) cc_final: 0.6985 (tp30) REVERT: O 365 LYS cc_start: 0.7669 (tppt) cc_final: 0.7139 (tttm) REVERT: O 388 GLN cc_start: 0.8099 (mt0) cc_final: 0.7811 (mm-40) REVERT: O 421 ASN cc_start: 0.8403 (m-40) cc_final: 0.7863 (t0) REVERT: O 436 GLU cc_start: 0.8037 (tp30) cc_final: 0.7814 (tp30) REVERT: R 16 GLU cc_start: 0.7943 (tp30) cc_final: 0.7624 (tm-30) REVERT: R 52 MET cc_start: 0.8599 (mmm) cc_final: 0.8169 (mmm) REVERT: R 119 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7651 (tttt) REVERT: R 270 THR cc_start: 0.8261 (m) cc_final: 0.7908 (p) REVERT: R 277 THR cc_start: 0.8385 (t) cc_final: 0.8144 (m) REVERT: R 365 LYS cc_start: 0.7575 (mmtm) cc_final: 0.7127 (tttm) REVERT: S 16 GLU cc_start: 0.7662 (tp30) cc_final: 0.7268 (tm-30) REVERT: S 151 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8053 (mm-30) REVERT: S 155 ASP cc_start: 0.8069 (t0) cc_final: 0.7806 (t70) REVERT: S 266 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6322 (mp0) REVERT: S 365 LYS cc_start: 0.7776 (mmtm) cc_final: 0.7322 (tttm) REVERT: S 421 ASN cc_start: 0.8569 (m-40) cc_final: 0.7925 (t0) REVERT: T 13 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7471 (tttp) REVERT: T 119 LYS cc_start: 0.7782 (tptp) cc_final: 0.7420 (tttt) REVERT: T 151 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8059 (mm-30) REVERT: T 155 ASP cc_start: 0.8109 (t0) cc_final: 0.7787 (t70) REVERT: T 365 LYS cc_start: 0.7665 (tppt) cc_final: 0.7136 (tttm) REVERT: T 421 ASN cc_start: 0.8397 (m-40) cc_final: 0.7869 (t0) outliers start: 83 outliers final: 38 residues processed: 776 average time/residue: 0.7369 time to fit residues: 700.6396 Evaluate side-chains 771 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 718 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 169 ASN 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 39 VAL 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 436 GLU 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 385 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 226 LYS Chi-restraints excluded: chain N residue 366 VAL 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 385 VAL Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 169 ASN Chi-restraints excluded: chain R residue 366 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 266 GLU Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 169 ASN Chi-restraints excluded: chain T residue 277 THR 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: [166, 467, 25, 398, 3, 499, 64, 206, 225, 403, 342] chunk 166 optimal weight: 0.8980 chunk 467 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 398 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 499 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 403 optimal weight: 7.9990 chunk 342 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 36 ASN 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** O 36 ASN R 36 ASN S 36 ASN S 413 ASN T 36 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.152131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.132068 restraints weight = 39080.906| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.01 r_work: 0.3397 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 44100 Z= 0.158 Angle : 0.532 6.311 59700 Z= 0.289 Chirality : 0.044 0.153 6444 Planarity : 0.004 0.040 7860 Dihedral : 6.509 59.671 5898 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.66 % Allowed : 15.20 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.11), residues: 5316 helix: 1.37 (0.11), residues: 2292 sheet: -1.59 (0.15), residues: 744 loop : -0.16 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG X 4 TYR 0.031 0.002 TYR G 298 PHE 0.018 0.002 PHE F 287 TRP 0.015 0.002 TRP A 427 HIS 0.005 0.001 HIS H 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (44100) covalent geometry : angle 0.53165 / 0.29 (59700) hydrogen bonds : bond 0.05365 / 3.55 ( 1545) hydrogen bonds : angle 4.68036 / 3.32 ( 4413) ********************** 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 796 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 719 time to evaluate : 1.539 Fit side-chains REVERT: A 16 GLU cc_start: 0.7952 (tp30) cc_final: 0.7624 (tm-30) REVERT: A 52 MET cc_start: 0.8715 (mmm) cc_final: 0.8294 (mmm) REVERT: A 119 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7670 (tttt) REVERT: A 168 GLU cc_start: 0.5595 (OUTLIER) cc_final: 0.3457 (mt-10) REVERT: A 277 THR cc_start: 0.8378 (t) cc_final: 0.8146 (m) REVERT: A 365 LYS cc_start: 0.7575 (mmtm) cc_final: 0.7140 (tttm) REVERT: B 16 GLU cc_start: 0.7638 (tp30) cc_final: 0.7255 (tm-30) REVERT: B 155 ASP cc_start: 0.8043 (t0) cc_final: 0.7783 (t70) REVERT: B 168 GLU cc_start: 0.5411 (OUTLIER) cc_final: 0.4765 (tt0) REVERT: B 169 ASN cc_start: 0.6851 (OUTLIER) cc_final: 0.5539 (m-40) REVERT: B 365 LYS cc_start: 0.7782 (mmtm) cc_final: 0.7325 (tttm) REVERT: B 421 ASN cc_start: 0.8560 (m-40) cc_final: 0.7914 (t0) REVERT: B 436 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7313 (pm20) REVERT: C 13 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7434 (tttp) REVERT: C 119 LYS cc_start: 0.7742 (tptp) cc_final: 0.7391 (tttt) REVERT: C 121 MET cc_start: 0.8169 (ttp) cc_final: 0.7795 (ttp) REVERT: C 155 ASP cc_start: 0.8145 (t0) cc_final: 0.7897 (t70) REVERT: C 168 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.5514 (tt0) REVERT: C 365 LYS cc_start: 0.7635 (tppt) cc_final: 0.7130 (tttm) REVERT: C 388 GLN cc_start: 0.8096 (mt0) cc_final: 0.7808 (mm-40) REVERT: C 409 LYS cc_start: 0.8415 (ttmm) cc_final: 0.8119 (ttmm) REVERT: C 421 ASN cc_start: 0.8393 (m-40) cc_final: 0.7868 (t0) REVERT: F 16 GLU cc_start: 0.7913 (tp30) cc_final: 0.7592 (tm-30) REVERT: F 52 MET cc_start: 0.8706 (mmm) cc_final: 0.8282 (mmm) REVERT: F 119 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7658 (tttt) REVERT: F 168 GLU cc_start: 0.5253 (OUTLIER) cc_final: 0.4418 (tt0) REVERT: F 270 THR cc_start: 0.8236 (m) cc_final: 0.7865 (p) REVERT: F 277 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8134 (m) REVERT: F 365 LYS cc_start: 0.7577 (mmtm) cc_final: 0.7138 (tttm) REVERT: F 436 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7425 (pm20) REVERT: G 155 ASP cc_start: 0.8059 (t0) cc_final: 0.7796 (t70) REVERT: G 168 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5024 (tt0) REVERT: G 226 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8096 (tttt) REVERT: G 266 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6279 (mp0) REVERT: G 365 LYS cc_start: 0.7759 (mmtm) cc_final: 0.7318 (tttm) REVERT: G 421 ASN cc_start: 0.8555 (m-40) cc_final: 0.7921 (t0) REVERT: G 436 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7821 (mm-30) REVERT: H 13 LYS cc_start: 0.7981 (ttmm) cc_final: 0.7450 (tttp) REVERT: H 16 GLU cc_start: 0.7868 (tp30) cc_final: 0.7580 (tm-30) REVERT: H 53 MET cc_start: 0.8401 (mtm) cc_final: 0.8167 (mtp) REVERT: H 119 LYS cc_start: 0.7765 (tptp) cc_final: 0.7408 (tttt) REVERT: H 151 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8092 (mm-30) REVERT: H 155 ASP cc_start: 0.8101 (t0) cc_final: 0.7831 (t70) REVERT: H 168 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5242 (tt0) REVERT: H 271 GLU cc_start: 0.7236 (tp30) cc_final: 0.6984 (tp30) REVERT: H 365 LYS cc_start: 0.7631 (tppt) cc_final: 0.7133 (tttm) REVERT: H 388 GLN cc_start: 0.8061 (mt0) cc_final: 0.7778 (mm-40) REVERT: H 421 ASN cc_start: 0.8412 (m-40) cc_final: 0.7878 (t0) REVERT: L 16 GLU cc_start: 0.7916 (tp30) cc_final: 0.7593 (tm-30) REVERT: L 119 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7685 (tttt) REVERT: L 168 GLU cc_start: 0.5323 (OUTLIER) cc_final: 0.4494 (tt0) REVERT: L 270 THR cc_start: 0.8239 (m) cc_final: 0.7865 (p) REVERT: L 277 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8143 (m) REVERT: L 365 LYS cc_start: 0.7560 (mmtm) cc_final: 0.7117 (tttm) REVERT: N 16 GLU cc_start: 0.7650 (tp30) cc_final: 0.7257 (tm-30) REVERT: N 120 GLU cc_start: 0.7200 (pt0) cc_final: 0.6909 (mm-30) REVERT: N 226 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8078 (tttt) REVERT: N 365 LYS cc_start: 0.7776 (mmtm) cc_final: 0.7317 (tttm) REVERT: N 421 ASN cc_start: 0.8540 (m-40) cc_final: 0.7915 (t0) REVERT: O 13 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7432 (tttp) REVERT: O 16 GLU cc_start: 0.7852 (tp30) cc_final: 0.7627 (tm-30) REVERT: O 119 LYS cc_start: 0.7756 (tptp) cc_final: 0.7399 (tttt) REVERT: O 121 MET cc_start: 0.8162 (ttp) cc_final: 0.7784 (ttp) REVERT: O 151 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8083 (mm-30) REVERT: O 155 ASP cc_start: 0.8114 (t0) cc_final: 0.7843 (t70) REVERT: O 271 GLU cc_start: 0.7215 (tp30) cc_final: 0.6960 (tp30) REVERT: O 365 LYS cc_start: 0.7632 (tppt) cc_final: 0.7112 (tttm) REVERT: O 388 GLN cc_start: 0.8078 (mt0) cc_final: 0.7786 (mm-40) REVERT: O 421 ASN cc_start: 0.8406 (m-40) cc_final: 0.7871 (t0) REVERT: O 436 GLU cc_start: 0.8026 (tp30) cc_final: 0.7800 (tp30) REVERT: R 16 GLU cc_start: 0.7924 (tp30) cc_final: 0.7604 (tm-30) REVERT: R 52 MET cc_start: 0.8598 (mmm) cc_final: 0.8182 (mmm) REVERT: R 119 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7645 (tttt) REVERT: R 168 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5123 (tt0) REVERT: R 270 THR cc_start: 0.8242 (m) cc_final: 0.7878 (p) REVERT: R 277 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8143 (m) REVERT: R 365 LYS cc_start: 0.7563 (mmtm) cc_final: 0.7113 (tttm) REVERT: S 16 GLU cc_start: 0.7653 (tp30) cc_final: 0.7255 (tm-30) REVERT: S 151 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8049 (mm-30) REVERT: S 155 ASP cc_start: 0.8068 (t0) cc_final: 0.7805 (t70) REVERT: S 226 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7978 (tttt) REVERT: S 266 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6287 (mp0) REVERT: S 365 LYS cc_start: 0.7762 (mmtm) cc_final: 0.7307 (tttm) REVERT: S 421 ASN cc_start: 0.8570 (m-40) cc_final: 0.7929 (t0) REVERT: T 13 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7455 (tttp) REVERT: T 119 LYS cc_start: 0.7759 (tptp) cc_final: 0.7396 (tttt) REVERT: T 151 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8056 (mm-30) REVERT: T 155 ASP cc_start: 0.8109 (t0) cc_final: 0.7840 (t70) REVERT: T 365 LYS cc_start: 0.7617 (tppt) cc_final: 0.7092 (tttm) REVERT: T 421 ASN cc_start: 0.8407 (m-40) cc_final: 0.7876 (t0) outliers start: 77 outliers final: 43 residues processed: 771 average time/residue: 0.7274 time to fit residues: 686.4613 Evaluate side-chains 779 residues out of total 4716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 716 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 436 GLU 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 277 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain F residue 277 THR 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 39 VAL 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 436 GLU 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 L residue 39 VAL Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain L residue 277 THR Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain L residue 385 VAL Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 226 LYS Chi-restraints excluded: chain O residue 39 VAL 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 168 GLU Chi-restraints excluded: chain R residue 169 ASN Chi-restraints excluded: chain R residue 277 THR Chi-restraints excluded: chain R residue 366 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 68 SER 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 330 LEU Chi-restraints excluded: chain T residue 39 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: [171, 126, 184, 275, 272, 215, 232, 138, 206, 246, 347] chunk 171 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 272 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 246 optimal weight: 8.9990 chunk 347 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 36 ASN B 169 ASN C 36 ASN F 36 ASN F 169 ASN G 36 ASN G 413 ASN H 36 ASN L 36 ASN L 169 ASN N 36 ASN O 36 ASN R 36 ASN R 169 ASN S 36 ASN S 413 ASN T 36 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.149894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129705 restraints weight = 39085.842| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.01 r_work: 0.3368 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 44100 Z= 0.286 Angle : 0.705 8.419 59700 Z= 0.384 Chirality : 0.052 0.222 6444 Planarity : 0.006 0.048 7860 Dihedral : 6.945 59.471 5898 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.03 % Allowed : 14.92 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.11), residues: 5316 helix: 1.03 (0.11), residues: 2280 sheet: -1.72 (0.15), residues: 744 loop : -0.27 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 4 TYR 0.039 0.004 TYR B 298 PHE 0.027 0.003 PHE O 287 TRP 0.019 0.003 TRP L 427 HIS 0.007 0.002 HIS H 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.29 (44100) covalent geometry : angle 0.70460 / 0.38 (59700) hydrogen bonds : bond 0.06915 / 4.57 ( 1545) hydrogen bonds : angle 5.04057 / 3.58 ( 4413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19697.77 seconds wall clock time: 334 minutes 16.90 seconds (20056.90 seconds total)