Starting phenix.real_space_refine on Tue Aug 26 22:53:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tf6_25863/08_2025/7tf6_25863.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf6_25863/08_2025/7tf6_25863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tf6_25863/08_2025/7tf6_25863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf6_25863/08_2025/7tf6_25863.map" model { file = "/net/cci-nas-00/data/ceres_data/7tf6_25863/08_2025/7tf6_25863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf6_25863/08_2025/7tf6_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.94, per 1000 atoms: 0.21 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: 2.96 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.42 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: 8.91 Time building geometry restraints manager: 4.05 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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.280 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 34.910 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 44100 Z= 0.115 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 aren 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 covalent geometry : bond 0.00241 (44100) covalent geometry : angle 0.50517 (59700) hydrogen bonds : bond 0.14194 ( 1545) hydrogen bonds : angle 5.37894 ( 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 : 1.427 Fit side-chains REVERT: A 13 LYS cc_start: 0.6176 (ttmm) cc_final: 0.5737 (ttpt) REVERT: A 16 GLU cc_start: 0.6706 (tp30) cc_final: 0.6271 (tm-30) REVERT: A 52 MET cc_start: 0.7233 (mmm) cc_final: 0.6676 (mmm) REVERT: A 66 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6927 (mt-10) REVERT: A 119 LYS cc_start: 0.6649 (ttpt) cc_final: 0.6342 (tttm) REVERT: A 120 GLU cc_start: 0.6347 (pt0) cc_final: 0.5702 (mt-10) REVERT: A 122 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6323 (mt-10) REVERT: A 128 ASP cc_start: 0.6851 (m-30) cc_final: 0.6597 (m-30) REVERT: A 151 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6440 (mt-10) REVERT: A 155 ASP cc_start: 0.6566 (t0) cc_final: 0.6337 (t70) REVERT: A 173 ASP cc_start: 0.6956 (m-30) cc_final: 0.6546 (m-30) REVERT: A 184 ASP cc_start: 0.7262 (m-30) cc_final: 0.6963 (m-30) REVERT: A 201 PHE cc_start: 0.6809 (m-80) cc_final: 0.5949 (m-80) REVERT: A 203 TYR cc_start: 0.6273 (p90) cc_final: 0.5732 (p90) REVERT: A 225 ARG cc_start: 0.6475 (ttp-170) cc_final: 0.5923 (ttt180) REVERT: A 257 GLU cc_start: 0.6253 (tm-30) cc_final: 0.5725 (pp20) REVERT: A 271 GLU cc_start: 0.6323 (tp30) cc_final: 0.6001 (tp30) REVERT: A 282 LYS cc_start: 0.6528 (tptm) cc_final: 0.5925 (tttm) REVERT: A 354 GLU cc_start: 0.7178 (tp30) cc_final: 0.6962 (mm-30) REVERT: A 365 LYS cc_start: 0.6394 (mmtm) cc_final: 0.5609 (tttm) REVERT: A 399 LYS cc_start: 0.6726 (ttmt) cc_final: 0.5966 (ttmm) REVERT: A 409 LYS cc_start: 0.6285 (ttmm) cc_final: 0.5871 (tttt) REVERT: A 418 GLN cc_start: 0.6860 (mm110) cc_final: 0.6634 (mm110) REVERT: A 428 ASP cc_start: 0.7182 (t70) cc_final: 0.6580 (m-30) REVERT: A 445 GLN cc_start: 0.6331 (tt0) cc_final: 0.5437 (tp40) REVERT: B 13 LYS cc_start: 0.5987 (ttmm) cc_final: 0.5228 (tttp) REVERT: B 16 GLU cc_start: 0.6417 (tp30) cc_final: 0.5752 (tt0) REVERT: B 66 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6500 (mt-10) REVERT: B 75 ASP cc_start: 0.6440 (t0) cc_final: 0.6151 (t0) REVERT: B 120 GLU cc_start: 0.6490 (pt0) cc_final: 0.5426 (mm-30) REVERT: B 128 ASP cc_start: 0.7007 (m-30) cc_final: 0.6778 (m-30) REVERT: B 151 GLU cc_start: 0.6476 (mt-10) cc_final: 0.5707 (mm-30) REVERT: B 169 ASN cc_start: 0.5515 (OUTLIER) cc_final: 0.5113 (m-40) REVERT: B 173 ASP cc_start: 0.6778 (m-30) cc_final: 0.6508 (m-30) REVERT: B 201 PHE cc_start: 0.6892 (m-80) cc_final: 0.5946 (m-80) REVERT: B 225 ARG cc_start: 0.6211 (ttp-170) cc_final: 0.5989 (ttm170) REVERT: B 257 GLU cc_start: 0.6537 (tm-30) cc_final: 0.6175 (tm-30) REVERT: B 270 THR cc_start: 0.6962 (m) cc_final: 0.6414 (p) REVERT: B 271 GLU cc_start: 0.6235 (tp30) cc_final: 0.5931 (tp30) REVERT: B 330 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7633 (mt) REVERT: B 365 LYS cc_start: 0.6631 (mmtm) cc_final: 0.5845 (tttm) REVERT: B 409 LYS cc_start: 0.6442 (ttmm) cc_final: 0.5917 (tttt) REVERT: B 418 GLN cc_start: 0.7034 (mm-40) cc_final: 0.6829 (mm-40) REVERT: B 421 ASN cc_start: 0.6108 (m-40) cc_final: 0.4762 (t0) REVERT: B 428 ASP cc_start: 0.7044 (t70) cc_final: 0.6432 (t0) REVERT: B 445 GLN cc_start: 0.6949 (tt0) cc_final: 0.5988 (tp40) REVERT: C 13 LYS cc_start: 0.5969 (ttmm) cc_final: 0.5259 (tttp) REVERT: C 16 GLU cc_start: 0.6727 (tp30) cc_final: 0.6358 (tm-30) REVERT: C 21 ARG cc_start: 0.6693 (mtp85) cc_final: 0.6484 (mmm160) REVERT: C 53 MET cc_start: 0.7303 (mtm) cc_final: 0.6830 (mtp) REVERT: C 66 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6555 (mt-10) REVERT: C 119 LYS cc_start: 0.6032 (tptp) cc_final: 0.5444 (tttm) REVERT: C 120 GLU cc_start: 0.6318 (pt0) cc_final: 0.5327 (mm-30) REVERT: C 122 GLU cc_start: 0.6542 (mt-10) cc_final: 0.6251 (mt-10) REVERT: C 128 ASP cc_start: 0.6937 (m-30) cc_final: 0.6687 (m-30) REVERT: C 151 GLU cc_start: 0.6618 (mt-10) cc_final: 0.5771 (mm-30) REVERT: C 155 ASP cc_start: 0.6577 (t0) cc_final: 0.6046 (t70) REVERT: C 173 ASP cc_start: 0.6725 (m-30) cc_final: 0.6348 (m-30) REVERT: C 184 ASP cc_start: 0.7206 (m-30) cc_final: 0.6960 (m-30) REVERT: C 201 PHE cc_start: 0.7116 (m-80) cc_final: 0.6336 (m-80) REVERT: C 225 ARG cc_start: 0.6522 (ttt180) cc_final: 0.6097 (ttt180) REVERT: C 257 GLU cc_start: 0.6264 (tm-30) cc_final: 0.5786 (pp20) REVERT: C 270 THR cc_start: 0.6997 (m) cc_final: 0.6499 (p) REVERT: C 271 GLU cc_start: 0.5812 (tp30) cc_final: 0.5404 (tp30) REVERT: C 354 GLU cc_start: 0.7310 (tp30) cc_final: 0.7038 (mm-30) REVERT: C 365 LYS cc_start: 0.6271 (tppt) cc_final: 0.5495 (tttm) REVERT: C 388 GLN cc_start: 0.6358 (mt0) cc_final: 0.6158 (mt0) REVERT: C 399 LYS cc_start: 0.6518 (ttmt) cc_final: 0.5714 (ttmm) REVERT: C 405 GLU cc_start: 0.5708 (mm-30) cc_final: 0.5224 (tm-30) REVERT: C 408 LYS cc_start: 0.6765 (tttt) cc_final: 0.6472 (ttpp) REVERT: C 409 LYS cc_start: 0.6534 (ttmm) cc_final: 0.6208 (ttpt) REVERT: C 421 ASN cc_start: 0.5864 (m-40) cc_final: 0.4565 (t0) REVERT: C 428 ASP cc_start: 0.6993 (t70) cc_final: 0.6328 (m-30) REVERT: C 436 GLU cc_start: 0.5564 (pm20) cc_final: 0.5038 (pm20) REVERT: C 443 MET cc_start: 0.6590 (ttp) cc_final: 0.6248 (ttt) REVERT: C 445 GLN cc_start: 0.6662 (tt0) cc_final: 0.5610 (tp40) REVERT: D 4 ARG cc_start: 0.6243 (tmt170) cc_final: 0.5763 (tpt90) REVERT: E 11 ILE cc_start: 0.6662 (mt) cc_final: 0.6417 (mp) REVERT: F 13 LYS cc_start: 0.6174 (ttmm) cc_final: 0.5742 (ttpt) REVERT: F 16 GLU cc_start: 0.6684 (tp30) cc_final: 0.6268 (tm-30) REVERT: F 21 ARG cc_start: 0.6639 (mtp85) cc_final: 0.6267 (mmp-170) REVERT: F 52 MET cc_start: 0.7223 (mmm) cc_final: 0.6662 (mmm) REVERT: F 66 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6939 (mt-10) REVERT: F 119 LYS cc_start: 0.6637 (ttpt) cc_final: 0.6078 (tttt) REVERT: F 120 GLU cc_start: 0.6268 (pt0) cc_final: 0.5616 (mt-10) REVERT: F 122 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6309 (mt-10) REVERT: F 128 ASP cc_start: 0.6829 (m-30) cc_final: 0.6584 (m-30) REVERT: F 151 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6369 (mt-10) REVERT: F 155 ASP cc_start: 0.6560 (t0) cc_final: 0.6321 (t70) REVERT: F 173 ASP cc_start: 0.6906 (m-30) cc_final: 0.6458 (m-30) REVERT: F 184 ASP cc_start: 0.7180 (m-30) cc_final: 0.6872 (m-30) REVERT: F 201 PHE cc_start: 0.6902 (m-80) cc_final: 0.6081 (m-80) REVERT: F 225 ARG cc_start: 0.6390 (ttp-170) cc_final: 0.5980 (ttt180) REVERT: F 257 GLU cc_start: 0.6450 (tm-30) cc_final: 0.5913 (pp20) REVERT: F 270 THR cc_start: 0.7012 (m) cc_final: 0.6324 (p) REVERT: F 271 GLU cc_start: 0.6028 (tp30) cc_final: 0.5622 (tp30) REVERT: F 282 LYS cc_start: 0.6528 (tptm) cc_final: 0.5918 (tttm) REVERT: F 354 GLU cc_start: 0.7120 (tp30) cc_final: 0.6910 (mm-30) REVERT: F 365 LYS cc_start: 0.6383 (mmtm) cc_final: 0.5598 (tttm) REVERT: F 399 LYS cc_start: 0.6712 (ttmt) cc_final: 0.5951 (ttmm) REVERT: F 409 LYS cc_start: 0.6276 (ttmm) cc_final: 0.5864 (tttt) REVERT: F 418 GLN cc_start: 0.6851 (mm110) cc_final: 0.6626 (mm110) REVERT: F 428 ASP cc_start: 0.7202 (t70) cc_final: 0.6574 (m-30) REVERT: F 445 GLN cc_start: 0.6341 (tt0) cc_final: 0.5443 (tp40) REVERT: G 16 GLU cc_start: 0.6588 (tp30) cc_final: 0.5915 (tt0) REVERT: G 17 GLU cc_start: 0.6394 (mt-10) cc_final: 0.6152 (mt-10) REVERT: G 51 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6554 (mt-10) REVERT: G 66 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6362 (mt-10) REVERT: G 75 ASP cc_start: 0.6451 (t0) cc_final: 0.6135 (t0) REVERT: G 120 GLU cc_start: 0.6358 (pt0) cc_final: 0.5288 (mm-30) REVERT: G 122 GLU cc_start: 0.6694 (mt-10) cc_final: 0.6365 (mt-10) REVERT: G 128 ASP cc_start: 0.7021 (m-30) cc_final: 0.6781 (m-30) REVERT: G 151 GLU cc_start: 0.6506 (mt-10) cc_final: 0.5738 (mm-30) REVERT: G 173 ASP cc_start: 0.6780 (m-30) cc_final: 0.6510 (m-30) REVERT: G 201 PHE cc_start: 0.6946 (m-80) cc_final: 0.6001 (m-80) REVERT: G 225 ARG cc_start: 0.6241 (ttp-170) cc_final: 0.6003 (ttm170) REVERT: G 257 GLU cc_start: 0.6538 (tm-30) cc_final: 0.6179 (tm-30) REVERT: G 270 THR cc_start: 0.6943 (m) cc_final: 0.6378 (p) REVERT: G 271 GLU cc_start: 0.6201 (tp30) cc_final: 0.5862 (tp30) REVERT: G 330 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7640 (mt) REVERT: G 347 MET cc_start: 0.7336 (mtp) cc_final: 0.6928 (mtp) REVERT: G 365 LYS cc_start: 0.6635 (mmtm) cc_final: 0.5844 (tttm) REVERT: G 409 LYS cc_start: 0.6445 (ttmm) cc_final: 0.5901 (tttt) REVERT: G 421 ASN cc_start: 0.6123 (m-40) cc_final: 0.4790 (t0) REVERT: G 428 ASP cc_start: 0.7052 (t70) cc_final: 0.6761 (t0) REVERT: G 436 GLU cc_start: 0.5428 (pm20) cc_final: 0.5060 (pm20) REVERT: G 445 GLN cc_start: 0.6754 (tt0) cc_final: 0.6497 (tt0) REVERT: H 13 LYS cc_start: 0.5983 (ttmm) cc_final: 0.5283 (tttp) REVERT: H 16 GLU cc_start: 0.6745 (tp30) cc_final: 0.6329 (tm-30) REVERT: H 21 ARG cc_start: 0.6706 (mtp85) cc_final: 0.6488 (mmm160) REVERT: H 53 MET cc_start: 0.7379 (mtm) cc_final: 0.6886 (mtp) REVERT: H 66 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6562 (mt-10) REVERT: H 119 LYS cc_start: 0.6077 (tptp) cc_final: 0.5520 (tttm) REVERT: H 120 GLU cc_start: 0.6312 (pt0) cc_final: 0.5340 (mm-30) REVERT: H 128 ASP cc_start: 0.6937 (m-30) cc_final: 0.6692 (m-30) REVERT: H 151 GLU cc_start: 0.6617 (mt-10) cc_final: 0.5754 (mm-30) REVERT: H 155 ASP cc_start: 0.6587 (t0) cc_final: 0.6155 (t70) REVERT: H 173 ASP cc_start: 0.6727 (m-30) cc_final: 0.6360 (m-30) REVERT: H 184 ASP cc_start: 0.7133 (m-30) cc_final: 0.6913 (m-30) REVERT: H 201 PHE cc_start: 0.7046 (m-80) cc_final: 0.6258 (m-80) REVERT: H 225 ARG cc_start: 0.6576 (ttp-170) cc_final: 0.6204 (ttt180) REVERT: H 257 GLU cc_start: 0.6251 (tm-30) cc_final: 0.5789 (pp20) REVERT: H 270 THR cc_start: 0.6937 (m) cc_final: 0.6461 (p) REVERT: H 271 GLU cc_start: 0.5801 (tp30) cc_final: 0.5392 (tp30) REVERT: H 354 GLU cc_start: 0.7307 (tp30) cc_final: 0.7042 (mm-30) REVERT: H 365 LYS cc_start: 0.6275 (tppt) cc_final: 0.5499 (tttm) REVERT: H 388 GLN cc_start: 0.6363 (mt0) cc_final: 0.6162 (mt0) REVERT: H 399 LYS cc_start: 0.6514 (ttmt) cc_final: 0.5710 (ttmm) REVERT: H 408 LYS cc_start: 0.6751 (tttt) cc_final: 0.6468 (ttpp) REVERT: H 409 LYS cc_start: 0.6537 (ttmm) cc_final: 0.6033 (ttpt) REVERT: H 421 ASN cc_start: 0.5873 (m-40) cc_final: 0.4575 (t0) REVERT: H 428 ASP cc_start: 0.6928 (t0) cc_final: 0.6301 (m-30) REVERT: H 436 GLU cc_start: 0.5561 (pm20) cc_final: 0.5067 (pm20) REVERT: H 443 MET cc_start: 0.6579 (ttp) cc_final: 0.6343 (ttt) REVERT: H 445 GLN cc_start: 0.6630 (tt0) cc_final: 0.5628 (tp40) REVERT: I 4 ARG cc_start: 0.6227 (tmt170) cc_final: 0.5790 (tpt90) REVERT: K 3 ASN cc_start: 0.6578 (p0) cc_final: 0.6046 (p0) REVERT: K 4 ARG cc_start: 0.6389 (tmt170) cc_final: 0.5992 (tpt90) REVERT: L 13 LYS cc_start: 0.6129 (ttmm) cc_final: 0.5705 (ttpt) REVERT: L 16 GLU cc_start: 0.6742 (tp30) cc_final: 0.6330 (tm-30) REVERT: L 52 MET cc_start: 0.7130 (mmm) cc_final: 0.6608 (mmm) REVERT: L 66 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6945 (mt-10) REVERT: L 119 LYS cc_start: 0.6496 (ttpt) cc_final: 0.6012 (tttt) REVERT: L 120 GLU cc_start: 0.6399 (pt0) cc_final: 0.5766 (mt-10) REVERT: L 122 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6302 (mt-10) REVERT: L 128 ASP cc_start: 0.6898 (m-30) cc_final: 0.6640 (m-30) REVERT: L 151 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6412 (mt-10) REVERT: L 155 ASP cc_start: 0.6559 (t0) cc_final: 0.6308 (t70) REVERT: L 173 ASP cc_start: 0.6903 (m-30) cc_final: 0.6451 (m-30) REVERT: L 184 ASP cc_start: 0.7182 (m-30) cc_final: 0.6868 (m-30) REVERT: L 201 PHE cc_start: 0.6886 (m-80) cc_final: 0.6103 (m-80) REVERT: L 225 ARG cc_start: 0.6452 (ttp-170) cc_final: 0.5981 (ttt180) REVERT: L 257 GLU cc_start: 0.6383 (tm-30) cc_final: 0.5774 (pp20) REVERT: L 270 THR cc_start: 0.7009 (m) cc_final: 0.6323 (p) REVERT: L 271 GLU cc_start: 0.6085 (tp30) cc_final: 0.5716 (tp30) REVERT: L 282 LYS cc_start: 0.6547 (tptm) cc_final: 0.5940 (tttm) REVERT: L 354 GLU cc_start: 0.7163 (tp30) cc_final: 0.6945 (mm-30) REVERT: L 365 LYS cc_start: 0.6387 (mmtm) cc_final: 0.5602 (tttm) REVERT: L 399 LYS cc_start: 0.6759 (ttmt) cc_final: 0.5989 (ttmm) REVERT: L 409 LYS cc_start: 0.6289 (ttmm) cc_final: 0.5877 (tttt) REVERT: L 418 GLN cc_start: 0.6842 (mm110) cc_final: 0.6607 (mm-40) REVERT: L 428 ASP cc_start: 0.7204 (t70) cc_final: 0.6598 (m-30) REVERT: L 445 GLN cc_start: 0.6265 (tt0) cc_final: 0.5412 (tp40) REVERT: M 3 ASN cc_start: 0.6684 (p0) cc_final: 0.6210 (p0) REVERT: N 13 LYS cc_start: 0.5988 (ttmm) cc_final: 0.5238 (tttp) REVERT: N 16 GLU cc_start: 0.6424 (tp30) cc_final: 0.5749 (tt0) REVERT: N 51 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6548 (mt-10) REVERT: N 66 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6334 (mt-10) REVERT: N 75 ASP cc_start: 0.6475 (t0) cc_final: 0.6162 (t0) REVERT: N 120 GLU cc_start: 0.6405 (pt0) cc_final: 0.5416 (mm-30) REVERT: N 122 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6351 (mt-10) REVERT: N 128 ASP cc_start: 0.7001 (m-30) cc_final: 0.6772 (m-30) REVERT: N 151 GLU cc_start: 0.6479 (mt-10) cc_final: 0.5711 (mm-30) REVERT: N 173 ASP cc_start: 0.6795 (m-30) cc_final: 0.6498 (m-30) REVERT: N 201 PHE cc_start: 0.6959 (m-80) cc_final: 0.6015 (m-80) REVERT: N 225 ARG cc_start: 0.6209 (ttp-170) cc_final: 0.5971 (ttm170) REVERT: N 257 GLU cc_start: 0.6532 (tm-30) cc_final: 0.6172 (tm-30) REVERT: N 270 THR cc_start: 0.6956 (m) cc_final: 0.6409 (p) REVERT: N 271 GLU cc_start: 0.6231 (tp30) cc_final: 0.5923 (tp30) REVERT: N 330 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7626 (mt) REVERT: N 365 LYS cc_start: 0.6635 (mmtm) cc_final: 0.5889 (tttm) REVERT: N 409 LYS cc_start: 0.6448 (ttmm) cc_final: 0.5902 (tttt) REVERT: N 421 ASN cc_start: 0.6111 (m-40) cc_final: 0.4773 (t0) REVERT: N 428 ASP cc_start: 0.7036 (t70) cc_final: 0.6425 (t0) REVERT: N 445 GLN cc_start: 0.6792 (tt0) cc_final: 0.5842 (tp40) REVERT: O 13 LYS cc_start: 0.5950 (ttmm) cc_final: 0.5250 (tttp) REVERT: O 16 GLU cc_start: 0.6731 (tp30) cc_final: 0.6316 (tm-30) REVERT: O 21 ARG cc_start: 0.6699 (mtp85) cc_final: 0.6488 (mmm160) REVERT: O 51 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6651 (mt-10) REVERT: O 53 MET cc_start: 0.7287 (mtm) cc_final: 0.6822 (mtp) REVERT: O 66 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6567 (mt-10) REVERT: O 119 LYS cc_start: 0.6087 (tptp) cc_final: 0.5493 (tttm) REVERT: O 120 GLU cc_start: 0.6312 (pt0) cc_final: 0.5342 (mm-30) REVERT: O 122 GLU cc_start: 0.6556 (mt-10) cc_final: 0.6266 (mt-10) REVERT: O 128 ASP cc_start: 0.6932 (m-30) cc_final: 0.6684 (m-30) REVERT: O 151 GLU cc_start: 0.6607 (mt-10) cc_final: 0.5737 (mm-30) REVERT: O 155 ASP cc_start: 0.6585 (t0) cc_final: 0.6157 (t70) REVERT: O 173 ASP cc_start: 0.6715 (m-30) cc_final: 0.6336 (m-30) REVERT: O 184 ASP cc_start: 0.7192 (m-30) cc_final: 0.6991 (m-30) REVERT: O 201 PHE cc_start: 0.7045 (m-80) cc_final: 0.6278 (m-80) REVERT: O 225 ARG cc_start: 0.6524 (ttt180) cc_final: 0.5986 (ttt180) REVERT: O 257 GLU cc_start: 0.6391 (tm-30) cc_final: 0.5950 (pp20) REVERT: O 270 THR cc_start: 0.6933 (m) cc_final: 0.6458 (p) REVERT: O 271 GLU cc_start: 0.5811 (tp30) cc_final: 0.5401 (tp30) REVERT: O 354 GLU cc_start: 0.7306 (tp30) cc_final: 0.7067 (tp30) REVERT: O 365 LYS cc_start: 0.6273 (tppt) cc_final: 0.5499 (tttm) REVERT: O 388 GLN cc_start: 0.6370 (mt0) cc_final: 0.6167 (mt0) REVERT: O 399 LYS cc_start: 0.6511 (ttmt) cc_final: 0.5708 (ttmm) REVERT: O 408 LYS cc_start: 0.6772 (tttt) cc_final: 0.6487 (ttpp) REVERT: O 409 LYS cc_start: 0.6494 (ttmm) cc_final: 0.5954 (ttpt) REVERT: O 421 ASN cc_start: 0.5852 (m-40) cc_final: 0.4562 (t0) REVERT: O 428 ASP cc_start: 0.7002 (t70) cc_final: 0.6321 (m-30) REVERT: O 436 GLU cc_start: 0.6476 (tp30) cc_final: 0.6041 (tp30) REVERT: O 443 MET cc_start: 0.6620 (ttp) cc_final: 0.6277 (ttt) REVERT: O 445 GLN cc_start: 0.6642 (tt0) cc_final: 0.5622 (tp40) REVERT: P 4 ARG cc_start: 0.6216 (tmt170) cc_final: 0.5878 (tpt90) REVERT: Q 4 ARG cc_start: 0.6235 (tmt170) cc_final: 0.5998 (tpt90) REVERT: R 13 LYS cc_start: 0.6136 (ttmm) cc_final: 0.5712 (ttpt) REVERT: R 16 GLU cc_start: 0.6734 (tp30) cc_final: 0.6284 (tm-30) REVERT: R 51 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6718 (mt-10) REVERT: R 52 MET cc_start: 0.7305 (mmm) cc_final: 0.6629 (mmm) REVERT: R 66 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6991 (mt-10) REVERT: R 70 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7475 (mtt) REVERT: R 119 LYS cc_start: 0.6556 (ttpt) cc_final: 0.6082 (tttt) REVERT: R 120 GLU cc_start: 0.6266 (pt0) cc_final: 0.5201 (mm-30) REVERT: R 122 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6272 (mt-10) REVERT: R 128 ASP cc_start: 0.6847 (m-30) cc_final: 0.6596 (m-30) REVERT: R 151 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6500 (mt-10) REVERT: R 155 ASP cc_start: 0.6593 (t0) cc_final: 0.6341 (t70) REVERT: R 168 GLU cc_start: 0.4287 (OUTLIER) cc_final: 0.3928 (pp20) REVERT: R 173 ASP cc_start: 0.6894 (m-30) cc_final: 0.6428 (m-30) REVERT: R 184 ASP cc_start: 0.7205 (m-30) cc_final: 0.6891 (m-30) REVERT: R 201 PHE cc_start: 0.6903 (m-80) cc_final: 0.6107 (m-80) REVERT: R 203 TYR cc_start: 0.6344 (p90) cc_final: 0.5808 (p90) REVERT: R 225 ARG cc_start: 0.6507 (ttp-170) cc_final: 0.6097 (ttt180) REVERT: R 257 GLU cc_start: 0.6362 (tm-30) cc_final: 0.5839 (pp20) REVERT: R 270 THR cc_start: 0.7005 (m) cc_final: 0.6311 (p) REVERT: R 271 GLU cc_start: 0.6010 (tp30) cc_final: 0.5637 (tp30) REVERT: R 282 LYS cc_start: 0.6529 (tptm) cc_final: 0.5922 (tttm) REVERT: R 354 GLU cc_start: 0.7104 (tp30) cc_final: 0.6887 (mm-30) REVERT: R 365 LYS cc_start: 0.6390 (mmtm) cc_final: 0.5603 (tttm) REVERT: R 399 LYS cc_start: 0.6724 (ttmt) cc_final: 0.5969 (ttmm) REVERT: R 409 LYS cc_start: 0.6282 (ttmm) cc_final: 0.5870 (tttt) REVERT: R 418 GLN cc_start: 0.6852 (mm110) cc_final: 0.6617 (mm-40) REVERT: R 428 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6591 (m-30) REVERT: R 445 GLN cc_start: 0.6374 (tt0) cc_final: 0.5510 (tp40) REVERT: S 16 GLU cc_start: 0.6439 (tp30) cc_final: 0.5749 (tt0) REVERT: S 51 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6516 (mt-10) REVERT: S 66 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6396 (mt-10) REVERT: S 75 ASP cc_start: 0.6506 (t0) cc_final: 0.6236 (t0) REVERT: S 120 GLU cc_start: 0.6498 (pt0) cc_final: 0.5430 (mm-30) REVERT: S 122 GLU cc_start: 0.6709 (mt-10) cc_final: 0.6377 (mt-10) REVERT: S 128 ASP cc_start: 0.6864 (m-30) cc_final: 0.6578 (m-30) REVERT: S 151 GLU cc_start: 0.6528 (mt-10) cc_final: 0.5727 (mm-30) REVERT: S 169 ASN cc_start: 0.5515 (OUTLIER) cc_final: 0.5251 (m-40) REVERT: S 173 ASP cc_start: 0.6765 (m-30) cc_final: 0.6469 (m-30) REVERT: S 201 PHE cc_start: 0.6792 (m-80) cc_final: 0.5822 (m-80) REVERT: S 225 ARG cc_start: 0.6262 (ttp-170) cc_final: 0.5876 (ttt180) REVERT: S 257 GLU cc_start: 0.6494 (tm-30) cc_final: 0.6187 (tm-30) REVERT: S 270 THR cc_start: 0.6966 (m) cc_final: 0.6421 (p) REVERT: S 271 GLU cc_start: 0.6249 (tp30) cc_final: 0.5785 (tp30) REVERT: S 330 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7610 (mt) REVERT: S 365 LYS cc_start: 0.6774 (mmtm) cc_final: 0.5982 (tttm) REVERT: S 409 LYS cc_start: 0.6429 (ttmm) cc_final: 0.5871 (tttt) REVERT: S 421 ASN cc_start: 0.6149 (m-40) cc_final: 0.4819 (t0) REVERT: S 428 ASP cc_start: 0.7023 (t70) cc_final: 0.6391 (t0) REVERT: S 445 GLN cc_start: 0.6779 (tt0) cc_final: 0.6504 (tt0) REVERT: T 13 LYS cc_start: 0.5960 (ttmm) cc_final: 0.5255 (tttp) REVERT: T 16 GLU cc_start: 0.6752 (tp30) cc_final: 0.6377 (tm-30) REVERT: T 21 ARG cc_start: 0.6203 (mmm-85) cc_final: 0.5746 (mmm160) REVERT: T 53 MET cc_start: 0.7286 (mtm) cc_final: 0.6824 (mtp) REVERT: T 66 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6534 (mt-10) REVERT: T 119 LYS cc_start: 0.6060 (tptp) cc_final: 0.5463 (tttm) REVERT: T 120 GLU cc_start: 0.6333 (pt0) cc_final: 0.5344 (mm-30) REVERT: T 122 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6251 (mt-10) REVERT: T 128 ASP cc_start: 0.6929 (m-30) cc_final: 0.6678 (m-30) REVERT: T 151 GLU cc_start: 0.6610 (mt-10) cc_final: 0.5741 (mm-30) REVERT: T 155 ASP cc_start: 0.6579 (t0) cc_final: 0.6175 (t70) REVERT: T 173 ASP cc_start: 0.6765 (m-30) cc_final: 0.6408 (m-30) REVERT: T 184 ASP cc_start: 0.7179 (m-30) cc_final: 0.6930 (m-30) REVERT: T 201 PHE cc_start: 0.7026 (m-80) cc_final: 0.6244 (m-80) REVERT: T 225 ARG cc_start: 0.6491 (ttt180) cc_final: 0.6097 (ttt180) REVERT: T 270 THR cc_start: 0.6984 (m) cc_final: 0.6487 (p) REVERT: T 271 GLU cc_start: 0.5802 (tp30) cc_final: 0.5455 (tp30) REVERT: T 354 GLU cc_start: 0.7306 (tp30) cc_final: 0.7043 (mm-30) REVERT: T 365 LYS cc_start: 0.6281 (tppt) cc_final: 0.5505 (tttm) REVERT: T 399 LYS cc_start: 0.6512 (ttmt) cc_final: 0.5709 (ttmm) REVERT: T 405 GLU cc_start: 0.5710 (mm-30) cc_final: 0.5227 (tm-30) REVERT: T 408 LYS cc_start: 0.6778 (tttt) cc_final: 0.6487 (ttpp) REVERT: T 409 LYS cc_start: 0.6518 (ttmm) cc_final: 0.6074 (ttpt) REVERT: T 421 ASN cc_start: 0.5850 (m-40) cc_final: 0.4554 (t0) REVERT: T 428 ASP cc_start: 0.6950 (t0) cc_final: 0.6306 (m-30) REVERT: T 436 GLU cc_start: 0.6416 (tp30) cc_final: 0.5968 (tp30) REVERT: T 443 MET cc_start: 0.6619 (ttp) cc_final: 0.6276 (ttt) REVERT: T 445 GLN cc_start: 0.6624 (tt0) cc_final: 0.5622 (tp40) REVERT: U 4 ARG cc_start: 0.6251 (tmt170) cc_final: 0.5887 (tpt90) REVERT: V 11 ILE cc_start: 0.6707 (mt) cc_final: 0.6506 (mp) REVERT: X 3 ASN cc_start: 0.6631 (p0) cc_final: 0.6125 (p0) outliers start: 62 outliers final: 32 residues processed: 965 average time/residue: 0.6831 time to fit residues: 794.9324 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 : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 169 ASN Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 169 ASN Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 169 ASN Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 68 SER Chi-restraints excluded: chain N residue 169 ASN Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain O residue 36 ASN Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 169 ASN Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 169 ASN Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 330 LEU Chi-restraints excluded: chain T residue 36 ASN Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 169 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 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... Flipped N/Q/H residues before XYZ refinement: 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 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 aren 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 covalent geometry : bond 0.00439 (44100) covalent geometry : angle 0.58100 (59700) hydrogen bonds : bond 0.06035 ( 1545) hydrogen bonds : angle 4.88449 ( 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 : 1.301 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: 0.7701 (tttt) REVERT: A 120 GLU cc_start: 0.7064 (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: 0.7657 (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: 0.7107 (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: 0.8136 (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: 0.7131 (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: 0.6851 time to fit residues: 740.0503 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 : 1.437 ------------------------------------------------------------------------------- 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: 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... Flipped N/Q/H residues before XYZ refinement: 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 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 aren 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 covalent geometry : bond 0.00176 (44100) covalent geometry : angle 0.41966 (59700) hydrogen bonds : bond 0.03972 ( 1545) hydrogen bonds : angle 4.37887 ( 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 : 1.160 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: 0.7481 (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: 0.7665 (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: 0.8341 (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: 0.8093 (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: 0.8466 (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: 0.7788 (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: 0.6308 time to fit residues: 625.6304 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 : 1.243 ------------------------------------------------------------------------------- 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.5441 > 50: distance: 50 - 55: 8.011 distance: 55 - 56: 7.312 distance: 56 - 57: 9.708 distance: 56 - 59: 9.993 distance: 57 - 58: 11.449 distance: 57 - 62: 15.303 distance: 59 - 60: 5.574 distance: 59 - 61: 12.534 distance: 63 - 64: 5.051 distance: 63 - 66: 3.863 distance: 64 - 65: 4.581 distance: 64 - 74: 9.573 distance: 66 - 67: 6.225 distance: 67 - 68: 13.156 distance: 67 - 69: 15.793 distance: 68 - 70: 7.831 distance: 69 - 71: 6.582 distance: 70 - 72: 16.433 distance: 71 - 72: 11.801 distance: 72 - 73: 7.145 distance: 74 - 75: 10.494 distance: 75 - 76: 10.317 distance: 75 - 78: 3.923 distance: 76 - 77: 13.897 distance: 76 - 83: 3.308 distance: 78 - 79: 16.705 distance: 79 - 80: 11.869 distance: 80 - 81: 10.859 distance: 81 - 82: 26.680 distance: 83 - 84: 7.111 distance: 84 - 85: 12.619 distance: 84 - 87: 11.624 distance: 85 - 86: 4.964 distance: 85 - 90: 13.496 distance: 87 - 88: 11.722 distance: 87 - 89: 9.211 distance: 90 - 91: 8.801 distance: 91 - 92: 10.253 distance: 91 - 94: 5.405 distance: 92 - 93: 19.975 distance: 92 - 98: 24.079 distance: 94 - 95: 11.804 distance: 95 - 96: 6.545 distance: 95 - 97: 6.201 distance: 98 - 99: 9.889 distance: 99 - 100: 8.214 distance: 100 - 101: 6.377 distance: 100 - 102: 13.559 distance: 102 - 103: 8.458 distance: 103 - 104: 18.463 distance: 104 - 105: 27.777 distance: 104 - 109: 16.949 distance: 106 - 107: 22.515 distance: 106 - 108: 14.313 distance: 109 - 110: 20.688 distance: 109 - 115: 13.786 distance: 110 - 111: 17.293 distance: 110 - 113: 18.366 distance: 111 - 112: 14.072 distance: 111 - 116: 8.017 distance: 113 - 114: 10.615 distance: 116 - 117: 3.552 distance: 117 - 118: 5.337 distance: 117 - 120: 6.519 distance: 118 - 119: 7.369 distance: 118 - 127: 3.530 distance: 120 - 121: 7.169 distance: 121 - 122: 12.019 distance: 121 - 123: 12.853 distance: 122 - 124: 9.610 distance: 123 - 125: 8.564 distance: 124 - 126: 13.845 distance: 125 - 126: 11.966 distance: 128 - 129: 3.385 distance: 129 - 130: 5.721 distance: 129 - 136: 6.328 distance: 131 - 132: 6.775 distance: 132 - 133: 9.982 distance: 133 - 134: 7.258 distance: 133 - 135: 10.886